Contacts of the strand formed by residues 631 - 640 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507E GLN* 2.7 33.4 + - - +
601F PRO* 4.2 11.2 - - + -
602F SER 5.4 0.9 - - - +
623F LYS* 5.9 0.2 - - + -
624F GLN 5.1 5.2 - - - +
626F ASP* 3.3 30.5 - - + -
630F PRO* 1.3 74.7 - - - +
632F ARG* 1.3 61.8 + - - +
633F HIS 3.6 21.3 - - - +
634F TYR* 3.7 28.9 - - + +
653F SER* 3.2 20.9 - - - -
675F ALA* 3.8 23.8 - - + -
676F GLU 3.6 10.5 - - - +
677F ASN* 4.2 0.9 - - - -
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Residues in contact with ARG 632 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629F SER* 5.0 2.2 + - - -
630F PRO* 3.5 11.3 + - + +
631F ILE* 1.3 75.2 - - - +
633F HIS* 1.3 85.8 + - + +
652F PRO* 4.9 1.4 - - - +
653F SER* 4.4 9.5 + - - -
676F GLU* 2.7 16.2 + - - +
677F ASN* 4.0 5.4 - - - -
678F GLN* 3.3 60.9 + - - +
1700F SO4 3.2 32.4 + - - +
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Residues in contact with HIS 633 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631F ILE* 3.6 11.3 - - - +
632F ARG* 1.3 98.7 + - + +
634F TYR* 1.3 63.4 + - - +
635F LEU* 4.0 9.6 - - + -
650F ARG* 2.8 32.1 + - + +
651F LEU 3.4 17.9 + - - +
652F PRO* 5.2 1.2 - - - +
653F SER 4.8 1.6 - - - +
675F ALA 3.8 0.2 - - - -
676F GLU* 2.8 57.3 + - - +
1700F SO4 2.6 36.6 + - - -
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Residues in contact with TYR 634 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604F PRO* 4.0 17.2 - - + +
621F LEU* 4.4 13.7 - - + -
623F LYS* 3.0 38.7 - - + +
624F GLN 5.3 0.5 + - - -
631F ILE* 3.7 21.2 - - + +
633F HIS* 1.3 75.1 - - - +
635F LEU* 1.3 62.9 + - - +
636F VAL* 3.8 5.0 + - + +
649F ILE 3.7 2.3 - - - +
650F ARG* 3.8 1.9 - - - -
651F LEU* 3.0 40.2 + - + +
652F PRO 3.6 17.7 - - - -
653F SER* 3.5 25.4 - - - -
655F SER* 4.3 9.4 - - - -
673F VAL* 4.2 18.4 - - + -
674F VAL 3.2 13.2 - - - -
675F ALA* 4.0 21.1 - - + -
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Residues in contact with LEU 635 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633F HIS* 4.4 4.9 - - + -
634F TYR* 1.3 74.0 - - - +
636F VAL* 1.3 60.2 + - - +
648F GLU* 3.5 29.8 - - - +
649F ILE 3.7 2.0 - - - -
650F ARG* 3.9 24.7 - - + +
672F TYR* 3.6 6.1 - - + +
673F VAL* 3.3 4.3 - - - -
674F VAL* 2.7 56.2 + - + +
676F GLU* 4.3 26.9 - - + +
681F LYS* 3.7 41.3 - - + +
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Residues in contact with VAL 636 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621F LEU* 6.2 2.0 - - + -
634F TYR* 4.2 8.1 - - + +
635F LEU* 1.3 77.5 - - - +
637F ARG* 1.3 74.6 + - - +
638F TYR* 5.9 0.9 - - + -
648F GLU* 4.5 0.6 - - - +
649F ILE* 2.6 60.0 + - + +
651F LEU* 3.6 28.3 - - + -
658F VAL* 3.8 23.6 - - + -
660F LEU* 5.8 2.5 - - + -
671F VAL* 4.4 6.7 - - + -
672F TYR 3.2 8.7 - - - +
673F VAL* 4.4 21.1 - - + -
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Residues in contact with ARG 637 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636F VAL* 1.3 84.7 - - - +
638F TYR* 1.3 62.8 + - - +
645F TRP* 3.6 41.6 - - + +
646F LYS 4.1 13.0 - - - +
647F PRO 5.3 1.8 - - - -
648F GLU* 2.9 46.4 + - + +
649F ILE* 5.3 1.3 - - - -
671F VAL* 3.4 1.9 - - - +
672F TYR* 2.6 87.3 + - + +
681F LYS* 5.8 2.2 - - - +
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Residues in contact with TYR 638 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636F VAL* 5.9 0.7 - - + -
637F ARG* 1.3 78.5 - - - +
639F ARG* 1.3 64.2 + - - +
645F TRP* 3.5 2.6 - - - -
646F LYS* 3.1 68.9 + - + +
647F PRO 5.9 2.0 - - - -
649F ILE* 4.9 12.6 - - + -
660F LEU* 3.9 43.3 - - + -
661F LYS 5.4 2.4 + - - -
663F LEU* 3.6 26.2 - - + +
669F TYR* 4.1 18.2 - + + -
670F GLU 3.2 12.1 - - - +
671F VAL* 4.2 5.2 - - + -
689F PHE* 5.9 0.2 - - + -
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Residues in contact with ARG 639 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594D LYS* 5.0 4.0 - - - +
638F TYR* 1.3 81.1 - - - +
640F ALA* 1.3 63.6 + - - +
641F LEU* 4.0 8.7 - - - +
643F SER 2.9 23.1 + - - +
644F GLU* 3.5 20.2 - - - +
645F TRP* 3.3 38.4 - - + +
646F LYS* 4.8 5.4 - - - +
669F TYR* 3.2 9.5 - - - +
670F GLU* 2.7 63.5 + - + +
1696F SO4 2.9 45.6 + - - -
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Residues in contact with ALA 640 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541D GLY* 6.4 0.2 - - - -
639F ARG* 1.3 74.4 - - - +
641F LEU* 1.3 71.4 + - - +
643F SER* 2.9 27.1 + - - +
646F LYS* 5.3 2.4 - - - +
664F ASP* 6.0 0.7 - - - +
667F ALA* 6.0 2.0 - - + -
668F GLU 3.6 4.3 - - - +
669F TYR* 3.5 29.0 - - + +
1699F SO4 4.2 22.8 + - - +
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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