Contacts of the helix formed by residues 539 - 561 (chain D) in PDB entry 2PPB
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 ASP 539 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537D THR 3.4 5.8 + - - +
538D SER* 1.3 74.6 + - - +
540D LEU* 1.3 62.7 + - - +
542D ASP* 2.9 31.3 + - - +
543D LEU* 3.5 6.6 + - - +
592D THR* 4.7 2.3 + - - -
598D ARG* 2.8 44.3 + - - -
600D LEU* 3.7 18.8 - - + +
601D ARG* 4.0 24.2 + - + +
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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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520D LEU* 3.5 35.7 - - + -
525D ARG* 4.6 8.7 - - + -
538D SER* 2.9 12.8 + - - +
539D ASP* 1.3 78.0 - - - +
541D ASN* 1.3 51.3 + - - +
543D LEU* 3.1 9.6 + - + +
544D TYR* 2.8 66.9 + - + +
581D LEU* 4.2 28.7 - - + +
601D ARG 4.6 16.6 + - - +
603D LEU* 4.5 17.3 - - + +
606D ILE* 4.8 9.6 - - + -
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Residues in contact with ASN 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D THR* 5.3 4.5 - - + -
44D LEU* 4.0 16.2 - - + +
45D PHE* 4.0 6.6 - - - -
525D ARG* 3.0 48.7 + - - +
537D THR* 2.4 34.8 + - + +
538D SER 2.7 20.7 + - - +
539D ASP 2.9 0.2 + - - -
540D LEU* 1.3 78.1 - - - +
542D ASP* 1.3 62.3 + - - +
544D TYR* 3.0 8.7 + - - +
545D ARG* 2.8 31.4 + - - +
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Residues in contact with ASP 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537D THR* 4.7 9.9 - - - +
538D SER 4.3 2.8 - - - +
539D ASP* 2.9 17.0 + - - +
541D ASN* 1.3 82.2 - - - +
543D LEU* 1.3 59.1 + - - +
545D ARG* 3.5 25.8 + - - +
546D ARG* 2.8 30.1 + - - +
592D THR* 3.5 26.8 + - - +
600D LEU* 4.5 14.2 - - + +
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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
----------------------------------------------------------
539D ASP 3.5 3.3 + - - +
540D LEU* 3.1 15.6 + - + +
541D ASN 3.1 0.6 - - - -
542D ASP* 1.3 76.0 - - - +
544D TYR* 1.3 66.4 + - - +
546D ARG* 3.2 26.3 - - - +
547D LEU* 3.2 8.8 + - - +
577D ALA 5.3 2.3 - - - +
580D ALA* 3.3 50.4 - - + +
581D LEU* 3.6 20.2 - - + +
584D ASN* 4.9 1.3 - - - +
590D PRO* 4.3 9.2 - - + -
600D LEU* 3.6 48.5 - - + +
601D ARG 4.8 1.3 - - - +
602D SER* 4.3 7.4 - - - +
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Residues in contact with TYR 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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1094C ALA* 4.1 7.1 - - - +
44D LEU* 4.3 13.0 - - + -
93D ILE* 4.2 17.5 - - + -
517D VAL* 5.2 0.2 - - + -
518D PRO 3.1 20.2 + - - -
519D VAL* 3.6 16.2 - - + -
520D LEU* 2.7 37.4 + - + +
525D ARG* 4.3 10.5 - - - -
540D LEU* 2.8 50.0 + - + +
541D ASN* 3.0 10.5 + - - +
543D LEU* 1.3 73.4 - - - +
545D ARG* 1.3 67.1 + - - +
547D LEU* 3.2 3.8 + - - +
548D ILE* 2.9 29.1 + - + +
581D LEU* 3.5 35.4 - - + +
603D LEU* 5.0 0.7 - - - +
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Residues in contact with ARG 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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29D PRO* 4.5 14.3 - - + +
31D THR* 5.7 2.8 + - - -
44D LEU* 5.3 5.9 - - + +
541D ASN 2.8 16.0 + - - +
542D ASP* 3.7 27.8 + - - +
544D TYR* 1.3 71.8 - - - +
546D ARG* 1.3 59.2 + - - +
548D ILE* 3.1 8.5 + - - +
549D ASN* 2.7 54.3 + - - +
593D ASN* 6.0 0.2 + - - -
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Residues in contact with ARG 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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542D ASP* 2.8 25.1 - - - +
543D LEU* 3.2 24.9 - - + +
545D ARG* 1.3 81.4 - - - +
547D LEU* 1.3 63.6 + - - +
549D ASN* 3.6 4.6 - - - +
550D ARG* 2.7 71.4 + - + +
573D MET* 5.3 0.2 - - - +
576D GLU* 3.8 21.5 + - - -
577D ALA* 4.5 8.1 - - + -
580D ALA* 5.5 0.9 - - + -
590D PRO* 4.2 21.4 - - - +
591D VAL 5.7 0.4 - - - +
600D LEU* 5.4 4.3 - - - -
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Residues in contact with LEU 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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93D ILE* 4.5 11.2 - - + -
95D LEU* 3.9 29.8 - - + -
517D VAL* 3.4 31.9 - - + -
543D LEU 3.2 6.8 + - - +
544D TYR 3.2 8.2 + - - +
546D ARG* 1.3 81.0 - - - +
548D ILE* 1.3 66.0 + - + +
550D ARG* 3.1 0.7 + - - +
551D ASN* 2.9 24.9 + - + +
574D LEU* 5.1 3.4 - - + +
577D ALA* 4.1 15.1 - - + +
578D VAL* 4.1 24.5 - - + +
581D LEU* 3.3 29.6 - - + -
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Residues in contact with ILE 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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26D VAL* 4.7 12.6 - - + +
27D GLU 4.7 7.0 - - - +
28D LYS* 4.6 7.2 - - - +
29D PRO* 3.9 35.9 - - + -
44D LEU* 5.6 6.3 - - + -
93D ILE* 3.4 44.2 - - + -
519D VAL* 5.3 2.0 - - + -
544D TYR* 2.9 33.7 + - + +
545D ARG* 3.5 7.6 - - - +
547D LEU* 1.3 75.1 - - - +
549D ASN* 1.3 65.8 + - - +
551D ASN* 3.9 4.4 - - - +
552D ASN* 2.9 29.5 + - + +
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Residues in contact with ASN 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D PRO* 4.1 25.3 - - - +
545D ARG* 2.7 34.3 + - - +
546D ARG* 3.6 5.8 - - - +
548D ILE* 1.3 73.4 - - - +
550D ARG* 1.3 54.6 + - + +
552D ASN* 3.7 4.5 - - - +
553D ARG* 2.8 49.7 + - + +
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Residues in contact with ARG 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 ARG* 2.7 56.6 + - - +
547D LEU* 3.4 8.1 - - - +
549D ASN* 1.3 77.6 - - - +
551D ASN* 1.3 53.1 + - - +
553D ARG* 2.7 31.6 - - - +
554D LEU* 2.8 31.5 + - - +
570D GLU* 3.2 18.9 + - - -
573D MET* 3.1 37.3 + - - +
574D LEU* 3.2 26.4 - - + +
576D GLU* 3.0 28.7 + - - -
577D ALA* 4.3 9.2 - - + +
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Residues in contact with ASN 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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93D ILE* 4.6 9.5 - - + +
94D GLU 2.8 16.8 + - - -
95D LEU* 3.5 16.0 - - + +
96D ALA* 2.6 24.4 + - - +
547D LEU* 2.9 21.4 + - + +
548D ILE* 3.9 5.2 - - - +
550D ARG* 1.3 71.9 - - - +
552D ASN* 1.3 65.3 + - - +
554D LEU* 3.1 4.3 + - - +
555D LYS* 2.5 62.3 + - - +
574D LEU* 3.4 9.3 - - - +
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Residues in contact with ASN 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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27D GLU 4.3 13.3 - - - +
28D LYS* 4.1 21.0 + - - +
548D ILE* 2.9 23.9 + - + +
549D ASN* 3.7 5.6 - - - +
551D ASN* 1.3 76.7 + - - +
553D ARG* 1.3 65.0 + - - +
554D LEU 2.9 1.4 + - - -
555D LYS* 3.0 19.7 + - - +
556D LYS* 3.1 33.3 + - - +
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Residues in contact with ARG 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 ASN* 2.8 23.9 + - - +
550D ARG* 2.7 52.4 - - - +
552D ASN* 1.3 72.5 - - - +
554D LEU* 1.3 57.1 + - - +
556D LYS* 3.8 10.6 - - - +
557D LEU* 2.9 48.0 + - + +
570D GLU* 2.9 26.6 + - - +
573D MET* 5.0 7.4 - - - +
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Residues in contact with LEU 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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96D ALA* 3.3 29.4 - - + -
97D THR* 4.2 7.9 - - - +
550D ARG 2.8 13.5 + - - +
551D ASN 3.2 8.5 - - - +
552D ASN 3.0 0.2 - - - -
553D ARG* 1.3 74.8 - - - +
555D LYS* 1.3 59.5 + - - +
557D LEU* 2.7 32.5 + - + +
558D LEU* 2.8 21.8 + - + +
567D ILE* 4.1 19.5 - - + +
570D GLU* 4.5 10.8 - - + -
571D LYS* 3.7 34.3 - - - +
574D LEU* 3.9 22.4 - - + -
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Residues in contact with LYS 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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94D GLU* 2.9 10.2 + - - +
95D LEU 3.4 0.2 - - - -
96D ALA* 2.8 29.6 - - + +
551D ASN* 2.5 58.0 + - - +
552D ASN* 3.0 13.1 + - - +
554D LEU* 1.3 79.1 - - - +
556D LYS* 1.3 59.2 + - + +
558D LEU* 3.2 8.9 + - - +
559D ALA* 3.0 29.1 + - - +
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Residues in contact with LYS 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 ASN* 3.1 31.1 + - - +
553D ARG* 3.8 11.0 - - - +
555D LYS* 1.3 80.1 - - + +
557D LEU* 1.3 54.3 + - - +
559D ALA* 3.1 6.6 + - - +
560D GLN* 2.7 53.5 + - + +
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Residues in contact with LEU 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 ARG* 2.9 32.3 + - + +
554D LEU* 2.7 19.3 + - + +
556D LYS* 1.3 72.9 - - + +
558D LEU* 1.3 55.9 + - - -
560D GLN* 3.9 16.3 - - - +
561D GLY 2.7 31.0 + - - +
562D ALA* 3.9 3.6 - - - +
563D PRO* 5.1 2.4 - - + +
566D ILE* 4.5 24.2 - - + +
567D ILE* 5.2 8.2 - - + +
570D GLU* 3.6 38.8 - - + +
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Residues in contact with LEU 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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96D ALA* 6.1 2.9 - - + -
97D THR* 5.3 8.1 - - - +
554D LEU* 2.8 21.7 + - + +
555D LYS* 3.6 11.0 - - - +
557D LEU* 1.3 79.0 - - - +
559D ALA* 1.3 62.0 + - - +
561D GLY* 4.0 6.2 + - - -
562D ALA* 3.9 26.1 + - + +
567D ILE* 4.1 24.2 - - + -
571D LYS* 6.0 0.9 - - - -
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Residues in contact with ALA 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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555D LYS 3.0 16.5 + - - +
556D LYS* 3.7 6.3 - - - +
558D LEU* 1.3 78.2 - - - +
560D GLN* 1.3 66.8 + - + +
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Residues in contact with GLN 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 LYS* 2.7 40.7 + - + +
557D LEU* 3.9 23.8 - - - +
559D ALA* 1.3 76.1 - - - +
561D GLY* 1.3 60.8 + - - +
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Residues in contact with GLY 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 LEU* 2.7 13.9 - - - +
558D LEU 4.3 3.6 - - - -
559D ALA 3.4 1.6 - - - -
560D GLN* 1.3 82.3 - - - +
562D ALA* 1.3 62.2 + - - -
563D PRO* 3.1 13.3 - - - +
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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
------------------------------------------------------------
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