Contacts of the strand formed by residues 1560 - 1566 (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 TYR1560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1556A ASN* 2.9 22.7 + - - -
1558A SER* 3.0 20.4 + - - -
1559A GLY* 1.3 81.9 - - - +
1561A LEU* 1.3 63.0 + - - +
1579A LYS* 3.8 24.0 - - + -
1580A ASP 3.6 8.7 - - - +
1581A THR* 3.5 48.5 - - + -
1583A VAL 3.3 11.4 - - - -
1584A LEU* 3.6 21.1 - - + +
1585A GLU* 3.3 8.1 - - - +
1613A ARG* 2.9 30.3 + - - -
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Residues in contact with LEU1561 (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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1553A PHE* 3.7 35.2 - - + -
1554A MET 4.2 0.7 - - - +
1556A ASN* 4.2 0.9 - - - +
1560A TYR* 1.3 74.0 - - - +
1562A ASN* 1.3 79.4 + - - +
1563A ILE* 3.9 20.0 - - + -
1579A LYS* 3.4 0.7 - - - -
1580A ASP* 2.9 35.4 + - + +
1583A VAL* 2.8 41.1 + - + +
1585A GLU* 3.5 9.0 - - + +
1590A LEU* 3.7 31.4 - - + -
1607A PHE* 4.1 5.2 - - + -
1642A TRP* 4.3 9.4 - - + -
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Residues in contact with ASN1562 (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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1517A ARG* 4.1 9.9 - - - +
1537A LEU* 3.6 14.1 - - + +
1552A LEU 3.7 0.3 - - - +
1553A PHE* 3.5 1.2 - - - -
1554A MET* 2.9 37.7 + - + +
1556A ASN* 3.3 43.0 + - - +
1558A SER* 3.5 10.6 + - - -
1561A LEU* 1.3 86.6 - - - +
1563A ILE* 1.3 67.8 + - - +
1577A VAL* 3.7 15.6 - - + +
1578A GLU 3.1 10.7 - - - +
1579A LYS* 3.9 9.4 - - - +
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Residues in contact with ILE1563 (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 LYS* 3.8 30.7 - - + +
1552A LEU 3.3 7.2 - - - +
1553A PHE* 4.1 13.9 - - + -
1554A MET* 4.0 2.7 - - - -
1561A LEU* 3.9 28.7 - - + +
1562A ASN* 1.3 81.0 - - - +
1564A ALA* 1.3 70.7 + - - +
1565A THR* 5.0 0.5 + - - -
1576A THR 4.4 0.9 - - - +
1577A VAL* 3.7 1.3 - - - -
1578A GLU* 2.8 53.1 + - + +
1580A ASP* 4.7 13.2 - - + +
1640A PHE* 3.8 26.7 - - + -
1642A TRP* 5.2 0.4 - - + -
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Residues in contact with ALA1564 (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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1513A PRO* 3.5 39.5 - - + -
1550A LEU 3.8 0.2 - - - +
1551A LYS* 3.2 6.4 - - - -
1552A LEU* 2.8 33.8 + - + +
1554A MET* 3.6 9.1 - - + +
1563A ILE* 1.3 76.8 - - - +
1565A THR* 1.3 63.0 + - - +
1573A TRP* 3.7 11.9 - - + -
1574A ASP 5.6 0.9 - - - +
1576A THR 4.8 3.1 - - - -
1577A VAL* 4.4 7.2 - - + -
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Residues in contact with THR1565 (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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1549A GLN* 3.2 35.9 - - + +
1550A LEU 3.3 4.5 - - - +
1551A LYS* 2.8 23.6 + - - +
1563A ILE* 5.0 0.3 + - - +
1564A ALA* 1.3 75.8 - - - +
1566A SER* 1.3 61.1 + - - +
1567A PHE* 3.8 13.6 + - + -
1573A TRP* 3.3 7.7 - - - +
1574A ASP* 2.8 39.5 + - - +
1576A THR 5.0 4.8 + - - -
1578A GLU* 4.2 5.4 + - - -
1631A TYR* 3.4 20.6 + - - +
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Residues in contact with SER1566 (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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1549A GLN* 3.4 8.2 - - - +
1550A LEU* 2.9 33.7 + - - -
1565A THR* 1.3 73.2 - - - +
1567A PHE* 1.3 62.1 + - - +
1568A ASP* 2.9 14.9 + - - -
1569A GLY 4.6 1.7 + - - -
1570A GLY 2.9 21.1 + - - -
1572A THR 2.7 25.7 + - - -
1573A TRP* 3.4 22.0 - - - +
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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