Contacts of the strand formed by residues 1278 - 1285 (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 LEU1278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1270A LEU* 4.6 6.1 - - + -
1271A PHE 3.4 3.1 - - - +
1272A LYS* 3.7 32.5 - - + -
1276A GLY 4.4 3.8 - - - +
1277A THR* 1.3 75.6 - - - +
1279A ILE* 1.3 62.2 + - - +
1280A ALA 4.1 0.2 - - - -
1302A ARG 3.9 0.2 - - - +
1303A ARG* 3.2 6.2 - - - -
1304A SER* 2.9 35.1 + - - +
1307A GLY* 3.7 4.9 - - - -
1308A GLY* 3.5 37.2 - - - +
1311A TRP* 3.7 22.1 - - + -
1659A THR* 4.5 4.7 - - + -
1661A LEU* 3.7 32.5 - - + -
1662A SER 5.9 0.2 - - - +
1680A TYR* 3.7 9.9 - - + +
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Residues in contact with ILE1279 (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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1270A LEU* 3.4 5.6 - - - +
1271A PHE* 2.8 38.3 + - + +
1273A THR* 3.6 28.5 - - + -
1277A THR* 4.4 7.4 - - + -
1278A LEU* 1.3 79.3 - - - +
1280A ALA* 1.3 64.6 + - - +
1281A SER 4.2 0.4 - - - +
1301A VAL* 3.7 25.6 - - + -
1302A ARG 3.6 1.8 - - - -
1303A ARG* 4.4 8.1 - - + -
1331A LEU* 3.6 25.5 - - + +
1340A ILE* 3.7 26.9 - - + -
1439A ASP 4.1 1.1 - - - +
1440A GLY* 4.0 16.2 - - - -
1443A TRP* 4.5 4.7 - - + -
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Residues in contact with ALA1280 (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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1254A LEU* 3.7 30.1 - - + -
1255A PHE* 3.9 9.0 - - + -
1269A ALA 3.2 8.5 - - - +
1270A LEU* 4.2 5.2 - - + -
1279A ILE* 1.3 75.0 - - - +
1281A SER* 1.3 60.5 + - - +
1301A VAL* 3.2 5.2 - - - +
1302A ARG* 2.9 35.1 + - + +
1311A TRP* 3.9 10.7 - - + -
1669A LEU* 4.0 10.8 - - + -
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Residues in contact with SER1281 (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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1268A PRO* 3.7 2.6 - - - +
1269A ALA* 2.9 42.7 + - - +
1279A ILE* 4.2 1.0 - - - -
1280A ALA* 1.3 74.6 - - - +
1282A ILE* 1.3 66.6 + - - +
1299A THR* 4.8 0.4 - - - -
1300A ALA 3.2 10.8 - - - -
1301A VAL* 4.0 4.3 - - - -
1329A THR* 2.8 28.4 + - - -
1331A LEU* 3.7 12.1 - - - +
1342A LEU* 3.8 22.6 - - - +
1669A LEU* 4.5 2.4 - - - +
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Residues in contact with ILE1282 (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* 3.5 42.4 - - + -
1265A TYR* 3.6 33.0 - - + -
1266A ARG 3.2 30.5 - - - +
1267A ILE 3.6 17.7 - - - +
1268A PRO* 3.6 13.2 - - + -
1281A SER* 1.3 75.2 - - - +
1283A ASP* 1.3 59.5 + - - +
1299A THR* 3.6 6.8 - - - +
1300A ALA* 3.0 35.8 + - + +
1329A THR* 4.0 5.0 + - - -
1669A LEU* 4.9 0.4 - - + -
1678A MET* 3.9 19.3 - - + -
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Residues in contact with ASP1283 (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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1265A TYR* 3.2 12.9 - - - -
1266A ARG 2.8 37.8 + - - +
1267A ILE* 3.4 7.3 + - - +
1282A ILE* 1.3 71.8 - - - +
1284A ALA* 1.3 57.1 + - - +
1285A ARG* 2.8 40.6 + - - +
1297A ILE* 3.6 18.5 - - + +
1298A ASP 3.6 5.6 - - - -
1299A THR* 4.9 1.1 + - - +
1326A VAL 4.2 1.4 - - - +
1327A ILE* 3.5 11.9 - - - +
1328A ASP* 3.0 25.5 + - - -
1329A THR* 4.4 6.9 + - - +
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Residues in contact with ALA1284 (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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1262A SER* 3.5 21.5 - - - +
1264A ASN 3.8 2.5 - - - -
1265A TYR* 3.8 16.6 - - + -
1282A ILE 3.7 2.2 + - - -
1283A ASP* 1.3 68.1 - - - +
1285A ARG* 1.3 62.6 + - - +
1286A ARG* 3.5 10.6 + - - +
1297A ILE* 3.4 2.5 - - - -
1298A ASP 2.8 38.5 + - - +
1300A ALA* 4.4 2.9 - - + -
1316A ILE* 4.2 23.1 - - + -
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Residues in contact with ARG1285 (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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1262A SER* 3.8 0.7 - - - -
1263A SER* 3.6 0.3 + - - -
1264A ASN* 2.9 41.8 + - + +
1266A ARG* 3.7 29.9 - - - +
1267A ILE* 3.4 7.5 - - - +
1283A ASP* 2.8 41.6 + - + +
1284A ALA* 1.3 69.6 - - - +
1286A ARG* 1.3 60.6 + - - +
1287A HIS 3.4 2.5 - - - -
1288A GLY 3.2 13.9 - - - +
1289A GLY* 2.9 27.2 + - - -
1290A ALA 3.5 8.2 + - - -
1291A ASP* 2.9 22.4 + - - +
1295A ASN* 3.7 4.0 - - - +
1296A ASP 4.2 2.9 - - - -
1297A ILE* 3.7 21.5 - - + +
1327A ILE* 3.3 9.4 - - - +
2693A FSI 2.9 26.9 + - - -
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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