Contacts of the strand formed by residues 469 - 472 (chain A) in PDB entry 2V3V
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 GLY 469 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LEU* 3.6 16.6 - - - +
115A GLU* 3.4 18.8 - - - -
468A ASP* 1.3 77.4 - - - +
470A VAL* 1.3 64.5 + - - -
471A TYR 4.1 0.3 + - - -
479A SER 4.0 0.2 - - - +
480A LEU* 3.9 6.5 - - - +
481A THR* 3.0 35.8 + - - +
517A ALA* 4.7 0.4 - - - -
540A ARG* 4.7 0.4 - - - -
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Residues in contact with VAL 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 3.8 0.5 - - - -
114A THR* 3.0 33.6 + - - +
115A GLU* 2.9 9.8 + - - +
348A ASN* 3.3 1.2 + - - -
469A GLY* 1.3 73.8 - - - -
471A TYR* 1.3 76.9 + - - +
478A TYR* 3.9 16.6 - - + -
479A SER 3.5 11.9 - - - +
480A LEU* 4.1 10.3 - - + -
521A TRP* 3.5 43.3 - - + -
540A ARG* 3.6 23.3 - - - +
543A LEU* 4.3 9.9 - - + -
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Residues in contact with TYR 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 4.1 30.1 - - + -
13A CYS 4.1 9.0 - - - -
14A ARG* 3.7 27.7 + - - -
111A GLN* 2.5 32.3 + - - -
112A CYS 3.6 12.6 - - - -
113A LEU* 4.0 15.2 - - + +
347A PRO* 3.6 31.9 - - + +
348A ASN* 3.3 20.9 - - + -
416A GLU* 4.4 0.9 + - - -
464A TRP* 5.2 7.0 - + - -
467A ARG* 5.5 3.3 + - - -
469A GLY 4.1 0.8 + - - -
470A VAL* 1.3 84.6 - - - +
472A GLY* 1.3 59.9 + - - +
473A CYS* 3.9 1.4 + - + +
477A ARG 3.6 1.7 - - - +
478A TYR* 3.6 0.3 - - - -
479A SER* 2.8 36.0 + - - +
481A THR* 5.0 6.3 - - - +
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Residues in contact with GLY 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 4.4 1.0 + - - -
344A THR* 6.0 0.2 - - - +
347A PRO 3.0 12.5 - - - +
348A ASN* 2.6 21.1 + - - +
350A CYS* 3.4 5.2 + - - +
351A GLY* 3.4 20.0 + - - -
470A VAL 4.2 0.2 - - - -
471A TYR* 1.3 71.8 - - - +
473A CYS* 1.3 66.8 + - - +
477A ARG 3.3 8.5 - - - -
478A TYR* 3.7 18.4 - - - -
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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