Contacts of the strand formed by residues 1480 - 1487 (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 ILE1480 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1332B ILE* 3.8 35.2 - - + -
1333B GLN 4.8 2.0 - - - +
1334B ASP* 4.0 27.6 - - + +
1341B PHE* 4.0 11.2 - - + -
1469B ILE 3.5 3.6 - - - -
1470B GLN* 3.8 23.8 - - + +
1478B GLY 3.9 2.0 - - - +
1479B ARG* 1.3 71.7 - - - +
1481B VAL* 1.3 61.1 + - - +
1482B VAL* 4.2 1.3 - - + -
1498B ILE 3.9 0.2 - - - +
1499B TYR* 3.0 8.3 - - - +
1500B SER* 2.9 34.2 + - - +
1503B SER* 4.1 7.0 - - - +
1504B GLY* 4.0 23.8 - - - +
1507B TRP* 3.9 19.5 - - + -
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Residues in contact with VAL1481 (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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1468B GLY* 3.2 5.5 - - - -
1469B ILE* 2.8 45.7 + - + +
1471B ILE* 4.0 23.1 - - + -
1479B ARG* 3.8 25.1 - - + +
1480B ILE* 1.3 77.8 - - - +
1482B VAL* 1.3 66.5 + - - +
1483B PRO* 3.8 1.7 - - - +
1497B VAL* 3.6 36.3 - - + -
1498B ILE 3.5 2.7 - - - -
1499B TYR* 4.3 1.6 - - + -
1542B VAL* 4.1 12.3 - - + -
1550B LEU* 4.5 9.4 - - + -
1569B GLY 4.4 3.4 - - - +
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Residues in contact with VAL1482 (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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1330B THR* 3.7 28.5 - - + +
1332B ILE* 4.2 20.2 - - + -
1343B LEU* 4.2 9.0 - - + -
1463B ILE* 4.0 13.2 - - + -
1468B GLY* 4.6 2.9 - - - -
1480B ILE* 4.4 0.9 - - + -
1481B VAL* 1.3 78.9 - - - +
1483B PRO* 1.3 75.7 - - + +
1497B VAL* 4.2 2.5 - - - -
1498B ILE* 2.8 51.4 + - + +
1507B TRP* 3.8 25.8 - - + -
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Residues in contact with PRO1483 (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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1330B THR* 5.2 1.1 - - - +
1463B ILE* 4.0 0.9 - - - +
1464B ALA* 3.1 22.0 + - + +
1467B ARG 3.6 18.2 - - - +
1468B GLY* 4.1 1.8 - - - -
1481B VAL 3.8 7.6 - - - +
1482B VAL* 1.3 91.6 - - + +
1484B VAL* 1.3 63.2 + - - +
1496B ALA 3.6 7.0 - - - +
1497B VAL* 4.0 5.2 - - + -
1540B CYS* 3.2 33.7 - - - +
1541B GLN* 3.8 20.9 - - - +
1542B VAL* 3.9 24.9 - - + +
1552B LEU* 4.6 0.4 - - + -
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Residues in contact with VAL1484 (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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1431B ILE* 5.1 3.4 - - + -
1461B LEU* 3.9 20.0 - - + -
1462B GLY 3.2 17.0 - - - +
1463B ILE* 4.1 15.0 - - + -
1464B ALA* 3.8 4.5 - - - +
1482B VAL 3.7 8.5 - - - +
1483B PRO* 1.3 78.7 - - - +
1485B TYR* 1.3 69.3 - - - +
1496B ALA* 2.9 44.0 + - + +
1497B VAL 4.1 0.7 - - - +
1498B ILE* 4.0 24.9 - - + -
1509B ILE* 4.0 16.8 - - + -
1540B CYS* 3.5 8.5 - - - -
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Residues in contact with TYR1485 (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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1328B ASP* 4.6 1.7 + - - -
1353B PHE* 4.1 4.3 - + - -
1460B PHE* 3.5 31.2 - + - -
1461B LEU* 3.5 1.9 - - - +
1462B GLY 2.9 35.5 + - - +
1463B ILE 3.8 17.7 - - - -
1464B ALA* 4.3 1.8 - - + -
1465B PRO* 5.1 0.2 - - + -
1484B VAL* 1.3 81.6 - - - +
1486B TYR* 1.3 66.6 + - - +
1493B GLN* 3.3 32.1 - - + -
1494B SER 3.3 13.7 - - - +
1495B SER* 4.0 0.4 - - - +
1538B THR* 3.4 30.5 - - - +
1539B GLU* 3.7 26.3 + - + +
2692B FSI 2.8 40.3 + - - -
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Residues in contact with TYR1486 (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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1455B LYS* 5.3 2.4 + - - -
1457B TRP* 3.6 19.5 - + - -
1458B MET* 3.6 40.0 - - + +
1460B PHE* 3.0 18.2 - - - +
1461B LEU* 3.9 16.4 - - + -
1485B TYR* 1.3 80.7 - - - +
1487B THR* 1.3 69.5 + - - +
1488B ASN 4.8 0.2 - - - -
1492B LYS 3.6 0.4 - - - +
1493B GLN* 3.2 5.2 - - - -
1494B SER* 2.9 44.2 + - - -
1496B ALA* 3.9 22.9 - - + -
1509B ILE* 4.1 5.2 - - + -
1510B GLY 5.0 2.3 + - - -
1511B GLU* 4.8 0.3 - - - -
1512B SER* 3.3 20.9 + - - -
1515B ASP* 3.9 1.7 + - - -
1527B SER* 2.7 38.2 + - - -
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Residues in contact with THR1487 (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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1353B PHE* 3.8 24.4 + - + +
1458B MET* 3.3 9.5 - - - +
1459B LYS* 2.9 31.4 + - - +
1460B PHE* 2.8 34.3 + - + +
1486B TYR* 1.3 78.1 - - - +
1488B ASN* 1.3 62.5 + - - +
1491B GLY* 3.5 28.2 - - - +
1492B LYS 3.2 4.5 - - - -
1493B GLN* 3.6 23.6 - - + -
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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