Contacts of the strand formed by residues 1340 - 1347 (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 ILE1340 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1271B PHE* 5.2 5.2 - - + -
1273B THR* 3.7 20.0 - - + -
1279B ILE* 3.9 9.9 - - + -
1331B LEU* 4.6 6.7 - - + -
1332B ILE 3.6 12.1 - - - +
1333B GLN* 3.5 28.0 - - + +
1338B GLY 3.9 1.3 - - - +
1339B ARG* 1.3 72.2 - - - +
1341B PHE* 1.3 67.0 + - - +
1435B TYR* 3.0 8.0 - - - +
1436B SER* 2.8 37.6 + - - +
1439B ASP* 3.6 35.7 - - - +
1440B GLY 3.6 10.3 - - - +
1443B TRP* 3.8 19.8 - - + -
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Residues in contact with PHE1341 (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 3.8 0.2 - - - +
1331B LEU* 3.4 8.1 - - - +
1332B ILE* 2.8 59.4 + - + +
1333B GLN 4.6 0.4 - - - -
1334B ASP* 4.0 19.1 - - + -
1339B ARG* 3.5 46.7 - - + -
1340B ILE* 1.3 73.9 - - - +
1342B LEU* 1.3 61.0 + - - +
1343B LEU* 4.1 4.7 - - + -
1433B LEU* 3.5 30.1 - - + -
1434B VAL 3.4 1.8 - - - -
1435B TYR* 3.9 12.8 - + + -
1443B TRP* 4.4 0.7 - - - -
1480B ILE* 4.0 12.1 - - + -
1503B SER 3.3 24.5 - - - -
1504B GLY* 3.9 16.2 - - - -
1507B TRP* 4.9 5.2 - + + -
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Residues in contact with LEU1342 (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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1281B SER* 3.6 20.0 - - - +
1299B THR* 4.4 4.5 - - + -
1301B VAL* 3.8 17.3 - - + -
1317B ILE* 3.4 30.5 - - + -
1318B MET* 5.1 3.6 - - + +
1329B THR* 3.7 16.4 - - + -
1330B THR 2.9 29.6 - - - +
1331B LEU* 3.4 20.0 - - + -
1341B PHE* 1.3 74.1 - - - +
1343B LEU* 1.3 60.9 + - - +
1432B ASN 4.1 0.2 - - - +
1433B LEU* 3.6 1.0 - - - -
1434B VAL* 2.9 46.9 + - + +
1443B TRP* 3.7 11.8 - - + -
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Residues in contact with LEU1343 (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 3.8 0.3 - - - +
1329B THR* 3.2 6.1 - - - -
1330B THR* 3.0 45.9 + - + +
1332B ILE* 4.8 2.7 - - + -
1341B PHE* 4.1 13.0 - - + +
1342B LEU* 1.3 78.6 - - - +
1344B VAL* 1.3 62.9 + - - +
1431B ILE* 4.1 11.9 - - + -
1432B ASN 3.1 7.9 - - - +
1433B LEU* 3.6 28.3 - - + -
1449B ILE* 4.2 8.7 - - + -
1463B ILE* 3.6 19.0 - - + +
1482B VAL* 4.2 16.2 - - + -
1498B ILE* 4.0 27.1 - - + -
1507B TRP* 4.7 9.0 - - + -
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Residues in contact with VAL1344 (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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1299B THR* 4.0 1.6 - - - +
1318B MET* 3.4 35.7 - - + -
1326B VAL* 3.8 21.5 - - + -
1327B ILE 3.4 31.6 - - - +
1328B ASP 3.4 10.8 - - - +
1329B THR* 3.6 18.8 - - + -
1343B LEU* 1.3 76.6 - - - +
1345B THR* 1.3 66.4 + - - +
1431B ILE* 3.7 3.3 - - - -
1432B ASN* 2.9 39.8 + - + +
1463B ILE* 3.7 8.3 - - - +
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Residues in contact with THR1345 (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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1326B VAL* 3.2 4.0 - - - -
1327B ILE* 2.8 49.2 + - - +
1328B ASP* 3.7 2.6 + - - +
1344B VAL* 1.3 72.7 - - - +
1346B HIS* 1.3 62.6 - - - +
1347B PHE* 3.8 24.2 - - + -
1429B SER* 4.0 21.1 - - - -
1430B TYR 3.5 5.2 - - - +
1431B ILE* 4.8 1.1 - - - +
1460B PHE* 4.2 4.5 - - + -
1461B LEU 4.0 1.1 - - - +
1462B GLY* 3.3 13.2 - - - -
1463B ILE* 2.9 30.9 + - - +
2692B FSI 5.4 0.9 - - - -
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Residues in contact with HIS1346 (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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1320B TYR* 3.4 33.1 + + - -
1324B SER* 2.9 23.4 + - - -
1325B SER 3.3 13.7 - - - -
1326B VAL* 4.1 2.9 - - + -
1345B THR* 1.3 74.5 - - - +
1347B PHE* 1.3 75.1 + - - +
1348B PRO 4.7 0.7 - - - -
1417B ASN* 3.2 29.6 - - - -
1429B SER* 3.5 4.3 - - - -
1430B TYR* 2.7 58.3 + + + +
1432B ASN* 3.5 30.7 + - - +
1448B ASN* 6.0 0.2 + - - -
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Residues in contact with PHE1347 (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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1292B ALA* 4.0 7.4 - - + -
1324B SER* 2.7 23.2 + - - -
1325B SER 2.9 21.4 + - - +
1327B ILE* 3.7 31.6 - - + -
1345B THR* 3.8 7.2 - - + -
1346B HIS* 1.3 76.8 - - - +
1348B PRO* 1.3 64.8 - - + +
1351B TYR* 3.2 21.1 - - + +
1352B GLY* 3.4 46.4 - - - -
1353B PHE 3.6 3.4 - - - -
1356B ALA* 4.3 3.8 - - + -
1428B THR 3.7 15.7 - - - -
1429B SER* 3.6 23.1 - - - -
1460B PHE* 3.8 21.3 - + - -
2692B FSI 4.2 7.2 - - + -
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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