Contacts of the helix formed by residues 538 - 560 (chain J) in PDB entry 4XLN
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 SER 538 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016I ILE* 5.8 0.3 - - - +
524J LEU 4.7 0.3 + - - -
525J ARG* 3.4 10.9 - - - -
526J PRO* 3.2 31.5 + - - +
537J THR* 1.3 86.1 + - - +
539J ASP* 1.3 65.0 + - - +
540J LEU* 3.3 6.7 - - - -
541J ASN* 3.3 30.7 + - - +
542J ASP* 4.0 4.0 + - - +
332L LEU* 3.4 8.6 - - - +
333L GLU* 3.8 12.4 + - - -
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Residues in contact with ASP 539 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537J THR 4.0 0.2 + - - -
538J SER* 1.3 70.0 - - - +
540J LEU* 1.3 64.7 + - - +
541J ASN 3.1 2.0 - - - -
542J ASP* 3.0 10.3 + - - +
543J LEU* 2.9 25.9 + - - +
593J ASN* 3.9 9.9 + - - -
598J ARG* 5.3 4.5 + - - +
599J PRO 4.0 2.4 - - - +
600J LEU* 3.4 43.4 - - + +
601J ARG 3.8 8.5 + - - +
331L SER* 3.2 23.7 + - - -
333L GLU* 3.1 38.5 + - + +
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Residues in contact with LEU 540 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520J LEU* 3.7 33.2 - - + -
525J ARG* 4.2 16.8 - - + -
538J SER* 3.3 3.7 - - - -
539J ASP* 1.3 79.4 - - - +
541J ASN* 1.3 55.4 + - - +
543J LEU* 3.4 11.6 + - + +
544J TYR* 2.9 61.4 + - + -
581J VAL* 4.3 6.7 - - + +
601J ARG 4.1 5.7 + - - +
602J SER* 4.0 11.0 - - - -
603J LEU* 3.8 39.3 - - + +
606J ILE* 5.5 9.9 - - + -
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Residues in contact with ASN 541 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J THR* 5.4 3.1 - - + -
44J LEU* 3.6 15.9 - - + +
45J PHE* 3.4 16.9 - - + -
525J ARG* 2.6 59.7 + - - +
526J PRO 4.1 0.2 + - - -
537J THR* 3.5 14.3 + - - +
538J SER* 3.3 31.0 - - - +
539J ASP 3.1 0.2 - - - -
540J LEU* 1.3 78.9 - - - +
542J ASP* 1.3 57.0 + - - +
544J TYR 3.6 0.2 + - - -
545J ARG* 2.9 29.3 + - - +
272L THR* 5.1 8.5 - - + -
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Residues in contact with ASP 542 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537J THR* 4.9 5.0 - - - +
538J SER 4.5 5.2 - - - +
539J ASP* 3.0 14.9 + - - +
541J ASN* 1.3 74.9 - - - +
543J LEU* 1.3 66.6 + - - +
545J ARG* 3.1 21.2 + - - +
546J ARG* 2.9 31.8 + - - +
593J ASN* 4.0 23.8 + - - +
600J LEU* 3.8 15.0 - - + -
272L THR* 3.3 36.2 + - - +
331L SER* 6.1 0.2 - - - -
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Residues in contact with LEU 543 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539J ASP 2.9 18.3 + - - +
540J LEU* 3.5 14.6 - - + +
541J ASN 3.3 0.2 - - - -
542J ASP* 1.3 77.9 - - - +
544J TYR* 1.3 63.6 + - - +
546J ARG* 3.2 7.9 + - - +
547J LEU* 3.0 22.2 + - - +
577J ALA* 5.4 0.5 - - - +
580J ALA* 3.4 32.9 - - + +
581J VAL* 3.9 15.1 - - + +
584J ASN* 4.6 0.7 - - - +
591J VAL* 3.7 28.5 - - + -
600J LEU* 3.6 21.5 - - + +
601J ARG 3.8 21.5 - - - +
602J SER* 3.9 12.3 - - - -
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Residues in contact with TYR 544 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094I ALA* 4.0 12.0 + - - +
44J LEU* 3.6 17.7 - - + -
93J ILE* 3.9 22.9 - - + -
517J VAL* 4.5 3.8 - - + -
518J PRO 2.9 28.7 + - - -
519J VAL* 3.8 16.4 - - + -
520J LEU* 3.5 16.7 + - - +
525J ARG* 4.3 12.8 - - - -
540J LEU* 2.9 57.7 + - + +
543J LEU* 1.3 72.9 - - - +
545J ARG* 1.3 57.3 + - - +
547J LEU* 3.2 7.3 + - + +
548J ILE* 2.9 40.0 + - + +
581J VAL* 3.6 25.9 - - + +
603J LEU* 4.3 5.2 - - - +
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Residues in contact with ARG 545 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J PRO* 3.2 45.1 + - + +
30J GLU* 4.9 1.3 - - - +
31J THR* 4.9 4.0 - - - -
44J LEU* 4.4 8.2 - - + +
541J ASN 2.9 18.6 + - - +
542J ASP* 3.3 22.5 + - - +
543J LEU 3.1 0.4 - - - -
544J TYR* 1.3 77.0 - - - +
546J ARG* 1.3 62.5 + - - +
548J ILE* 3.9 0.6 - - - -
549J ASN* 2.9 35.9 + - - +
221L GLY 5.3 2.4 + - - -
268L ASP 4.9 1.2 + - - -
269L GLN* 3.0 41.0 + - - +
270L ALA 2.9 26.5 + - - -
271L ARG 3.4 14.2 + - - -
272L THR* 3.8 23.3 + - - +
274L ARG* 6.3 0.4 - - - +
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Residues in contact with ARG 546 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542J ASP* 2.9 21.9 + - - +
543J LEU* 3.8 6.8 - - - +
545J ARG* 1.3 80.3 - - + +
547J LEU* 1.3 64.3 + - - +
549J ASN* 3.3 7.1 - - - +
550J ARG* 2.9 56.4 + - - +
576J GLU* 5.5 2.2 + - - -
577J ALA* 5.0 2.2 - - + +
591J VAL* 3.8 32.4 - - - +
600J LEU* 6.0 2.9 - - - -
221L GLY 5.0 3.7 + - - -
222L LEU* 3.9 16.8 - - + +
223L SER* 4.2 20.2 - - - +
226L ASP* 3.2 23.3 + - - +
269L GLN* 4.0 14.1 - - + +
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Residues in contact with LEU 547 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93J ILE* 3.9 24.7 - - + -
95J LEU* 5.0 7.0 - - + -
517J VAL* 4.3 18.2 - - + -
543J LEU 3.0 13.3 + - - +
544J TYR* 3.3 10.5 - - + +
546J ARG* 1.3 77.0 - - - +
548J ILE* 1.3 60.8 + - - +
550J ARG* 3.2 2.9 + - - +
551J ASN* 2.9 26.8 + - + +
574J LEU* 3.8 15.9 - - + -
577J ALA* 3.9 12.4 - - + +
578J VAL* 3.6 39.7 - - + +
581J VAL* 3.7 25.4 - - + -
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Residues in contact with ILE 548 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J VAL* 3.4 35.2 - - + +
27J GLU* 3.1 26.7 - - - +
29J PRO* 4.9 3.1 - - + -
44J LEU* 4.0 22.4 - - + -
93J ILE* 3.5 38.4 - - + -
544J TYR* 2.9 22.6 + - + +
545J ARG* 4.1 2.2 - - - +
547J LEU* 1.3 72.5 - - - +
549J ASN* 1.3 58.0 + - - +
551J ASN* 3.5 6.0 - - - +
552J ASN* 2.9 39.5 + - - +
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Residues in contact with ASN 549 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J PRO* 3.3 38.9 - - - +
545J ARG* 2.9 23.0 + - - +
546J ARG 3.3 5.2 - - - +
548J ILE* 1.3 77.4 - - - +
550J ARG* 1.3 65.9 + - + +
552J ASN* 3.7 4.5 - - - +
553J ARG* 3.0 28.3 + - - +
226L ASP* 6.0 0.2 - - - +
268L ASP 5.0 1.9 + - - +
269L GLN* 2.9 48.7 + - - +
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Residues in contact with ARG 550 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546J ARG* 2.9 36.3 + - - +
547J LEU 3.6 4.0 - - - +
549J ASN* 1.3 77.1 - - + +
551J ASN* 1.3 57.6 + - - +
553J ARG* 3.9 8.0 - - - +
554J LEU* 2.9 30.6 + - - +
570J GLU* 3.2 19.0 - - - +
573J MET* 3.1 48.6 + - + +
574J LEU* 4.4 11.7 - - + -
576J GLU* 3.6 26.5 + - - +
577J ALA* 3.7 18.3 - - - +
223L SER* 5.4 4.2 - - - -
225L LEU* 4.9 2.8 - - - +
226L ASP* 3.0 50.9 + - - +
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Residues in contact with ASN 551 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J GLU* 4.9 0.2 + - - -
93J ILE* 4.1 11.6 - - + +
94J GLU 3.4 16.0 + - - +
95J LEU* 3.3 35.1 - - + +
96J ALA 3.4 8.0 + - - -
547J LEU* 2.9 14.3 + - + +
548J ILE* 3.5 10.5 - - - +
549J ASN 3.1 0.2 - - - -
550J ARG* 1.3 78.5 - - - +
552J ASN* 1.3 76.8 + - - +
554J LEU* 3.1 5.3 - - - +
555J LYS* 2.9 40.9 + - - +
574J LEU* 3.7 17.3 - - + +
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Residues in contact with ASN 552 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J GLU* 3.5 36.2 + - - +
28J LYS* 5.2 0.6 - - - +
29J PRO* 5.1 4.2 - - + +
548J ILE* 2.9 29.8 + - - +
549J ASN* 3.8 4.5 - - - +
551J ASN* 1.3 82.5 + - - +
553J ARG* 1.3 66.8 - - - +
555J LYS* 3.3 21.4 + - - +
556J LYS* 2.9 24.7 + - - +
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Residues in contact with ARG 553 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549J ASN* 3.0 15.9 + - - +
550J ARG* 3.9 12.9 - - - +
552J ASN* 1.3 73.8 - - - +
554J LEU* 1.3 62.9 + - - +
556J LYS* 3.1 7.9 + - - +
557J LEU* 3.0 43.0 + - + +
570J GLU* 2.8 39.6 + - - -
573J MET* 3.4 9.7 - - - +
222L LEU* 4.6 4.8 - - - +
226L ASP* 2.4 42.3 + - - -
229L GLN* 3.3 20.9 - - - +
230L GLU* 3.3 43.3 - - - +
233L GLN* 4.6 3.8 - - - +
269L GLN* 5.3 4.2 - - - +
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Residues in contact with LEU 554 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96J ALA* 3.7 17.0 - - + +
97J THR* 3.6 26.5 - - + -
550J ARG 2.9 20.2 + - - +
551J ASN* 3.1 6.3 - - - +
553J ARG* 1.3 77.0 - - - +
555J LYS* 1.3 64.6 + - - +
557J LEU* 3.8 4.5 - - + +
558J LEU* 2.9 46.8 + - + +
567J ILE* 4.3 10.5 - - + +
570J GLU* 3.5 31.9 - - + -
571J LYS* 4.3 8.3 - - + -
574J LEU* 3.6 22.7 - - + -
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Residues in contact with LYS 555 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J GLU* 4.4 10.9 + - - -
27J GLU* 4.0 18.6 + - - +
94J GLU 4.6 5.4 + - - +
95J LEU 5.7 0.2 - - - -
96J ALA* 3.6 24.7 - - + +
551J ASN* 2.9 39.4 + - - +
552J ASN* 3.3 30.6 + - - +
554J LEU* 1.3 72.7 - - - +
556J LYS* 1.3 63.2 + - - +
558J LEU* 3.5 6.2 - - - +
559J ALA* 2.9 28.8 + - - +
159L ILE 6.0 0.7 - - - +
160L PRO 5.0 16.1 - - - +
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Residues in contact with LYS 556 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552J ASN 2.9 13.8 + - - +
553J ARG* 3.3 13.0 - - - +
554J LEU 3.1 0.2 - - - -
555J LYS* 1.3 78.5 - - - +
557J LEU* 1.3 62.9 + - - +
559J ALA* 4.1 1.8 - - - +
560J GLN* 3.2 21.8 + - - +
233L GLN* 4.5 11.7 - - - +
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Residues in contact with LEU 557 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553J ARG* 3.0 44.8 + - + +
554J LEU* 3.8 5.4 - - + +
556J LYS* 1.3 73.3 - - - +
558J LEU* 1.3 57.5 + - - +
560J GLN* 3.7 9.5 - - - +
561J GLY 3.6 1.4 + - - -
562J ALA* 3.1 40.3 + - + +
566J ILE* 4.0 22.4 - - + -
567J ILE* 3.3 31.7 - - + +
570J GLU* 3.6 21.8 - - + +
229L GLN* 4.9 3.6 - - - +
233L GLN* 3.4 36.3 - - + +
236L ILE* 5.0 1.6 - - + -
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Residues in contact with LEU 558 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96J ALA* 4.0 24.5 - - + -
97J THR* 5.2 1.6 - - + +
554J LEU* 2.9 35.2 + - + +
555J LYS* 3.5 4.7 - - - +
556J LYS 3.1 0.2 - - - -
557J LEU* 1.3 75.0 - - - +
559J ALA* 1.3 59.2 + - - +
560J GLN 3.0 3.6 - - - -
561J GLY* 3.0 21.0 + - - -
562J ALA 4.4 0.3 + - - -
567J ILE* 3.7 32.8 - - + +
571J LYS* 5.1 6.1 - - - -
151L LEU* 5.1 3.1 - - + +
155L ARG* 4.7 20.9 - - - +
156L ILE* 4.9 17.3 - - + +
159L ILE* 5.0 13.5 - - + +
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Residues in contact with ALA 559 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555J LYS 2.9 16.1 + - - +
556J LYS 4.4 1.6 - - - +
558J LEU* 1.3 76.3 - - - +
560J GLN* 1.3 60.4 + - - +
561J GLY* 3.2 1.0 + - - -
144L GLU* 3.9 15.2 - - - +
147L ARG* 5.8 0.2 - - - -
156L ILE* 4.8 16.6 - - - +
159L ILE 5.9 0.6 + - - -
160L PRO* 4.6 27.6 - - + +
164L GLU* 5.6 4.7 - - + -
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Residues in contact with GLN 560 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556J LYS 3.2 19.2 + - - +
557J LEU* 3.7 7.6 - - - +
558J LEU 3.0 0.4 - - - -
559J ALA* 1.3 78.5 - - - +
561J GLY* 1.3 57.0 + - - +
562J ALA* 3.8 12.5 - - - +
144L GLU* 5.2 1.1 - - - -
147L ARG* 2.7 39.0 + - - +
199L ARG* 4.4 7.4 + - - +
233L GLN* 3.9 16.9 + - - +
236L ILE* 3.3 40.5 - - - +
237L ARG* 6.0 4.0 - - - +
240L GLU* 4.9 4.9 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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