Contacts of the helix formed by residues 638 - 656 (chain B) in PDB entry 5J3V
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 LYS 638 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619B THR* 4.2 12.1 - - + -
623B ALA* 4.9 16.1 - - - +
636B PRO* 3.2 13.9 + - + +
637B ASP* 1.3 70.1 + - - +
639B ASP* 1.3 58.5 + - - +
640B PHE 3.2 0.7 - - - -
641B MET* 3.1 22.9 + - + +
642B ILE* 3.0 31.4 + - - +
678B ASP* 3.0 38.9 + - - +
679B LYS* 4.6 10.1 - - - +
680B MET* 3.7 41.2 - - + +
683B VAL* 4.1 2.5 - - + -
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Residues in contact with ASP 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584B PHE* 3.5 26.1 - - + -
637B ASP* 3.0 21.3 + - - +
638B LYS* 1.3 76.4 - - - +
640B PHE* 1.3 58.6 + - - +
642B ILE* 3.7 18.2 - - - +
643B VAL* 2.9 38.1 + - + +
680B MET* 5.7 1.4 - - - +
18D LYS* 4.4 18.3 + - - +
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Residues in contact with PHE 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B ASP 3.2 24.0 - - - -
579B GLU* 3.7 14.1 - - - -
580B ASP 3.3 33.9 - - - -
581B LYS* 3.8 12.3 - - + -
583B LEU* 4.1 12.3 - - + -
584B PHE* 3.5 31.2 - + - -
615B LEU* 4.4 19.6 - - + +
619B THR* 3.9 12.3 - - - +
637B ASP* 3.1 34.9 + - + +
639B ASP* 1.3 77.8 - - - +
641B MET* 1.3 57.6 + - - +
643B VAL* 4.3 1.8 - - - +
644B ALA* 3.1 29.6 + - - +
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Residues in contact with MET 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616B VAL* 4.2 20.8 - - + +
619B THR* 3.7 24.8 + - + -
620B LEU* 3.6 34.5 - - + -
623B ALA* 6.4 0.7 - - + -
638B LYS* 3.1 27.6 + - + +
640B PHE* 1.3 79.3 - - - +
642B ILE* 1.3 65.0 + - + +
644B ALA* 3.4 3.6 + - - +
645B LEU* 3.0 34.8 + - + +
675B CYS* 4.0 13.7 - - - -
678B ASP* 3.9 10.5 - - - +
683B VAL* 3.7 31.0 - - + -
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Residues in contact with ILE 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638B LYS 3.0 16.5 + - - +
639B ASP* 3.7 23.1 - - - +
641B MET* 1.3 75.7 - - - +
643B VAL* 1.3 65.7 + - + +
645B LEU* 3.4 3.9 + - - +
646B ASP* 3.1 37.3 + - - +
680B MET* 4.1 13.5 - - - -
682B GLU* 3.6 33.2 - - + +
683B VAL* 4.1 15.3 - - + -
686B SER* 3.3 23.1 + - - +
18D LYS* 4.8 20.4 - - + +
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Residues in contact with VAL 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B LEU 4.2 0.9 - - - +
584B PHE* 3.7 44.4 - - + +
587B LEU* 3.4 33.4 - - + +
588B GLU* 4.2 9.8 - - + +
639B ASP* 2.9 22.1 + - + +
640B PHE* 4.3 3.1 - - - +
642B ILE* 1.3 80.1 - - + +
644B ALA* 1.3 61.6 + - - +
646B ASP* 3.5 9.6 + - - +
647B LEU* 3.3 20.1 + - - +
20D LEU* 5.5 6.7 - - + -
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Residues in contact with ALA 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587B LEU* 4.7 3.6 - - - +
612B CYS* 3.6 34.3 - - - +
615B LEU* 3.9 18.6 - - + -
616B VAL* 3.9 9.0 - - + -
640B PHE 3.1 21.5 + - - +
641B MET 3.9 0.2 - - - +
643B VAL* 1.3 76.7 - - - +
645B LEU* 1.3 64.1 + - - +
647B LEU* 3.4 4.3 + - - +
648B LEU* 3.2 25.9 + - - +
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Residues in contact with LEU 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616B VAL* 3.7 27.1 - - + -
641B MET* 3.0 26.4 + - + +
642B ILE* 3.7 4.9 - - - +
644B ALA* 1.3 76.7 - - - +
646B ASP* 1.3 59.3 + - - +
648B LEU* 3.3 10.5 + - + +
649B SER* 3.0 25.6 + - - -
668B ILE* 5.2 3.6 - - + -
672B MET* 5.4 3.8 - - + -
675B CYS* 4.0 23.3 - - + -
683B VAL* 4.1 8.5 - - + +
686B SER* 3.9 18.6 - - - +
687B SER* 4.0 25.6 - - - +
690B LEU* 3.8 27.4 - - + +
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Residues in contact with ASP 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588B GLU* 6.1 3.4 - - + +
591B SER* 3.8 10.7 - - - -
642B ILE* 3.1 25.6 + - - +
643B VAL* 3.8 8.1 - - - +
644B ALA 3.3 0.4 - - - -
645B LEU* 1.3 74.3 - - - +
647B LEU* 1.3 60.0 + - - +
649B SER* 3.3 9.5 + - - -
650B GLY* 2.9 21.7 + - - -
686B SER* 3.1 29.3 + - - +
689B ALA* 5.4 3.1 - - - +
17D ARG* 3.8 39.4 + - - +
18D LYS* 4.9 3.6 + - - +
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Residues in contact with LEU 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573B TRP* 4.0 6.5 - - + -
587B LEU* 3.7 33.7 - - + +
590B LEU* 3.8 12.1 - - + +
591B SER* 3.6 32.3 - - - +
594B ALA* 4.7 4.7 - - + -
601B PHE* 5.7 0.4 - - + -
608B VAL* 3.7 23.8 - - + -
612B CYS* 3.5 24.5 - - - -
643B VAL 3.3 10.6 + - - +
644B ALA* 3.7 8.7 - - - +
645B LEU 3.2 0.4 - - - -
646B ASP* 1.3 76.0 - - - +
648B LEU* 1.3 60.8 + - - +
650B GLY 3.2 0.9 + - - -
651B LEU* 3.0 31.4 + - + +
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Residues in contact with LEU 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B TYR* 3.6 40.4 - - + +
612B CYS* 3.7 26.9 - - + +
613B VAL* 4.2 10.5 - - + +
616B VAL* 4.8 1.6 - - + -
644B ALA 3.2 16.2 + - - +
645B LEU* 3.3 16.6 + - + +
647B LEU* 1.3 76.5 - - - +
649B SER* 1.3 60.6 + - - +
651B LEU* 3.5 7.4 + - + +
652B ALA* 3.1 23.6 + - - +
659B ILE* 4.5 3.7 - - + +
668B ILE* 3.8 24.9 - - + -
690B LEU* 3.5 24.7 - - + +
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Residues in contact with SER 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645B LEU 3.0 13.0 + - - -
646B ASP* 3.3 14.4 - - - -
648B LEU* 1.3 77.2 - - - +
650B GLY* 1.3 57.0 + - - +
652B ALA* 3.4 2.2 + - - +
653B GLU* 3.0 31.3 + - - +
686B SER 5.4 0.4 - - - -
689B ALA* 4.0 4.4 + - - -
690B LEU* 3.6 19.2 - - - +
693B ASP* 2.3 32.2 + - - +
14D LYS* 3.7 16.8 - - - +
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Residues in contact with GLY 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591B SER* 3.9 11.9 - - - -
594B ALA* 4.0 6.4 - - - -
595B THR* 3.2 28.4 + - - -
646B ASP 2.9 13.9 + - - -
647B LEU 3.2 4.8 + - - -
649B SER* 1.3 77.6 + - - +
651B LEU* 1.3 55.6 + - - +
653B GLU* 4.6 2.9 - - - -
654B GLY* 3.0 23.9 + - - -
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Residues in contact with LEU 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594B ALA* 3.7 13.2 - - + -
601B PHE* 3.5 37.0 - - + -
605B CYS 4.2 4.0 - - - +
608B VAL* 4.1 13.7 - - + -
609B TYR* 4.0 39.9 - - + +
647B LEU* 3.0 19.3 + - + +
648B LEU* 3.7 12.1 - - + +
650B GLY* 1.3 75.6 - - - +
652B ALA* 1.3 59.8 + - - +
655B LEU* 2.6 54.8 + - + +
659B ILE* 4.1 10.3 - - + -
662B LEU* 5.5 0.4 - - + -
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Residues in contact with ALA 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648B LEU 3.1 15.7 + - - +
649B SER* 3.4 0.9 + - - +
651B LEU* 1.3 77.3 - - - +
653B GLU* 1.3 61.2 + - - +
656B GLY* 3.2 22.5 + - - +
659B ILE* 3.8 12.5 - - + +
690B LEU* 4.7 0.4 - - + -
693B ASP* 3.7 29.2 - - + +
694B LEU* 3.7 28.0 - - + -
697B ALA* 3.8 8.6 - - + +
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Residues in contact with GLU 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595B THR* 3.6 29.7 + - + +
598B GLN* 4.5 5.0 + - - +
649B SER 3.0 17.8 + - - +
650B GLY* 4.1 4.1 - - - +
652B ALA* 1.3 77.2 - - - +
654B GLY* 1.3 61.2 + - - +
656B GLY* 4.3 3.6 + - - -
693B ASP* 4.2 13.8 - - - +
696B LYS* 6.0 7.0 - - - +
14D LYS* 3.4 29.4 + - - +
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Residues in contact with GLY 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594B ALA 3.8 14.6 - - - -
595B THR* 3.9 9.8 - - - +
598B GLN* 3.0 37.7 - - - +
599B SER 4.4 0.2 + - - -
650B GLY 3.0 17.5 + - - -
653B GLU* 1.3 77.3 - - - +
655B LEU* 1.3 63.4 + - - +
656B GLY* 3.2 2.2 + - - -
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Residues in contact with LEU 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594B ALA 4.9 0.9 + - - +
598B GLN 3.3 21.1 - - - +
599B SER* 4.5 3.6 - - - +
601B PHE* 4.3 7.0 - - + -
602B LEU* 3.7 37.7 - - + +
605B CYS* 3.6 28.0 - - + -
651B LEU* 2.6 41.5 + - + +
654B GLY* 1.3 74.0 - - - +
656B GLY* 1.3 62.1 + - - +
657B GLY 3.4 0.5 + - - -
658B ASN* 3.1 32.3 + - + +
659B ILE* 4.6 17.5 - - + +
662B LEU* 5.0 3.1 - - + -
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Residues in contact with GLY 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651B LEU 3.7 0.2 + - - -
652B ALA 3.2 19.8 + - - +
653B GLU 4.7 3.1 - - - -
654B GLY 3.2 2.9 - - - -
655B LEU* 1.3 72.2 - - - +
657B GLY* 1.3 59.4 + - - -
658B ASN 3.1 9.8 + - - -
659B ILE* 3.3 14.6 + - - +
697B ALA* 3.2 23.4 - - - +
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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) + - + + + + + -
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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