Contacts of the strand formed by residues 1572 - 1576 (chain B) in PDB entry 2V5P
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 ILE1572 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1566B CYS* 3.3 3.6 - - - -
1567B PHE* 3.2 51.7 + - + +
1570B THR* 3.2 30.3 + - - +
1571B ARG* 1.3 68.5 - - - +
1573B SER* 1.3 63.0 + - - +
1574B VAL 3.5 0.3 + - - -
1596B SER* 3.2 22.7 - - - +
1597B PRO 5.6 0.4 - - - +
1606B TYR* 4.0 13.2 - - + +
12C GLU* 3.7 28.5 - - + +
15C ASP* 3.9 10.3 - - + -
16C THR* 3.5 25.8 - - - +
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Residues in contact with SER1573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1560B PRO* 5.5 1.8 - - - -
1563B VAL* 3.3 37.4 - - - +
1565B ALA 3.8 6.1 - - - -
1566B CYS* 4.2 0.9 - - - -
1571B ARG 3.1 8.9 + - - -
1572B ILE* 1.3 70.9 - - - +
1574B VAL* 1.3 60.6 + - - +
1575B GLY 3.4 11.3 + - - -
1576B LYS* 5.5 0.3 - - - +
1594B ASP 4.5 1.7 + - - -
1595B GLY* 3.8 7.0 - - - -
1596B SER* 3.0 42.0 + - - -
1606B TYR* 3.6 7.3 - - - -
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Residues in contact with VAL1574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1548B VAL* 5.1 3.6 - - + -
1565B ALA* 3.0 34.2 + - + +
1566B CYS* 4.1 4.7 - - - +
1567B PHE* 3.5 33.7 - - + -
1572B ILE 3.5 0.4 + - - +
1573B SER* 1.3 76.3 - - - +
1575B GLY* 1.3 55.3 + - - +
1592B TYR* 4.9 0.2 - - - -
1606B TYR* 3.6 20.0 - - + -
1607B LYS 3.7 2.9 - - - -
1608B SER* 2.7 46.3 + - - +
1636B LEU* 3.8 32.8 - - + -
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Residues in contact with GLY1575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1563B VAL* 3.4 10.7 - - - +
1564B GLY 3.0 20.3 + - - -
1565B ALA 3.9 1.8 + - - -
1573B SER* 3.4 9.2 + - - -
1574B VAL* 1.3 78.6 - - - +
1576B LYS* 1.3 61.9 + - - -
1592B TYR* 3.5 18.8 - - - -
1593B LYS 3.4 10.8 - - - -
1594B ASP 4.5 0.2 - - - -
1595B GLY* 3.7 7.3 - - - -
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Residues in contact with LYS1576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1562B GLY 3.4 13.5 - - - +
1563B VAL* 5.3 3.6 - - + -
1564B GLY 4.1 0.2 - - - -
1573B SER* 5.5 1.3 - - - +
1575B GLY* 1.3 73.5 - - - -
1577B ALA* 1.3 63.2 + - - +
1578B ASN* 3.0 22.5 + - - -
1592B TYR* 3.1 10.7 - - - -
1593B LYS* 2.6 27.7 + - + +
1594B ASP* 3.4 42.8 + - + +
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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