Contacts of the strand formed by residues 658 - 662 (chain C) in PDB entry 6VVT
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 ARG 658 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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642C GLU* 3.3 36.1 + - - +
643C GLU* 5.4 3.0 + - - -
650C THR* 5.5 8.1 - - - +
651C VAL 3.8 7.6 - - - +
652C MET* 4.0 18.9 - - + +
656C GLY 4.7 1.8 - - - +
657C THR* 1.3 78.1 - - - +
659C GLN* 1.3 66.0 + - - +
660C SER* 4.3 5.1 + - - +
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Residues in contact with GLN 659 (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 ASP* 5.5 4.9 - - + -
637C LYS* 3.2 34.5 - - + +
649C ILE 4.1 0.3 - - - +
650C THR* 3.4 3.6 - - - -
651C VAL* 2.9 45.8 + - + +
653C ALA* 4.2 5.4 - - - +
657C THR* 3.0 35.1 + - - +
658C ARG* 1.3 82.4 + - - +
660C SER* 1.3 63.2 + - - +
661C TYR* 3.8 24.7 - - + +
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Residues in contact with SER 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648C TYR* 4.8 6.7 - - - -
649C ILE 3.2 6.3 - - - -
650C THR* 2.8 30.2 - - - +
658C ARG* 4.3 5.2 + - - +
659C GLN* 1.3 74.5 - - - +
661C TYR* 1.3 73.1 + - - +
662C ARG* 6.0 2.0 - - - -
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Residues in contact with TYR 661 (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 VAL* 3.8 26.7 - - + -
634C VAL 3.7 11.7 - - - -
635C ALA* 3.8 1.6 - - - -
636C ASP* 2.7 43.7 + - - +
637C LYS 4.8 0.7 + - - -
648C TYR* 3.2 6.6 - - - -
649C ILE* 2.8 45.2 + - + +
651C VAL* 4.1 23.6 - - + +
659C GLN* 3.8 19.9 - - + +
660C SER* 1.3 81.1 - - - +
662C ARG* 1.3 64.7 + - - +
663C LEU* 3.7 6.9 + - + +
693C ILE* 3.7 21.8 - - + -
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Residues in contact with ARG 662 (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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111C ASP* 5.2 10.5 + - - +
633C VAL* 5.6 1.0 - - - +
647C ASP 3.8 6.7 - - - +
648C TYR* 4.1 11.2 - - + -
660C SER* 4.3 2.2 - - - -
661C TYR* 1.3 75.0 - - - +
663C LEU* 1.3 64.5 + - - +
664C ARG* 3.9 1.9 + - - +
677C GLN* 4.1 3.1 - - - +
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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