Contacts of the strand formed by residues 1297 - 1304 (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 ILE1297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1283A ASP* 3.6 27.8 - - + -
1284A ALA 3.4 8.5 - - - +
1285A ARG* 3.7 26.9 - - + +
1290A ALA 4.1 1.3 - - - +
1292A ALA 4.0 22.7 - - - +
1295A ASN* 3.8 17.3 - - + -
1296A ASP* 1.3 78.9 + - - +
1298A ASP* 1.3 69.8 + - - +
1320A TYR 5.2 1.2 + - - -
1324A SER 4.2 2.3 - - - +
1325A SER* 3.0 24.4 + - - +
1326A VAL* 3.1 43.3 + - - +
1327A ILE* 4.1 13.0 - - + -
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Residues in contact with ASP1298 (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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1283A ASP* 3.6 5.4 - - - -
1284A ALA* 2.8 39.1 + - + +
1286A ARG* 2.7 39.7 + - - +
1297A ILE* 1.3 77.5 - - - +
1299A THR* 1.3 59.7 + - - +
1316A ILE* 3.9 11.9 - - + -
1318A MET 3.4 11.4 - - - +
1319A ASP* 3.1 21.3 - - - +
1326A VAL* 3.8 3.5 - - - +
2694A CA 2.4 29.5 - - - -
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Residues in contact with THR1299 (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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1281A SER* 4.8 0.4 - - - -
1282A ILE 3.6 6.7 - - - +
1283A ASP* 4.9 1.3 + - - +
1298A ASP* 1.3 72.2 - - - +
1300A ALA* 1.3 64.3 + - - +
1316A ILE* 3.4 6.8 - - - +
1317A ILE* 2.8 57.0 + - + -
1318A MET* 3.0 22.8 + - + +
1326A VAL* 3.3 23.8 + - - +
1329A THR* 3.7 30.3 - - + +
1342A LEU* 4.3 6.7 - - + -
1344A VAL* 4.0 1.0 - - - +
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Residues in contact with ALA1300 (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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1255A PHE* 4.5 3.4 - - + -
1260A LEU* 3.9 13.5 - - + -
1265A TYR* 4.4 10.5 - - + -
1281A SER* 3.2 5.7 - - - -
1282A ILE* 3.0 49.9 + - + +
1284A ALA* 4.4 2.5 - - + -
1298A ASP 4.0 1.0 + - - -
1299A THR* 1.3 71.9 - - - +
1301A VAL* 1.3 66.9 + - - +
1315A GLN 3.3 7.6 - - - +
1316A ILE* 3.8 18.8 - - + -
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Residues in contact with VAL1301 (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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1255A PHE* 4.6 1.1 - - - -
1279A ILE* 3.7 26.5 - - + -
1280A ALA 3.2 4.5 - - - +
1281A SER* 4.0 14.4 - - - -
1299A THR* 4.7 0.4 - - + -
1300A ALA* 1.3 80.7 - - - +
1302A ARG* 1.3 71.8 + - - +
1303A ARG* 4.6 8.1 - - + -
1312A ASP* 4.3 0.9 - - - +
1314A GLY* 3.1 4.2 - - - -
1315A GLN* 2.9 45.4 + - + +
1317A ILE* 3.9 31.0 - - + -
1342A LEU* 4.1 5.2 - - + -
1443A TRP* 4.4 15.3 - - + +
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Residues in contact with ARG1302 (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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1253A ASP 4.4 3.6 + - - -
1254A LEU* 2.7 54.9 + - - +
1255A PHE* 3.6 19.7 - - + -
1256A HIS* 5.3 1.8 - - - -
1259A PHE* 3.4 32.9 - - + -
1279A ILE* 3.6 2.8 - - - -
1280A ALA* 2.9 33.6 + - + +
1301A VAL* 1.3 78.3 - - - +
1303A ARG* 1.3 63.4 + - - +
1311A TRP* 3.5 39.4 + - + +
1312A ASP* 2.8 31.1 + - - +
1313A GLU* 4.9 0.6 - - - +
1314A GLY* 3.9 12.1 - - - -
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Residues in contact with ARG1303 (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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1277A THR* 3.6 10.6 + - + +
1278A LEU 3.2 6.7 - - - +
1279A ILE* 4.4 12.3 - - + -
1301A VAL* 4.6 6.3 - - + -
1302A ARG* 1.3 78.3 - - - +
1304A SER* 1.3 60.2 + - - +
1305A GLU* 2.8 34.3 + - - +
1311A TRP* 3.4 5.4 - - - -
1312A ASP* 2.8 51.3 + - + +
1315A GLN* 4.9 3.4 - - - +
1439A ASP* 2.9 46.5 + - - +
1440A GLY 3.4 24.5 - - - +
1441A LYS* 3.6 27.5 - - - +
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Residues in contact with SER1304 (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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1276A GLY 4.6 0.5 - - - +
1277A THR* 3.4 7.1 - - - +
1278A LEU* 2.9 35.7 + - - +
1303A ARG* 1.3 75.1 - - - +
1305A GLU* 1.3 60.8 + - - +
1306A ASP* 2.9 7.1 + - - -
1307A GLY 4.7 0.3 + - - -
1308A GLY* 2.8 31.6 + - - -
1310A THR 2.7 25.0 + - - -
1311A TRP* 3.6 19.7 - - - -
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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