Contacts of the strand formed by residues 1325 - 1333 (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 SER1325 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1292B ALA* 4.1 23.7 - - - +
1295B ASN 3.7 7.1 + - - -
1296B ASP* 3.7 5.9 - - - -
1297B ILE* 3.0 44.2 + - - +
1320B TYR* 5.0 0.9 - - - -
1323B LYS 3.7 2.8 + - - -
1324B SER* 1.3 73.3 - - - +
1326B VAL* 1.3 61.6 + - - +
1327B ILE* 4.3 1.5 + - - -
1345B THR 3.9 0.3 - - - +
1346B HIS* 3.3 6.1 - - - -
1347B PHE* 2.9 35.2 + - - +
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Residues in contact with VAL1326 (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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1283B ASP* 4.2 1.6 - - - +
1297B ILE* 3.1 37.7 + - - +
1298B ASP* 3.8 3.4 - - - +
1299B THR* 3.3 35.0 + - - +
1318B MET* 3.9 16.2 - - + +
1319B ASP 4.8 0.2 - - - +
1320B TYR* 3.6 32.1 - - + -
1325B SER* 1.3 71.8 - - - +
1327B ILE* 1.3 61.4 + - - +
1344B VAL* 3.8 25.1 - - + -
1345B THR 3.2 4.7 - - - +
1346B HIS* 4.1 8.1 - - + -
1432B ASN* 4.3 1.6 - - - +
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Residues in contact with ILE1327 (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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1283B ASP* 3.4 17.5 - - - +
1285B ARG* 3.4 18.4 - - - +
1291B ASP* 4.1 2.7 - - + -
1292B ALA* 3.9 27.8 - - + +
1297B ILE* 4.1 9.0 - - + -
1325B SER* 4.7 1.6 - - - +
1326B VAL* 1.3 75.8 - - - +
1328B ASP* 1.3 78.0 + - - +
1344B VAL* 3.4 3.3 - - - +
1345B THR* 2.8 35.1 + - - +
1347B PHE* 3.7 31.4 - - + -
2692B FSI 3.7 26.7 - - + +
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Residues in contact with ASP1328 (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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1267B ILE* 3.5 18.0 - - - +
1283B ASP* 3.0 14.3 + - - -
1327B ILE* 1.3 81.1 - - - +
1329B THR* 1.3 61.2 + - - +
1344B VAL* 3.4 15.3 - - - +
1345B THR* 4.5 2.7 + - - +
1460B PHE* 5.4 0.3 - - - -
1463B ILE* 3.5 31.0 - - - +
1465B PRO* 4.0 15.9 - - + +
1485B TYR* 4.6 4.0 + - - -
1539B GLU* 4.7 0.2 - - - +
2692B FSI 2.7 57.9 + - - +
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Residues in contact with THR1329 (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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1267B ILE* 4.3 7.1 + - - +
1268B PRO 5.1 0.2 - - - +
1269B ALA* 3.7 9.0 - - - +
1281B SER* 2.8 31.5 + - - -
1282B ILE* 4.1 3.6 + - - +
1283B ASP* 4.4 9.3 + - - +
1299B THR* 3.7 29.6 - - + +
1328B ASP* 1.3 73.1 - - - +
1330B THR* 1.3 60.9 + - - +
1342B LEU* 3.7 8.7 - - + -
1343B LEU 3.2 4.9 - - - -
1344B VAL* 3.6 24.0 - - + -
1463B ILE* 4.1 0.7 - - - -
1465B PRO* 3.2 7.3 - - - +
1466B GLY 3.0 21.0 + - - -
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Residues in contact with THR1330 (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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1269B ALA* 4.5 0.4 - - - -
1329B THR* 1.3 76.6 - - - +
1331B LEU* 1.3 62.8 + - - +
1341B PHE 3.8 0.3 - - - +
1342B LEU* 2.9 20.0 - - - +
1343B LEU* 3.0 39.6 + - + +
1463B ILE* 3.5 23.8 - - + -
1464B ALA 4.3 3.8 + - - -
1466B GLY 3.2 8.9 + - - -
1467B ARG* 3.2 28.6 + - - -
1468B GLY* 3.6 2.3 + - - -
1482B VAL* 3.7 25.9 - - + +
1483B PRO* 5.2 0.3 - - - +
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Residues in contact with LEU1331 (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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1269B ALA* 3.9 16.8 - - + +
1270B LEU 5.3 0.2 - - - -
1271B PHE* 3.7 27.2 - - + -
1279B ILE* 3.6 42.2 - - + +
1281B SER* 3.7 15.9 - - - +
1330B THR* 1.3 75.2 + - - +
1332B ILE* 1.3 60.8 + - - +
1340B ILE* 4.6 6.3 - - + -
1341B PHE 3.4 10.1 - - - +
1342B LEU* 3.4 34.3 - - + -
1443B TRP* 4.4 7.4 - - + -
1466B GLY 3.1 7.4 + - - +
1467B ARG* 3.3 8.8 - - + +
1468B GLY 2.9 21.2 + - - -
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Residues in contact with ILE1332 (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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1271B PHE* 3.9 20.4 - - + -
1330B THR* 6.2 0.7 - - + -
1331B LEU* 1.3 75.8 - - - +
1333B GLN* 1.3 79.8 + - - +
1340B ILE* 3.6 5.2 - - - +
1341B PHE* 2.8 45.0 + - + +
1343B LEU* 4.8 4.0 - - + -
1468B GLY* 3.5 28.0 - - - +
1469B ILE* 3.6 29.2 - - - +
1470B GLN* 3.9 3.4 - - + +
1480B ILE* 3.8 23.8 - - + -
1482B VAL* 4.2 14.6 - - + -
1507B TRP* 5.4 0.2 - - + -
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Residues in contact with GLN1333 (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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1271B PHE* 3.7 16.0 - - + -
1273B THR* 3.3 11.2 - - - -
1274B LYS* 2.8 42.2 + - - +
1275B GLU* 5.3 2.6 - - - +
1332B ILE* 1.3 94.7 - - - +
1334B ASP* 1.3 71.7 + - - +
1335B ASP* 3.7 2.1 + - - +
1338B GLY* 2.8 28.9 + - - -
1339B ARG 3.3 14.1 - - - +
1340B ILE* 3.5 19.4 - - + +
1341B PHE* 4.4 3.8 - - - -
1439B ASP* 5.0 1.8 + - - +
1470B GLN* 3.6 13.5 - - - +
1480B ILE* 4.8 2.6 - - - +
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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