Contacts of the strand formed by residues 1587 - 1592 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1582A ARG 3.4 0.2 - - - +
1583A TYR* 3.3 5.7 - - - -
1584A VAL* 2.7 43.6 + - + +
1585A ASP 3.1 15.8 - - - +
1586A GLN* 1.3 82.7 - - + +
1588A LEU* 1.3 68.3 + - - +
1589A GLN* 3.8 4.3 - - + +
1611A SER* 3.8 28.7 - - - +
1612A PHE 3.4 16.8 - - - +
1613A VAL* 4.3 5.4 - - + -
1708A ALA 3.2 26.9 - - - +
1709A GLY* 3.7 13.2 - - - -
1726A ARG* 4.3 1.6 - - - +
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Residues in contact with LEU1588 (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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1518A VAL* 3.7 18.6 - - + -
1527A PHE* 3.6 41.5 - - + -
1529A LEU* 3.8 25.1 - - + -
1581A LEU* 4.3 7.8 - - + +
1582A ARG 3.1 7.9 - - - +
1583A TYR* 3.6 30.7 - - + -
1586A GLN 5.0 1.8 - - - +
1587A VAL* 1.3 72.2 - - - +
1589A GLN* 1.3 61.5 + - - +
1611A SER 3.8 0.2 - - - -
1612A PHE* 3.1 48.3 + - + +
1645A ALA* 3.8 18.4 - - + -
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Residues in contact with GLN1589 (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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1580A ARG 3.8 1.2 - - - +
1581A LEU* 3.4 9.0 - - - +
1582A ARG* 2.8 51.2 + - + +
1584A VAL* 3.5 31.4 - - + +
1587A VAL* 3.8 2.6 - - + -
1588A LEU* 1.3 73.6 - - - +
1590A LEU* 1.3 60.6 + - - +
1591A VAL* 4.2 9.5 + - + +
1609A VAL* 4.4 22.0 - - + +
1610A ILE 3.8 3.1 - - - +
1611A SER* 3.4 25.4 + - - +
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Residues in contact with LEU1590 (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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1552A ILE* 3.9 31.9 - - + -
1553A CYS* 4.0 9.9 - - - +
1578A ASN* 4.0 19.7 - - - +
1579A LYS 4.4 3.1 - - - -
1580A ARG 3.4 20.0 - - - +
1581A LEU* 3.9 17.7 - - + -
1589A GLN* 1.3 74.5 - - - +
1591A VAL* 1.3 62.1 + - - +
1592A TYR* 3.8 33.2 + - + +
1608A SER 3.6 1.9 - - - +
1609A VAL* 3.5 2.6 - - - -
1610A ILE* 2.7 53.2 + - + +
1612A PHE* 4.5 6.1 - - + -
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Residues in contact with VAL1591 (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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1578A ASN* 2.7 35.9 + - - +
1580A ARG* 3.9 16.7 + - + +
1582A ARG* 5.1 13.7 - - + -
1589A GLN* 5.1 11.0 - - + +
1590A LEU* 1.3 79.0 - - - +
1592A TYR* 1.3 63.6 + - - +
1593A LYS* 3.7 10.6 + - + +
1607A LYS* 5.8 5.6 - - + -
1608A SER 3.7 3.4 - - - +
1609A VAL* 3.9 23.6 - - + -
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Residues in contact with TYR1592 (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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1551A SER 2.7 30.3 + - - -
1552A ILE* 3.5 0.9 - - - -
1553A CYS 3.4 18.4 + - - -
1554A GLY 3.7 6.6 + - - -
1564A GLY* 3.8 22.0 - - - -
1565A ALA* 4.4 10.5 - - + -
1574A VAL 4.3 3.1 - - - +
1575A GLY* 3.6 15.6 - - - -
1576A LYS 3.1 17.7 - - - +
1577A ALA* 3.5 19.6 - - + +
1578A ASN* 3.6 10.1 - - - -
1590A LEU* 3.9 22.2 + - + -
1591A VAL* 1.3 79.2 - - - +
1593A LYS* 1.3 60.4 + - - +
1607A LYS* 3.3 8.0 - - - +
1608A SER* 2.8 43.0 + - - +
1610A ILE* 3.7 22.4 - - + -
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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