Contacts of the strand formed by residues 1537 - 1544 (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 LEU1537 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1493A GLN 3.0 6.3 + - - +
1494A SER* 3.0 28.6 + - - -
1495A SER* 3.0 20.9 + - - +
1512A SER* 4.9 0.4 - - - +
1513A PRO* 3.9 20.2 - - + -
1514A ASN* 3.3 26.6 - - - +
1517A ARG* 3.7 11.7 - - - +
1535A PRO 3.5 5.8 + - - +
1536A GLN* 1.3 81.0 - - - +
1538A THR* 1.4 60.9 + - - +
1554A MET* 3.7 31.4 - - + -
1555A ARG 3.7 2.2 - - - -
1556A ASN* 4.0 5.4 - - + -
1562A ASN* 3.6 27.8 - - - +
1577A VAL* 4.4 3.6 - - + -
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Residues in contact with THR1538 (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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1485A TYR* 3.4 24.7 - - - +
1493A GLN* 3.3 43.1 - - + +
1495A SER* 2.7 22.2 + - - -
1536A GLN* 4.4 6.1 - - + +
1537A LEU* 1.4 83.4 - - - +
1539A GLU* 1.3 74.6 + - - +
1540A CYS* 3.5 1.4 + - - -
1555A ARG* 2.9 41.4 + - - +
1556A ASN* 5.1 0.2 - - - -
1587A TYR* 4.0 14.8 - - + +
2693A FSI 4.8 0.6 + - - -
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Residues in contact with GLU1539 (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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1328A ASP* 4.7 0.5 - - - +
1464A ALA* 3.9 10.5 - - + -
1465A PRO* 3.6 17.0 - - + +
1485A TYR* 3.6 26.9 + - + -
1538A THR* 1.3 85.7 + - - +
1540A CYS* 1.3 60.9 + - - +
1554A MET* 3.6 0.3 - - - -
1555A ARG* 2.7 60.1 + - + +
1589A GLN* 3.2 25.3 - - + +
1590A LEU* 5.6 1.3 - - - +
1655A TYR* 2.8 31.7 + - - -
2693A FSI 3.9 11.9 - - - +
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Residues in contact with CYS1540 (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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1464A ALA* 3.4 7.0 - - - +
1465A PRO 4.9 0.2 - - - +
1483A PRO* 3.2 24.3 - - - +
1484A VAL 3.5 25.4 - - - -
1495A SER* 3.7 15.3 - - - -
1496A ALA 3.9 3.1 - - - -
1538A THR 3.8 1.6 - - - +
1539A GLU* 1.3 78.2 - - - +
1541A GLN* 1.3 81.5 + - - +
1552A LEU* 3.8 14.8 - - + -
1553A PHE 3.1 15.7 - - - +
1554A MET* 3.7 15.7 - - + -
1555A ARG 4.8 0.2 - - - +
1589A GLN* 6.1 0.4 - - - +
1590A LEU* 5.0 3.1 - - - -
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Residues in contact with GLN1541 (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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1464A ALA 3.5 17.8 + - - -
1465A PRO 3.7 8.9 + - - +
1466A GLY* 3.6 3.2 - - - -
1467A ARG* 2.9 53.7 + - - +
1483A PRO* 3.8 6.8 - - - +
1540A CYS* 1.3 89.6 + - - +
1542A VAL* 1.3 61.6 + - - +
1551A LYS 3.9 0.2 - - - +
1552A LEU* 3.6 2.9 - - - -
1553A PHE* 2.8 34.2 + - - +
1589A GLN* 5.2 1.0 + - + -
1590A LEU* 3.4 28.5 - - + +
1591A SER* 4.4 6.9 + - - -
1592A VAL* 3.9 26.7 - - + +
1657A CYS* 5.0 0.3 - - - -
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Residues in contact with VAL1542 (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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1467A ARG 5.4 1.0 + - - +
1468A GLY* 5.0 1.1 - - - -
1469A ILE* 3.4 42.7 - - + +
1481A VAL* 4.1 13.9 - - + +
1483A PRO* 3.8 19.7 - - + +
1497A VAL* 4.8 0.4 - - + -
1541A GLN* 1.3 76.7 - - - +
1543A VAL* 1.3 79.8 + - - +
1550A LEU* 4.0 23.6 - - + -
1551A LYS 3.3 14.1 - - - +
1552A LEU* 3.8 15.5 - - + -
1573A TRP* 4.7 3.4 - - + -
1592A VAL* 4.4 4.0 - - - +
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Residues in contact with VAL1543 (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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1469A ILE* 4.4 8.1 - - + -
1542A VAL* 1.3 80.9 - - - +
1544A GLU* 1.3 60.3 + - - +
1545A MET* 4.1 12.1 - - + -
1550A LEU* 3.5 4.0 - - - +
1551A LYS* 2.9 41.2 + - + +
1553A PHE* 3.8 28.3 - - + -
1592A VAL* 3.8 13.5 - - + +
1593A ILE* 3.6 39.0 - - - +
1594A ASN* 3.5 13.9 - - - +
1605A VAL* 4.1 9.2 - - + -
1640A PHE* 4.5 0.2 - - + -
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Residues in contact with GLU1544 (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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1469A ILE* 4.4 7.1 - - + +
1470A GLN 4.0 1.7 - - - +
1471A ILE* 3.3 15.5 - - - +
1472A LYS* 2.8 33.4 + - + +
1473A ASN* 2.9 44.6 + - - +
1543A VAL* 1.3 74.9 - - - +
1545A MET* 1.3 74.8 + - - +
1546A PRO* 4.9 0.2 - - - +
1548A GLY* 3.4 16.3 - - - +
1549A GLN 3.5 4.9 - - - +
1550A LEU* 4.2 8.5 - - + -
1594A ASN* 2.8 34.6 + - - +
1625A ILE* 4.9 1.4 - - - +
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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