Contacts of the strand formed by residues 1587 - 1592 (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 VAL1587 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1582B ARG 3.5 0.2 - - - +
1583B TYR* 3.4 6.1 - - - -
1584B VAL* 2.9 38.0 + - + +
1585B ASP 3.1 15.8 - - - +
1586B GLN* 1.3 82.5 - - - +
1588B LEU* 1.3 69.7 + - - +
1589B GLN* 3.8 7.3 + - + +
1611B SER* 3.6 29.8 - - - -
1612B PHE 3.4 15.3 - - - +
1613B VAL* 4.7 3.1 - - + -
1708B ALA* 3.1 32.3 - - + +
1709B GLY* 3.9 9.2 - - - +
1726B ARG* 4.2 1.1 - - - +
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Residues in contact with LEU1588 (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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1518B VAL* 3.8 10.3 - - + -
1527B PHE* 3.7 47.6 - - + -
1529B LEU* 4.2 21.1 - - + -
1581B LEU* 4.0 13.9 - - + -
1582B ARG 3.3 4.7 - - - +
1583B TYR* 3.7 30.3 - - + -
1586B GLN 5.4 0.9 - - - +
1587B VAL* 1.3 72.0 - - - +
1589B GLN* 1.3 61.3 + - - +
1611B SER* 3.7 0.5 - - - -
1612B PHE* 2.9 49.8 + - + +
1645B ALA* 4.0 20.2 - - + +
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Residues in contact with GLN1589 (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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1580B ARG 3.9 1.4 - - - +
1581B LEU* 3.4 6.8 - - - +
1582B ARG* 2.9 47.2 + - + +
1584B VAL* 3.5 30.6 - - + +
1587B VAL* 3.8 3.9 - - + +
1588B LEU* 1.3 72.3 - - - +
1590B LEU* 1.3 63.9 + - - +
1591B VAL* 5.2 8.2 - - + +
1609B VAL* 4.8 16.7 - - + +
1610B ILE 3.5 2.5 - - - +
1611B SER* 3.3 28.4 + - - +
1708B ALA* 5.8 1.8 - - - +
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Residues in contact with LEU1590 (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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1529B LEU* 5.3 0.2 - - + -
1552B ILE* 3.8 30.5 - - + -
1553B CYS* 4.3 14.1 - - - +
1578B ASN* 4.0 23.6 - - - +
1580B ARG 3.3 25.8 - - - +
1581B LEU* 3.7 16.8 - - + -
1588B LEU 3.8 0.6 + - - -
1589B GLN* 1.3 73.7 - - - +
1591B VAL* 1.3 62.7 + - - +
1592B TYR* 4.2 15.9 - - + +
1608B SER 3.7 0.2 - - - +
1609B VAL* 3.3 6.1 - - - +
1610B ILE* 2.6 44.5 + - + +
1612B PHE* 3.6 24.0 - - + -
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Residues in contact with VAL1591 (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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1578B ASN* 2.6 31.7 + - - +
1580B ARG* 4.1 12.9 + - + +
1582B ARG* 5.5 10.5 - - - -
1589B GLN* 5.2 11.0 - - + +
1590B LEU* 1.3 80.0 - - - +
1592B TYR* 1.3 63.7 + - - +
1593B LYS* 3.6 8.6 + - + +
1607B LYS* 5.4 8.5 - - + -
1608B SER 3.3 6.7 - - - +
1609B VAL* 3.8 20.4 - - + -
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Residues in contact with TYR1592 (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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1551B SER 2.8 29.4 + - - -
1552B ILE* 3.3 4.0 - - - +
1553B CYS 3.1 21.0 + - - -
1554B GLY 4.4 1.6 + - - -
1564B GLY* 4.2 21.5 - - - -
1565B ALA* 4.6 5.6 - - + -
1575B GLY* 3.5 16.2 - - - -
1576B LYS 3.1 18.6 - - - +
1577B ALA* 3.7 5.8 - - - -
1578B ASN* 3.5 33.9 - - - -
1590B LEU* 4.2 12.7 - - + +
1591B VAL* 1.3 74.3 - - - +
1593B LYS* 1.3 61.6 + - - +
1607B LYS* 3.3 10.0 - - - +
1608B SER* 2.7 44.0 + - - +
1610B ILE* 3.5 27.1 - - + -
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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