Contacts of the strand formed by residues 1560 - 1566 (chain B) 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 TYR1560 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1556B ASN* 2.9 23.2 + - - -
1558B SER* 3.0 22.5 + - - -
1559B GLY* 1.3 81.2 - - - +
1561B LEU* 1.3 63.4 + - - +
1579B LYS* 3.8 23.6 - - + -
1580B ASP 3.6 8.1 - - - +
1581B THR* 3.4 50.5 - - + -
1583B VAL 3.3 9.9 - - - -
1584B LEU* 3.6 19.6 - - + +
1585B GLU* 3.4 7.9 - - - +
1613B ARG* 3.0 28.6 + - - -
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Residues in contact with LEU1561 (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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1553B PHE* 3.8 36.8 - - + -
1554B MET 4.2 1.3 - - - +
1556B ASN* 4.2 0.4 - - - +
1560B TYR* 1.3 74.3 - - - +
1562B ASN* 1.3 79.6 + - - +
1563B ILE* 3.8 19.1 - - + -
1579B LYS* 3.4 0.7 - - - -
1580B ASP* 2.9 33.4 + - + +
1583B VAL* 2.8 42.0 + - + +
1585B GLU* 3.6 8.6 - - + +
1590B LEU* 3.7 29.6 - - + -
1607B PHE* 4.1 5.8 - - + -
1642B TRP* 4.3 9.2 - - + -
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Residues in contact with ASN1562 (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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1517B ARG* 4.1 9.7 - - - +
1537B LEU* 3.5 18.9 - - + +
1552B LEU 3.7 0.5 - - - +
1553B PHE* 3.5 1.6 - - - -
1554B MET* 2.9 37.3 + - + +
1556B ASN* 3.2 40.4 + - - +
1558B SER* 3.5 10.6 + - - -
1561B LEU* 1.3 83.9 - - - +
1563B ILE* 1.3 67.3 + - - +
1577B VAL* 3.7 18.8 - - + +
1578B GLU 3.1 7.0 - - - +
1579B LYS* 3.9 10.0 - - - +
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Residues in contact with ILE1563 (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 LYS* 3.8 38.4 - - + +
1552B LEU 3.3 6.7 - - - +
1553B PHE* 4.0 13.7 - - + -
1554B MET* 4.0 2.7 - - - -
1561B LEU* 3.8 27.8 - - + +
1562B ASN* 1.3 80.5 - - - +
1564B ALA* 1.3 64.3 + - - +
1565B THR* 5.1 0.2 + - - -
1576B THR 4.3 1.0 - - - +
1577B VAL* 3.6 1.7 - - - -
1578B GLU* 2.8 53.3 + - + +
1580B ASP* 4.7 14.8 - - + +
1640B PHE* 3.9 26.2 - - + -
1642B TRP* 5.1 0.2 - - + -
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Residues in contact with ALA1564 (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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1513B PRO* 3.6 39.5 - - + -
1550B LEU 3.7 0.2 - - - +
1551B LYS* 3.2 6.8 - - - -
1552B LEU* 2.8 33.0 + - + +
1554B MET* 3.6 9.6 - - + +
1563B ILE* 1.3 75.0 - - - +
1565B THR* 1.3 63.5 + - - +
1573B TRP* 3.7 11.9 - - + -
1574B ASP 5.5 1.1 - - - +
1576B THR 4.8 5.8 - - - -
1577B VAL* 4.5 4.0 - - + +
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Residues in contact with THR1565 (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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1549B GLN* 3.3 35.9 - - + +
1550B LEU 3.3 4.9 - - - +
1551B LYS* 2.9 24.0 + - - +
1563B ILE* 5.0 0.3 + - - +
1564B ALA* 1.3 75.0 - - - +
1566B SER* 1.3 59.0 + - - +
1567B PHE* 3.8 14.8 - - + -
1573B TRP* 3.3 8.9 - - - +
1574B ASP* 2.8 42.6 + - - +
1576B THR 5.1 4.0 + - - -
1578B GLU* 4.1 5.7 + - - -
1631B TYR* 3.5 19.1 + - - +
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Residues in contact with SER1566 (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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1549B GLN* 3.4 7.5 - - - +
1550B LEU* 2.9 33.8 + - - +
1565B THR* 1.3 73.2 - - - +
1567B PHE* 1.3 62.9 + - - +
1568B ASP* 2.9 15.4 + - - -
1569B GLY 4.6 0.9 + - - -
1570B GLY 2.9 21.3 + - - -
1572B THR 2.7 25.3 + - - -
1573B TRP* 3.4 22.6 - - - +
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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