Contacts of the strand formed by residues 667 - 674 (chain A) in PDB entry 3GVJ
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 667 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A ARG* 4.0 6.9 - - - +
304A LEU* 3.8 5.9 - - - +
306A TYR* 3.0 35.7 + - - -
645A SER* 3.7 0.9 - - - -
646A GLU* 2.8 65.8 + - - +
649A GLU* 5.2 2.7 - - + +
650A ASN* 3.6 22.2 - - - +
652A TRP* 3.7 4.4 - - - +
653A GLU* 2.9 40.2 + - - -
665A TYR 4.6 3.4 - - - +
666A PRO* 1.3 72.2 - - - +
668A THR* 1.3 61.6 + - - +
669A PHE* 3.5 29.6 - - + -
687A ASN* 3.6 17.9 - - - +
690A ASP* 3.5 13.7 - - - +
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Residues in contact with THR 668 (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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644A GLY 3.5 11.0 - - - +
645A SER* 2.8 22.6 + - - +
666A PRO 3.8 0.6 + - - -
667A ARG* 1.3 73.2 - - - +
669A PHE* 1.3 65.5 + - - +
687A ASN* 3.1 16.6 - - - +
688A ILE* 3.1 20.0 + - + -
689A THR* 3.0 28.1 + - + +
691A GLN* 2.7 26.9 + - - +
702A VAL* 5.1 0.5 - - - +
716A TYR* 3.8 21.1 - - + -
718A PHE* 3.6 4.1 - - + -
750A TYR* 6.1 0.2 - - + -
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Residues in contact with PHE 669 (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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304A LEU* 4.2 29.8 - - + -
306A TYR* 5.2 0.9 - - - -
643A PHE* 3.5 6.4 - - - +
644A GLY 2.9 31.7 + - - +
646A GLU* 4.9 0.4 - - - -
652A TRP* 3.5 43.7 - + + -
667A ARG* 3.5 48.7 - - + -
668A THR* 1.3 75.7 - - - +
670A TYR* 1.3 61.2 + - - +
685A TRP* 3.8 33.9 - - + -
686A VAL 3.2 8.5 - - - +
687A ASN* 3.5 30.1 - - + -
688A ILE* 4.5 4.3 - - - -
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Residues in contact with TYR 670 (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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311A PHE* 5.9 2.1 - - - -
312A VAL* 4.0 15.9 - - + +
641A ILE* 3.9 20.6 - - + -
642A MET 3.2 12.8 - - - +
643A PHE* 3.7 18.2 - - + -
669A PHE* 1.3 75.6 - - - +
671A ALA* 1.3 66.0 - - - +
672A ARG* 4.4 23.7 + - + -
684A GLU 3.6 1.6 - - - +
685A TRP* 3.9 3.6 - - - -
686A VAL* 2.9 50.8 + - + +
688A ILE* 3.7 25.1 - - + +
752A MET* 3.6 37.2 - - + +
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Residues in contact with ALA 671 (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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640A LEU 3.6 0.2 - - - +
641A ILE* 3.4 4.2 - - - +
642A MET* 2.9 36.2 + - + +
670A TYR* 1.3 81.7 - - - +
672A ARG* 1.3 62.8 + - - +
683A ILE* 3.7 24.7 - - + -
684A GLU 3.5 16.2 - - - +
685A TRP* 3.5 24.1 - - + -
686A VAL* 5.7 0.4 - - - -
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Residues in contact with ARG 672 (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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636A VAL* 4.8 6.1 + - - +
639A ASP* 2.9 36.3 + - - +
640A LEU 3.3 3.4 - - - -
641A ILE* 3.7 35.3 - - + +
670A TYR* 4.4 23.3 + - + -
671A ALA* 1.3 77.2 - - - +
673A LEU* 1.3 61.9 + - - +
674A ASN 4.2 0.2 - - - -
683A ILE* 4.4 13.0 - - - +
684A GLU 4.8 3.2 + - - -
752A MET* 5.4 2.2 - - - -
753A LYS 5.3 1.4 + - - -
754A ILE* 4.1 19.4 + - - +
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Residues in contact with LEU 673 (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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607A LEU* 3.5 30.5 - - + -
620A LEU* 4.6 6.5 - - + -
622A PHE* 3.7 30.7 - - + -
639A ASP* 3.4 3.8 - - - -
640A LEU* 2.9 37.0 + - + +
642A MET* 4.3 13.5 - - + -
671A ALA 4.2 0.2 - - - -
672A ARG* 1.3 74.5 - - - +
674A ASN* 1.3 75.4 + - - +
675A VAL* 3.4 2.8 + - - +
678A TRP* 4.5 14.4 - - + -
679A ASN 4.9 9.0 - - - +
680A ALA* 4.0 18.4 - - + -
683A ILE* 4.2 6.7 - - + -
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Residues in contact with ASN 674 (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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638A ASP* 3.4 25.6 + - - +
639A ASP* 3.4 11.2 + - - +
672A ARG 4.2 0.6 - - - -
673A LEU* 1.3 75.4 - - - +
675A VAL* 1.3 63.7 + - - +
676A ASN* 2.9 35.2 + - - +
677A ASN* 3.0 32.1 + - + +
678A TRP 3.2 17.5 + - - -
679A ASN 4.8 0.5 + - - -
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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