Contacts of the strand formed by residues 1656 - 1660 (chain A) in PDB entry 2VK7
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 SER1656 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1268A PRO* 3.8 5.5 - - - +
1589A GLN* 2.8 32.7 + - - +
1590A LEU* 4.7 0.5 - - - -
1591A SER* 3.5 7.9 + - - -
1608A SER* 2.7 39.3 + - - -
1609A ASN* 4.7 1.0 - - - -
1653A TYR* 3.6 17.8 - - - -
1654A ALA 4.5 1.0 + - - -
1655A TYR* 1.3 77.3 - - - +
1657A CYS* 1.3 62.8 + - - +
1668A LEU* 4.1 2.0 - - - -
1669A LEU 3.3 11.4 - - - -
1670A TYR* 3.9 5.2 - - - -
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Residues in contact with CYS1657 (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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1268A PRO 3.6 17.7 - - - +
1269A ALA* 3.9 1.1 - - - -
1270A LEU* 3.4 41.6 - - + +
1466A GLY* 3.7 24.0 - - - -
1467A ARG* 3.7 16.4 - - - -
1541A GLN* 5.0 0.4 - - - -
1591A SER* 3.5 6.3 - - - -
1656A SER* 1.3 78.4 - - - +
1658A LEU* 1.3 62.4 + - - +
1668A LEU* 3.5 6.4 - - - -
1669A LEU 2.9 35.5 + - - +
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Residues in contact with LEU1658 (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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1270A LEU* 3.5 5.0 - - - +
1467A ARG* 3.2 27.0 + - - -
1591A SER* 3.0 22.2 + - - +
1593A ILE* 3.8 16.1 - - + +
1606A ILE* 3.4 40.6 - - + +
1607A PHE 3.7 0.9 - - - -
1608A SER* 3.7 29.2 - - - +
1620A VAL* 4.5 8.3 - - + -
1657A CYS* 1.3 73.4 - - - +
1659A THR* 1.3 61.9 + - - +
1666A ILE* 3.6 27.4 - - + -
1667A GLY 3.3 3.6 - - - +
1668A LEU* 3.7 20.0 - - + -
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Residues in contact with THR1659 (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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1270A LEU* 3.7 31.2 - - + -
1272A LYS* 3.3 16.0 + - - +
1278A LEU* 4.5 7.9 - - + -
1467A ARG* 3.0 24.5 + - - +
1593A ILE* 3.7 8.7 - - - -
1658A LEU* 1.3 73.1 - - - +
1660A GLU* 1.3 74.2 + - - +
1661A LEU* 3.9 19.1 - - + -
1666A ILE* 3.5 4.3 - - - +
1667A GLY* 2.8 35.8 + - - +
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Residues in contact with GLU1660 (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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1272A LYS* 3.6 18.7 - - - +
1467A ARG* 4.7 1.6 - - - +
1593A ILE* 3.5 15.8 - - + +
1594A ASN 4.1 2.9 - - - +
1595A TYR* 3.3 33.8 - - + -
1596A SER* 2.6 48.5 + - - -
1597A GLN* 4.6 1.0 - - - +
1659A THR* 1.3 86.2 + - - +
1661A LEU* 1.3 71.6 + - - +
1664A GLY* 4.0 11.1 - - - -
1665A ASN 3.6 6.5 - - - +
1666A ILE* 4.3 4.3 - - + -
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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