Contacts of the strand formed by residues 1276 - 1283 (chain A) in PDB entry 4C2A
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 LEU1276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1274A ARG* 3.1 23.4 + - + +
1275A LEU* 1.3 73.9 - - - +
1277A ASP* 1.3 77.9 + - - +
1278A LEU* 4.1 17.0 - - + -
1307A LEU* 4.3 27.6 - - + -
1313A TRP 3.2 5.5 + - - +
1314A VAL* 3.4 11.4 - - + +
1315A ARG 2.9 27.4 + - - +
1377A ALA* 4.3 1.5 - - - +
1378A SER* 3.3 24.2 - - - +
1380A ILE* 3.6 28.5 - - + -
1457A LEU* 4.5 13.7 - - + +
1461A ALA* 4.4 4.5 - - + -
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Residues in contact with ASP1277 (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 LEU* 1.3 79.0 - - - +
1278A LEU* 1.3 59.9 + - - +
1315A ARG* 2.9 49.2 + - - +
1331A LEU* 4.2 12.6 - - + +
1369A PHE* 4.0 13.1 - - + -
1374A ARG* 4.4 8.3 + - - +
1377A ALA* 4.2 12.7 - - - +
1378A SER 2.8 12.9 + - - +
1379A ARG* 3.6 20.3 - - + +
1380A ILE 2.9 28.9 + - - +
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Residues in contact with LEU1278 (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 LEU* 4.1 12.3 - - + -
1277A ASP* 1.3 73.2 - - - +
1279A VAL* 1.3 65.4 + - - +
1280A PHE* 3.5 35.3 + - + -
1303A MET* 4.3 0.7 - - + -
1307A LEU* 3.5 29.2 - - + -
1314A VAL* 5.8 1.3 - - + -
1315A ARG 2.8 13.7 + - - +
1316A VAL* 3.1 14.1 - - + +
1317A ALA 2.9 23.6 + - - +
1331A LEU* 4.3 0.6 - - - +
1380A ILE* 3.7 30.3 - - + +
1382A LEU* 4.3 16.8 - - + -
1457A LEU* 4.0 14.6 - - + -
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Residues in contact with VAL1279 (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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1278A LEU* 1.3 77.1 - - - +
1280A PHE* 1.3 63.3 + - - +
1281A LEU* 3.6 27.2 + - + +
1317A ALA* 3.5 17.9 - - + +
1319A VAL* 4.7 1.1 - - + -
1331A LEU* 4.7 4.0 - - + -
1364A THR* 4.9 3.1 - - + -
1368A ILE* 3.9 29.4 - - + -
1369A PHE* 3.5 35.9 - - + -
1380A ILE 2.8 13.4 + - - +
1381A ALA* 3.6 5.7 - - + -
1382A LEU* 2.7 32.9 + - - +
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Residues in contact with PHE1280 (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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1278A LEU* 3.5 31.2 - - + -
1279A VAL* 1.3 72.7 - - - +
1281A LEU* 1.3 63.8 + - - +
1282A LEU* 4.0 13.0 - - + -
1300A VAL* 3.9 33.2 - - + -
1303A MET* 3.9 30.1 - - + -
1304A MET* 3.9 20.4 - - + -
1316A VAL* 4.2 9.6 - - + -
1317A ALA 2.8 20.1 + - - +
1318A VAL* 3.6 13.8 - - + +
1319A VAL 2.8 28.9 + - - +
1382A LEU* 3.6 32.1 - - + -
1384A LEU* 4.5 2.9 - - + -
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Residues in contact with LEU1281 (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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1279A VAL* 3.6 26.2 - - + +
1280A PHE* 1.3 75.0 - - - +
1282A LEU* 1.3 63.1 + - - +
1319A VAL* 3.4 22.2 - - + -
1321A TYR* 3.6 10.9 - - + -
1360A VAL* 3.8 17.3 - - + -
1361A LEU* 4.2 13.7 - - + -
1364A THR* 3.7 20.0 - - - +
1368A ILE* 5.1 0.2 - - + -
1381A ALA* 4.5 14.6 - - + -
1382A LEU 2.9 17.5 + - - +
1383A LEU* 3.8 28.5 - - + -
1384A LEU* 3.0 28.5 + - - +
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Residues in contact with LEU1282 (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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1280A PHE* 4.1 10.1 - - + -
1281A LEU* 1.3 71.5 - - - +
1283A ASP* 1.3 65.4 + - - +
1284A GLY 3.2 0.3 + - - -
1293A PHE* 4.3 17.0 - - + -
1296A LEU* 4.3 14.4 - - + -
1297A LYS* 4.3 24.2 - - + -
1300A VAL* 3.6 23.3 - - + -
1318A VAL* 4.6 14.4 - - + -
1319A VAL 2.7 20.6 + - - +
1320A GLU* 3.5 5.8 - - - +
1321A TYR* 3.0 29.9 + - - -
1344A ALA 5.4 1.1 - - - +
1347A VAL* 4.5 12.1 - - + -
1384A LEU* 3.5 27.4 - - + -
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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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1282A LEU* 1.3 68.5 - - - +
1284A GLY* 1.3 59.4 + - - +
1285A SER* 2.8 42.6 + - - +
1288A LEU* 4.0 13.1 - - + +
1293A PHE* 3.6 20.0 - - - -
1296A LEU* 4.3 4.0 - - + +
1321A TYR* 3.5 13.2 + - - +
1355A ALA* 3.3 7.2 - - - +
1384A LEU 3.1 24.7 + - - +
1385A MET* 3.7 1.7 - - - +
1386A ALA* 2.7 35.7 + - + +
1387A SER* 2.8 21.1 + - - -
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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