Contacts of the helix formed by residues 538 - 575 (chain D) in PDB entry 1NLW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 538 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536D ARG 3.3 3.2 + - - -
537D HIS* 1.3 74.4 - - - +
539D THR* 1.3 65.2 + - - +
540D LEU* 3.4 13.3 + - + +
541D SER* 2.9 34.6 + - - +
542D LEU* 3.2 24.5 + - - +
607H G 3.3 30.1 + - - +
608H C 2.7 33.5 + - - -
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Residues in contact with THR 539 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521D LEU* 3.4 32.3 - - + +
538D THR* 1.3 79.8 + - - +
540D LEU* 1.3 56.9 + - - +
542D LEU* 3.6 3.6 - - - +
543D LEU* 2.9 49.4 + - + +
714E ARG* 5.4 1.0 + - - -
718E ILE* 4.1 24.7 - - + -
722E PHE* 4.8 5.4 - - + -
608H C 3.4 19.6 + - - -
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Residues in contact with LEU 540 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538D THR* 3.2 11.1 + - + +
539D THR* 1.3 80.8 - - - +
541D SER* 1.3 64.3 + - - +
543D LEU* 3.2 4.4 + - - +
544D THR* 3.1 31.4 + - - +
714E ARG* 5.9 2.2 - - + +
717E HIS* 4.0 30.3 - - + +
718E ILE* 4.4 14.2 - - + +
721E SER* 3.1 30.5 - - - +
607H G 5.0 13.5 - - - +
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Residues in contact with SER 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537D HIS* 3.4 13.1 - - - +
538D THR* 2.9 42.3 + - - +
540D LEU* 1.3 74.4 - - - +
542D LEU* 1.3 54.8 + - - +
544D THR* 3.3 6.2 + - - -
545D LYS* 2.8 45.7 + - - +
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Residues in contact with LEU 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521D LEU* 3.5 48.5 - - + +
524D LEU* 4.4 7.9 - - + -
525D LYS* 3.6 37.2 - - + +
528D VAL* 3.9 15.5 - - + -
537D HIS* 5.1 1.3 - - + -
538D THR 3.2 16.7 + - - +
539D THR* 3.6 3.1 - - - +
541D SER* 1.3 79.1 + - - +
543D LEU* 1.3 66.5 + - - +
545D LYS* 3.3 25.1 - - - +
546D ALA* 2.9 27.2 + - - +
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Residues in contact with LEU 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521D LEU* 4.7 8.3 - - + -
524D LEU* 5.2 2.0 - - + -
539D THR* 2.9 32.1 + - + +
540D LEU* 3.2 5.6 + - - +
542D LEU* 1.3 76.0 - - - +
544D THR* 1.3 61.4 + - - +
546D ALA* 3.6 5.1 + - - +
547D LYS* 3.2 21.1 + - - +
718E ILE* 3.8 6.1 - - + +
721E SER* 3.7 30.5 - - - +
722E PHE* 3.5 42.8 - - + +
725E LEU* 3.9 29.7 - - + +
743E LEU* 4.1 18.2 - - + -
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Residues in contact with THR 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540D LEU* 3.1 18.6 + - - +
541D SER* 3.4 10.8 - - - +
543D LEU* 1.3 74.3 - - - +
545D LYS* 1.3 68.1 + - + +
547D LYS* 3.2 8.0 + - - +
548D LEU* 3.1 39.7 + - + +
721E SER* 4.3 11.9 + - - -
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Residues in contact with LYS 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525D LYS* 4.9 2.2 - - - +
528D VAL* 3.8 13.9 - - + +
530D LEU* 3.1 52.6 + - + +
531D GLY* 4.6 7.3 + - - -
534D SER* 4.6 0.8 + - - -
537D HIS* 3.4 26.8 - - + +
541D SER* 2.8 28.4 + - - +
542D LEU* 3.3 37.3 - - - +
544D THR* 1.3 74.8 - - + +
546D ALA* 1.3 53.7 + - - +
548D LEU* 3.2 8.9 + - - +
549D HIS* 2.7 37.7 + - - +
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Residues in contact with ALA 546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524D LEU* 4.0 32.8 - - + -
528D VAL* 4.2 13.7 - - + +
542D LEU 2.9 18.6 + - - +
543D LEU 3.6 5.6 - - - +
545D LYS* 1.3 76.8 - - - +
547D LYS* 1.3 63.8 + - - +
549D HIS* 3.2 3.1 + - - +
550D ILE* 3.0 27.2 + - - +
725E LEU* 4.4 12.8 - - + -
750E ILE* 4.7 4.2 - - + +
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Residues in contact with LYS 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ARG* 6.0 2.0 - - - +
543D LEU 3.2 9.1 + - - +
544D THR* 3.2 11.5 + - - +
546D ALA* 1.3 77.8 - - - +
548D LEU* 1.3 75.0 + - + +
550D ILE* 3.0 7.5 + - - +
551D LYS* 3.0 52.3 + - + +
721E SER 6.0 0.2 - - - +
724E SER* 3.7 44.8 + - - +
725E LEU* 4.1 14.5 - - + +
728E SER* 4.2 5.6 - - - +
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Residues in contact with LEU 548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544D THR* 3.1 30.6 + - + +
545D LYS* 3.8 7.6 - - - +
547D LYS* 1.3 92.7 - - + +
549D HIS* 1.3 57.0 + - - +
551D LYS* 3.2 12.1 + - + +
552D LYS* 2.9 28.3 + - - +
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Residues in contact with HIS 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527D LEU 3.8 10.3 + - - -
528D VAL* 4.5 7.9 - - + -
529D PRO* 3.0 48.2 - - + +
530D LEU* 6.4 0.2 - - + -
545D LYS 2.7 22.0 + - - +
546D ALA* 3.6 8.7 - - - +
548D LEU* 1.3 70.0 - - - +
550D ILE* 1.3 66.6 + - - +
552D LYS* 3.1 13.0 + - + +
553D LEU* 2.9 57.0 + - + +
750E ILE* 4.2 13.2 - - + +
754E ARG* 5.9 1.6 + - - -
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Residues in contact with ILE 550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546D ALA 3.0 12.3 + - - +
547D LYS 3.4 6.3 - - - +
549D HIS* 1.3 75.0 - - - +
551D LYS* 1.3 64.6 + - + +
553D LEU* 3.1 9.1 + - - +
554D GLU* 3.0 35.2 + - - +
725E LEU* 3.8 20.6 - - + -
728E SER* 3.7 32.1 - - - +
729E VAL* 4.1 13.9 - - + -
746E ALA* 4.3 6.1 - - + -
749E TYR* 3.5 32.8 - - + -
750E ILE* 3.5 31.2 - - + -
753E MET* 5.9 1.1 - - + -
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Residues in contact with LYS 551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLY* 4.8 15.5 + - - +
547D LYS* 3.0 49.9 + - + +
548D LEU* 3.5 15.3 - - + +
550D ILE* 1.3 78.8 - - + +
552D LYS* 1.3 61.6 + - - +
554D GLU* 3.5 21.7 + - - +
555D ASP* 3.1 23.0 + - - +
558D ARG* 5.3 1.0 + - - -
727E ASP 5.3 1.2 + - - -
728E SER* 3.7 25.4 + - - +
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Residues in contact with LYS 552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548D LEU 2.9 14.0 + - - +
549D HIS* 3.1 19.9 + - + +
551D LYS* 1.3 74.8 - - - +
553D LEU* 1.3 69.4 + - + +
555D ASP* 3.0 17.1 + - + +
556D SER* 3.0 35.8 + - - +
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Residues in contact with LEU 553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549D HIS* 2.9 42.0 + - + +
550D ILE* 3.6 8.3 - - + +
552D LYS* 1.3 78.8 - - + +
554D GLU* 1.3 63.3 + - - +
556D SER* 3.0 6.3 + - - +
557D ASP* 2.9 19.3 + - - -
750E ILE* 3.7 44.2 - - + +
753E MET* 4.1 17.5 - - + -
754E ARG* 4.9 16.2 - - + -
757E ASN* 3.5 23.3 + - + +
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Residues in contact with GLU 554 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550D ILE* 3.0 30.4 + - + +
551D LYS* 3.8 24.9 + - - +
553D LEU* 1.3 75.8 - - - +
555D ASP* 1.3 61.0 + - - +
557D ASP* 3.3 9.2 + - - +
558D ARG* 3.1 38.8 + - - +
728E SER 3.8 7.3 - - - +
730E PRO* 4.6 2.9 - - - +
749E TYR* 2.7 39.5 + - + +
753E MET* 4.6 7.6 - - + -
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Residues in contact with ASP 555 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLU* 4.8 8.7 - - - +
23A LYS* 5.3 2.9 + - - -
551D LYS 3.1 13.6 + - - +
552D LYS* 3.0 22.2 + - + +
554D GLU* 1.3 79.1 - - - +
556D SER* 1.3 60.0 + - - +
558D ARG* 3.4 32.0 + - - +
559D LYS* 3.1 32.7 + - - +
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Residues in contact with SER 556 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552D LYS* 3.0 34.5 + - - +
553D LEU* 3.0 10.5 + - - -
555D ASP* 1.3 76.5 + - - +
557D ASP* 1.3 59.3 + - - +
559D LYS* 3.6 12.0 - - - +
560D ALA* 2.8 30.0 + - - +
757E ASN* 3.4 12.1 - - - +
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Residues in contact with ASP 557 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553D LEU 2.9 12.6 + - - +
554D GLU* 3.5 13.2 - - - +
555D ASP 3.2 0.2 - - - -
556D SER* 1.3 76.2 - - - +
558D ARG* 1.3 62.9 + - - +
560D ALA* 3.4 2.9 + - - +
561D VAL* 3.0 32.7 + - - +
753E MET* 5.0 5.6 - - - -
756E LYS* 3.0 52.1 - - - +
757E ASN* 3.3 16.9 + - - +
760E HIS* 3.2 12.7 + - - -
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Residues in contact with ARG 558 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLU* 2.8 61.8 + - - +
25A LYS* 3.8 19.5 - - + +
26A GLY* 4.1 16.0 - - - +
35A SER* 6.5 1.1 - - - -
551D LYS 5.3 1.0 + - - -
554D GLU* 3.1 24.6 + - - +
555D ASP* 3.5 34.6 + - - +
557D ASP* 1.3 78.8 - - - +
559D LYS* 1.3 57.8 + - - +
561D VAL* 3.5 7.7 + - - +
562D HIS* 3.1 28.4 + - - +
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Residues in contact with LYS 559 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.4 19.8 - - - +
22A GLU* 6.0 1.5 - - - -
555D ASP* 3.1 23.5 + - - +
556D SER* 3.6 12.6 - - - +
557D ASP 3.2 0.2 - - - -
558D ARG* 1.3 75.9 - - - +
560D ALA* 1.3 59.8 + - - +
562D HIS* 3.3 12.8 + - + +
563D GLN* 2.9 26.8 + - + +
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Residues in contact with ALA 560 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556D SER 2.8 19.6 + - - +
557D ASP 3.7 4.5 - - - +
558D ARG 3.3 0.2 - - - -
559D LYS* 1.3 76.4 - - - +
561D VAL* 1.3 58.0 + - - +
563D GLN* 2.9 24.5 + - - +
564D ILE* 2.9 19.2 + - - +
757E ASN* 4.3 5.8 - - - +
760E HIS* 3.8 27.6 - - + +
761E GLN 5.6 0.2 - - - +
764E ILE* 4.1 11.4 - - + -
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Residues in contact with VAL 561 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557D ASP* 3.0 26.2 + - - +
558D ARG* 3.8 7.2 - - - +
559D LYS 3.3 0.2 - - - -
560D ALA* 1.3 74.9 - - - +
562D HIS* 1.3 62.2 + - - +
564D ILE* 3.5 11.4 + - + +
565D ASP* 3.1 21.0 + - + +
756E LYS* 5.5 1.6 - - - +
760E HIS* 3.4 26.2 - - + +
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Residues in contact with HIS 562 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG* 3.1 44.1 + - - -
22A GLU* 5.9 3.6 - - - +
558D ARG 3.1 18.1 + - - +
559D LYS* 3.5 12.3 - - + +
561D VAL* 1.3 75.4 - - - +
563D GLN* 1.3 67.5 + - - +
565D ASP* 3.3 6.2 + - - +
566D GLN* 3.0 57.8 + - + +
109F A 4.6 3.5 + - - -
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Residues in contact with GLN 563 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559D LYS* 2.9 13.2 + - + +
560D ALA* 2.9 14.6 + - - +
562D HIS* 1.3 79.3 - - - +
564D ILE* 1.3 60.7 + - - +
566D GLN* 3.1 9.6 + - - +
567D LEU* 3.1 32.0 + - + +
764E ILE* 3.4 43.7 - - + +
768E LYS* 4.5 13.1 - - - +
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Residues in contact with ILE 564 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560D ALA 2.9 17.2 + - - +
561D VAL* 3.8 11.0 - - + +
563D GLN* 1.3 74.7 - - - +
565D ASP* 1.3 65.4 + - - +
567D LEU* 3.1 2.5 + - - -
568D GLN* 3.0 45.6 + - - +
760E HIS* 4.0 26.9 - - + +
763E ASP* 3.7 31.2 - - + +
764E ILE* 3.7 16.6 - - + +
767E LEU* 3.5 22.7 - - + +
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Residues in contact with ASP 565 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561D VAL* 3.1 12.4 + - + +
562D HIS* 3.4 13.2 - - - +
563D GLN 3.2 0.2 - - - -
564D ILE* 1.3 81.4 - - - +
566D GLN* 1.3 83.6 + - - +
568D GLN* 3.2 12.5 + - - +
569D ARG* 2.5 44.7 + - - +
572D ARG* 5.1 2.2 + - - -
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Residues in contact with GLN 566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG* 4.6 2.0 - - - -
562D HIS* 3.0 50.8 + - + +
563D GLN* 3.1 12.1 + - - +
565D ASP* 1.3 98.9 + - - +
567D LEU* 1.3 60.6 + - + +
569D ARG* 2.7 35.0 + - - +
570D GLU* 3.1 27.2 + - - +
109F A 4.2 8.2 + - - +
110F C 4.1 12.9 + - - -
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Residues in contact with LEU 567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563D GLN* 3.1 29.7 + - + +
564D ILE 3.1 6.5 + - - +
566D GLN* 1.3 75.8 - - + +
568D GLN* 1.3 54.9 + - - +
570D GLU* 3.2 13.0 + - - +
571D GLN* 2.7 30.5 + - - +
764E ILE* 3.6 42.6 - - + +
767E LEU* 3.8 18.6 - - + -
768E LYS* 4.2 17.9 - - + -
771E ASN* 3.3 30.4 + - - +
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Residues in contact with GLN 568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564D ILE* 3.0 35.6 + - - +
565D ASP* 3.6 11.5 - - - +
567D LEU* 1.3 73.4 - - - +
569D ARG* 1.3 56.4 + - - +
570D GLU 2.9 4.9 - - - -
571D GLN* 3.0 10.1 + - - +
572D ARG* 2.8 47.8 + - + +
767E LEU* 3.8 19.0 - - + +
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Residues in contact with ARG 569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565D ASP* 2.5 46.5 + - - +
566D GLN* 2.7 35.0 + - - +
568D GLN* 1.3 76.6 - - - +
570D GLU* 1.3 58.8 + - - +
572D ARG* 3.5 33.4 + - - +
573D HIS* 3.5 18.7 + - - +
108F C 5.1 1.2 + - - -
109F A 3.4 37.4 + - - -
110F C 4.8 4.0 - - - -
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Residues in contact with GLU 570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566D GLN 3.1 17.8 + - - +
567D LEU* 3.4 14.9 - - - +
568D GLN 2.9 0.4 - - - -
569D ARG* 1.3 77.9 - - - +
571D GLN* 1.3 65.3 + - - +
572D ARG 3.3 0.2 - - - -
573D HIS* 3.1 10.2 + - + +
574D LEU* 3.0 31.9 + - + +
771E ASN* 3.3 30.2 + - - +
775E GLU* 4.7 6.9 - - - +
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Residues in contact with GLN 571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567D LEU 2.7 16.6 + - - +
568D GLN* 3.0 11.4 + - - +
570D GLU* 1.3 74.5 - - - +
572D ARG* 1.3 63.1 + - + +
574D LEU* 3.5 2.5 + - - +
575D LYS* 3.2 47.0 + - + +
767E LEU* 4.2 6.5 + - - +
770E GLN* 2.8 53.4 + - - +
771E ASN* 3.1 23.0 + - - +
774E LEU* 3.6 17.4 - - + +
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Residues in contact with ARG 572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565D ASP* 5.1 1.8 + - - -
568D GLN* 2.8 21.4 + - + +
569D ARG* 3.5 45.5 + - - +
571D GLN* 1.3 78.1 - - + +
573D HIS* 1.3 60.8 + - - +
575D LYS* 4.1 8.6 - - + +
576D ARG* 3.2 22.9 + - - +
314G C 4.4 4.0 + - - -
315G T 3.7 49.5 + - - +
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Residues in contact with HIS 573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569D ARG 3.5 14.3 + - - +
570D GLU* 3.2 15.5 - - + +
571D GLN 3.0 0.6 - - - -
572D ARG* 1.3 78.4 - - - +
574D LEU* 1.3 77.7 + - + +
576D ARG* 3.0 10.7 + - - +
577D GLN* 2.9 26.3 + - + +
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Residues in contact with LEU 574 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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570D GLU* 3.0 21.7 + - + +
571D GLN 3.9 3.6 - - - +
573D HIS* 1.3 86.3 - - + +
575D LYS* 1.3 58.3 + - - +
577D GLN* 2.8 26.2 + - + +
578D LEU* 2.9 17.7 + - - +
771E ASN* 3.6 23.8 - - + +
774E LEU* 3.5 35.0 - - + -
775E GLU* 3.7 17.7 - - + -
778E VAL* 4.3 21.1 - - + -
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Residues in contact with LYS 575 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571D GLN* 3.2 33.3 + - + +
572D ARG* 4.1 7.4 - - + +
574D LEU* 1.3 77.9 - - - +
576D ARG* 1.3 57.2 + - - +
578D LEU* 2.7 37.6 + - + +
774E LEU* 3.9 30.1 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il