Contacts of the helix formed by residues 635 - 652 (chain A) in PDB entry 2VWK
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 635 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629A ALA* 2.8 24.7 + - - +
630A ILE* 3.8 1.2 + - - -
633A HIS* 3.9 9.0 - - + +
634A GLY* 1.3 71.3 - - - +
636A VAL* 1.3 60.9 + - - +
637A GLU* 2.9 11.3 + - - +
638A GLU* 2.6 50.7 + - + +
639A ALA* 3.3 14.4 + - - +
641A ARG* 4.6 6.4 + - - -
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Residues in contact with VAL 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LEU* 4.6 11.4 - - + -
630A ILE* 4.2 20.4 - - + -
634A GLY 4.1 0.8 + - - +
635A ASP* 1.3 72.0 - - - +
637A GLU* 1.3 62.8 + - + +
639A ALA* 3.3 5.5 - - - +
640A VAL* 3.2 19.6 + - - +
745A LEU* 4.9 5.4 - - + -
748A PHE* 3.8 44.0 - - + -
750A TYR* 4.0 27.1 - - + +
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Residues in contact with GLU 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A ASP* 2.9 7.8 + - - +
636A VAL* 1.3 77.1 - - + +
638A GLU* 1.3 54.4 + - - +
640A VAL* 3.1 7.0 + - + +
641A ARG* 2.8 48.7 + - - +
750A TYR* 3.9 18.5 + - - +
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Residues in contact with GLU 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A ALA* 3.9 4.2 - - + +
633A HIS* 2.7 46.4 + - - +
635A ASP* 2.6 29.0 + - - +
637A GLU* 1.3 68.0 - - - +
639A ALA* 1.3 57.4 + - - +
641A ARG* 3.1 28.3 + - + +
642A ILE* 2.7 59.4 + - + +
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Residues in contact with ALA 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A VAL* 3.9 20.1 - - + +
629A ALA* 3.7 16.1 - - + +
630A ILE* 3.8 26.9 - - + -
635A ASP 3.3 4.1 + - - +
636A VAL 3.3 10.8 - - - +
637A GLU 3.3 0.2 - - - -
638A GLU* 1.3 78.3 - - - +
640A VAL* 1.3 60.9 + - - +
642A ILE* 3.4 6.5 + - - +
643A VAL* 3.3 28.3 + - - +
745A LEU* 4.2 6.7 - - + -
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Residues in contact with VAL 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A VAL 3.2 9.3 + - - +
637A GLU* 3.1 9.2 + - - +
639A ALA* 1.3 73.4 - - - +
641A ARG* 1.3 66.7 + - - +
643A VAL* 3.4 4.3 + - - +
644A LYS* 3.1 32.1 + - - +
745A LEU* 4.1 22.0 - - + -
750A TYR* 3.7 52.0 - - + +
754A ASP 3.8 22.0 - - - +
755A LEU* 4.2 5.8 - - + +
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Residues in contact with ARG 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A ASP* 4.6 7.3 + - - -
637A GLU* 2.8 25.5 + - - +
638A GLU* 3.4 46.3 - - + +
640A VAL* 1.3 76.5 - - - +
642A ILE* 1.3 57.4 + - + +
644A LYS* 3.0 11.6 + - - +
645A GLU* 2.9 51.9 + - - +
757A TYR* 4.2 12.6 - - - +
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Residues in contact with ILE 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622A THR* 4.8 7.2 - - + -
625A ARG* 3.5 69.3 - - + +
626A VAL* 5.0 3.6 - - + -
629A ALA* 4.3 2.7 - - + -
633A HIS* 6.2 0.7 - - + -
638A GLU* 2.7 50.8 + - + +
639A ALA* 3.7 5.8 - - - +
640A VAL 3.3 0.2 - - - -
641A ARG* 1.3 73.1 - - + +
643A VAL* 1.3 60.4 + - + +
645A GLU* 3.2 15.0 + - - +
646A VAL* 2.8 33.3 + - + +
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Residues in contact with VAL 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A THR* 4.4 6.3 - - + -
626A VAL* 3.5 24.0 - - + -
639A ALA 3.3 16.0 + - - +
640A VAL 3.8 6.3 - - - +
641A ARG 3.3 0.2 - - - -
642A ILE* 1.3 75.6 - - - +
644A LYS* 1.3 58.1 + - - +
646A VAL* 3.9 5.5 - - - +
647A THR* 2.9 32.6 + - + +
737A VAL* 5.0 5.2 - - + -
738A LEU* 3.9 21.8 - - + -
741A VAL* 3.9 22.0 - - + -
745A LEU* 4.0 7.4 - - + -
755A LEU* 3.8 22.9 - - + +
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Residues in contact with LYS 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A VAL* 3.1 27.3 + - - +
641A ARG* 3.0 12.4 + - - +
643A VAL* 1.3 76.3 - - - +
645A GLU* 1.3 58.3 + - - +
647A THR* 2.9 19.7 + - - -
648A GLU* 2.9 18.7 + - - +
754A ASP 3.2 18.8 - - - +
755A LEU 3.6 18.2 - - - -
756A ARG* 3.4 18.1 + - - +
757A TYR* 3.6 45.8 + - + +
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Residues in contact with GLU 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A ARG* 5.0 4.3 + - - -
641A ARG* 2.9 43.4 + - - +
642A ILE* 3.5 17.9 - - - +
644A LYS* 1.3 76.4 - - - +
646A VAL* 1.3 53.4 + - + +
648A GLU* 3.1 7.1 + - - +
649A LYS* 2.8 43.2 + - + +
757A TYR* 4.4 13.6 + - + +
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Residues in contact with VAL 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ILE* 4.5 18.8 - - + -
622A THR* 3.5 36.6 - - + +
625A ARG* 3.6 25.8 - - - +
642A ILE* 2.8 22.4 + - + +
643A VAL 3.9 3.6 - - - +
645A GLU* 1.3 73.3 - - + +
647A THR* 1.3 56.4 + - - +
649A LYS* 3.4 13.4 + - - +
650A LEU* 3.0 32.5 + - + +
655A VAL* 4.5 2.6 - - + +
737A VAL* 4.2 11.4 - - + -
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Residues in contact with THR 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A VAL* 2.9 18.8 + - + +
644A LYS* 2.9 17.2 + - - -
646A VAL* 1.3 71.9 - - - +
648A GLU* 1.3 64.3 + - - +
650A LEU* 3.4 6.9 + - - -
651A SER* 3.1 20.1 + - - -
733A ILE* 3.4 39.8 - - + +
737A VAL* 4.7 10.5 - - + -
738A LEU* 4.0 20.9 - - + -
755A LEU 3.4 11.0 + - - +
756A ARG* 3.9 16.8 - - + +
757A TYR 5.0 0.3 + - - -
760A THR* 5.7 2.0 + - - -
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Residues in contact with GLU 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A LYS 2.9 19.0 + - - +
645A GLU* 3.1 7.6 + - - +
647A THR* 1.3 75.7 + - - +
649A LYS* 1.3 65.5 + - + +
651A SER* 2.9 20.7 + - - -
652A LYS* 3.1 31.9 + - + +
757A TYR* 3.7 21.8 - - + +
760A THR* 3.1 31.7 - - + +
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Residues in contact with LYS 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A GLU* 2.8 25.9 + - + +
646A VAL* 3.7 12.1 - - - +
648A GLU* 1.3 74.2 - - + +
650A LEU* 1.3 61.7 + - - +
652A LYS* 3.4 1.8 + - - -
653A TYR 3.2 3.8 + - - -
654A GLU* 3.0 58.3 + - + +
655A VAL* 3.8 18.4 - - + +
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Residues in contact with LEU 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A ILE* 4.6 1.8 - - + -
646A VAL* 3.0 21.4 + - + +
647A THR* 3.5 10.8 - - - +
648A GLU 3.2 0.2 - - - -
649A LYS* 1.3 76.6 - - - +
651A SER* 1.3 61.9 + - - +
653A TYR* 3.2 10.2 + - - -
655A VAL* 3.7 26.0 - - + +
660A LEU* 3.9 21.5 - - + -
727A TYR* 3.3 20.6 + - + +
729A ALA* 3.2 18.5 - - + +
732A TYR* 3.9 15.5 - - + -
733A ILE* 3.7 26.2 - - + -
737A VAL* 3.8 29.4 - - + -
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Residues in contact with SER 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A THR 3.1 14.0 + - - -
648A GLU* 2.9 14.6 + - - -
650A LEU* 1.3 74.9 - - - +
652A LYS* 1.3 64.6 + - - +
653A TYR* 3.3 19.3 + - - -
729A ALA* 4.0 10.0 - - - +
730A GLU* 5.5 0.2 + - - -
733A ILE* 4.0 9.0 - - - +
756A ARG* 4.5 0.5 + - - -
760A THR* 2.8 34.9 + - - -
761A ARG* 4.0 11.2 - - - +
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Residues in contact with LYS 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A GLU* 3.1 35.8 + - + +
649A LYS* 3.4 0.4 + - - -
650A LEU 3.2 0.4 - - - -
651A SER* 1.3 80.4 - - - +
653A TYR* 1.3 76.5 + - - +
654A GLU* 3.1 31.0 + - - +
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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