Contacts of the strand formed by residues 1314 - 1321 (chain E) in PDB entry 4C2B
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 VAL1314 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1271E CYS* 5.8 1.6 - - - +
1272E ARG 5.9 0.7 - - - +
1274E ARG* 3.2 31.4 - - + +
1276E LEU* 3.2 26.7 - - + +
1278E LEU* 4.3 11.4 - - + -
1307E LEU* 4.4 29.6 - - + -
1308E ARG* 3.4 16.9 + - + +
1309E ILE* 3.3 7.8 - - + +
1310E SER 2.7 32.2 + - - -
1313E TRP* 1.3 78.2 - - + +
1315E ARG* 1.3 68.1 + - - +
1316E VAL* 4.8 4.5 - - + -
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Residues in contact with ARG1315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1276E LEU 2.9 7.3 + - - -
1277E ASP* 2.8 41.0 + - - +
1278E LEU* 2.6 36.2 + - - +
1309E ILE* 5.0 1.6 - - - -
1310E SER 3.4 12.3 - - - +
1311E GLN* 3.2 32.3 + - - +
1314E VAL* 1.3 72.8 - - - +
1316E VAL* 1.3 59.8 + - - +
1331E LEU* 3.2 38.1 + - + +
1332E LYS* 3.5 26.5 - - - +
1373E ASP* 3.1 29.3 + - - -
1374E ARG* 3.3 30.6 - - - +
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Residues in contact with VAL1316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1278E LEU* 3.3 24.0 - - + -
1280E PHE* 4.6 3.8 - - + -
1304E MET* 3.9 31.2 - - + -
1309E ILE* 3.6 32.0 - - + +
1314E VAL* 4.2 2.4 + - + -
1315E ARG* 1.3 77.4 - - - +
1317E ALA* 1.3 61.7 + - - +
1318E VAL* 5.6 0.4 - - + -
1329E ILE* 3.3 10.7 - - + +
1330E GLY 3.0 21.5 - - - +
1331E LEU* 3.9 2.0 - - - +
1340E LEU* 3.7 29.8 - - + +
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Residues in contact with ALA1317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1278E LEU 2.8 15.0 + - - +
1279E VAL* 3.2 21.3 - - + +
1280E PHE* 2.5 37.1 + - - +
1316E VAL* 1.3 77.4 - - - +
1318E VAL* 1.3 58.2 + - - +
1319E VAL* 4.1 3.1 - - + -
1329E ILE* 3.2 16.6 - - - +
1330E GLY* 4.2 0.7 - - - -
1331E LEU* 3.8 18.2 - - + +
1368E ILE* 5.7 2.9 - - + -
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Residues in contact with VAL1318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1280E PHE* 3.6 22.9 - - + -
1282E LEU* 4.4 19.3 - - + -
1300E VAL* 4.2 12.1 - - + -
1304E MET* 4.6 6.1 - - - -
1316E VAL* 5.6 0.4 - - + -
1317E ALA* 1.3 77.4 - - - +
1319E VAL* 1.3 65.8 + - - +
1320E GLU* 4.9 1.6 - - + +
1328E TYR* 2.9 29.7 + - + +
1329E ILE* 2.9 44.4 + - + +
1343E ILE* 6.3 0.2 - - + -
1344E ALA* 4.7 4.3 - - + -
1347E VAL* 4.3 24.2 - - + -
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Residues in contact with VAL1319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1279E VAL* 5.2 1.6 - - + -
1280E PHE 2.9 18.1 + - - +
1281E LEU* 3.7 19.6 - - + +
1282E LEU* 3.5 14.2 + - - -
1317E ALA* 5.0 3.4 - - + +
1318E VAL* 1.3 80.4 - - - +
1320E GLU* 1.3 60.7 + - - +
1321E TYR* 3.8 2.8 + - - +
1325E SER* 3.8 24.5 - - - +
1326E HIS 3.3 20.9 - - - +
1327E ALA* 3.8 19.3 - - + +
1329E ILE 4.4 7.0 - - - +
1360E VAL* 5.0 2.7 - - + -
1363E TYR* 4.5 16.6 - - + -
1368E ILE* 4.5 11.9 - - + -
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Residues in contact with GLU1320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1282E LEU* 4.2 13.0 - - + +
1284E GLY* 4.3 4.1 - - - -
1293E PHE* 4.4 12.3 - - + -
1318E VAL* 4.9 1.5 - - + +
1319E VAL* 1.3 71.4 - - - +
1321E TYR* 1.3 60.5 + - - +
1322E HIS* 3.0 27.7 + - - -
1326E HIS* 2.7 58.4 + - - +
1328E TYR* 3.5 33.8 + - + -
1347E VAL* 4.1 12.8 - - + -
1348E LYS* 4.1 19.3 - - - +
1350E ALA* 3.2 14.1 - - - +
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Residues in contact with TYR1321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1281E LEU* 3.8 17.3 - - + -
1282E LEU 3.1 31.7 + - - -
1283E ASP* 4.0 8.1 + - - -
1284E GLY* 3.1 28.2 + - - -
1319E VAL* 4.1 8.1 - - + +
1320E GLU* 1.3 77.4 - - - +
1322E HIS* 1.3 64.9 + - - +
1324E GLY 3.2 11.7 - - - +
1325E SER* 4.1 8.7 - - - +
1355E ALA* 4.0 16.3 - - + +
1356E SER 3.3 33.0 - - - -
1357E THR* 3.9 12.4 - - + +
1360E VAL* 3.6 34.8 - - + -
1383E LEU* 3.7 14.5 - - + +
1384E LEU 3.7 10.7 + - - -
1385E MET* 4.1 5.5 - - - -
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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