Contacts of the strand formed by residues 631 - 640 (chain C) in PDB entry 2VKX
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 ILE 631 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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601C PRO* 3.7 22.2 - - + -
624C GLN 5.7 2.0 - - - +
626C ASP* 3.7 28.5 - - + -
630C PRO* 1.3 74.4 - - - +
632C ARG* 1.3 60.6 + - - +
633C HIS 3.6 22.2 - - - +
634C TYR* 4.1 26.0 - - + +
653C SER* 3.3 21.3 + - - +
675C ALA* 4.1 12.1 - - + -
676C GLU 3.3 14.1 - - - +
677C ASN* 4.5 1.6 - - + -
507D GLN* 2.9 31.6 + - - +
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Residues in contact with ARG 632 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630C PRO 3.5 2.7 + - - +
631C ILE* 1.3 73.7 - - - +
633C HIS* 1.3 91.0 + - + +
650C ARG* 4.1 17.4 - - - +
652C PRO* 4.7 0.7 - - - +
653C SER* 4.2 9.8 + - - -
676C GLU* 2.5 47.7 + - - +
677C ASN* 4.1 13.1 + - - -
678C GLN* 4.9 14.1 - - - +
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Residues in contact with HIS 633 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631C ILE* 3.6 7.5 - - - +
632C ARG* 1.3 120.7 + - + +
634C TYR* 1.3 64.4 + - - +
635C LEU* 4.0 14.6 - - + -
650C ARG* 3.6 37.8 + - + +
651C LEU 3.2 20.9 + - - +
652C PRO* 4.7 2.9 - - + +
653C SER 4.9 1.3 - - - +
675C ALA* 3.8 0.3 - - - -
676C GLU* 2.9 45.9 + - - +
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Residues in contact with TYR 634 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604C PRO* 4.1 17.2 - - + +
621C LEU* 4.5 14.4 - - + -
623C LYS* 3.2 39.7 + - + +
624C GLN 5.3 1.0 + - - -
631C ILE* 4.1 19.1 - - + +
633C HIS* 1.3 74.4 - - - +
635C LEU* 1.3 62.9 + - - +
636C VAL* 3.6 3.0 + - - -
649C ILE 3.7 0.3 - - - +
650C ARG* 3.9 0.7 - - - -
651C LEU* 2.9 46.8 + - + +
652C PRO 3.5 18.6 - - - -
653C SER* 3.6 27.2 + - - -
655C SER* 4.5 2.9 - - - -
673C VAL* 4.3 20.9 - - + -
674C VAL 3.3 3.6 - - - +
675C ALA* 4.0 29.2 - - + -
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Residues in contact with LEU 635 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633C HIS* 4.3 13.2 - - + -
634C TYR* 1.3 73.3 - - - +
636C VAL* 1.3 60.9 + - - +
637C ARG* 5.5 0.6 - - - +
648C GLU* 4.0 25.6 - - - +
649C ILE 3.6 1.3 - - - -
650C ARG* 3.4 34.8 - - + +
672C TYR 3.6 2.1 - - - +
673C VAL* 3.5 2.9 - - - -
674C VAL* 2.8 47.6 + - + +
676C GLU* 3.7 29.4 - - + +
681C LYS* 3.9 22.0 - - + +
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Residues in contact with VAL 636 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621C LEU* 6.3 0.4 - - + -
634C TYR 4.2 2.0 - - - +
635C LEU* 1.3 74.8 - - - +
637C ARG* 1.3 79.2 + - - +
638C TYR* 5.2 3.4 - - + -
648C GLU* 3.3 1.9 - - - +
649C ILE* 2.9 60.5 + - + +
651C LEU* 3.6 33.9 - - + -
658C VAL* 4.5 17.3 - - + -
660C LEU* 5.9 1.8 - - + -
671C VAL* 4.5 10.8 - - + -
672C TYR 3.3 6.3 - - - +
673C VAL* 4.3 19.5 - - + -
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Residues in contact with ARG 637 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636C VAL* 1.3 83.5 - - - +
638C TYR* 1.3 64.6 + - - +
645C TRP* 3.7 51.0 - - + +
646C LYS 4.8 4.7 - - - +
647C PRO 5.4 1.1 - - - -
648C GLU* 3.7 38.8 + - + +
649C ILE* 5.7 0.2 - - - -
671C VAL* 3.4 2.8 - - - +
672C TYR* 2.7 46.0 + - + +
674C VAL* 6.2 2.4 - - - +
681C LYS* 6.0 2.2 - - - +
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Residues in contact with TYR 638 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636C VAL* 5.2 2.5 - - + -
637C ARG* 1.3 79.1 - - - +
639C ARG* 1.3 73.9 + - - +
645C TRP* 3.7 3.3 - - - -
646C LYS* 3.2 63.8 + - + +
647C PRO 5.0 3.1 + - - -
649C ILE* 4.1 23.3 - - + -
660C LEU* 3.9 34.5 - - + -
663C LEU* 4.5 15.7 - - + +
669C TYR* 4.8 9.2 - + + -
670C GLU 3.1 12.6 - - - +
671C VAL* 3.7 17.7 - - + -
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Residues in contact with ARG 639 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638C TYR* 1.3 85.9 - - - +
640C ALA* 1.3 78.3 + - - +
641C LEU* 3.4 9.5 + - - +
642C SER 3.5 1.8 - - - +
643C SER 3.4 18.1 + - - -
644C GLU 3.7 7.2 - - - +
645C TRP* 3.3 60.1 - - + +
646C LYS* 4.2 5.4 - - - +
669C TYR* 3.1 8.8 - - - -
670C GLU* 2.8 56.7 + - - +
1697C SO4 2.9 36.3 + - - -
594E LYS* 6.0 1.0 - - - +
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Residues in contact with ALA 640 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639C ARG* 1.3 79.3 + - - +
641C LEU* 1.3 70.0 + - - +
643C SER* 3.1 28.4 + - - +
646C LYS* 4.4 11.1 - - - +
664C ASP* 5.1 5.4 - - - +
667C ALA* 5.7 3.4 - - + -
668C GLU 3.5 5.4 - - - +
669C TYR* 3.3 30.1 - - + +
541E GLY* 6.6 0.2 - - - -
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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