Contacts of the helix formed by residues 1257 - 1271 (chain G) in PDB entry 2VKZ
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 ASP1257 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1255G MET 3.2 1.4 + - - -
1256G GLU* 1.5 59.5 - - - +
1258G ARG* 1.3 61.2 + - - +
1259G ASN* 3.4 2.7 - - - +
1260G GLN* 3.5 31.0 + - + +
1261G ARG* 3.1 31.9 + - + +
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Residues in contact with ARG1258 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1161G GLN* 5.6 3.5 - - - +
1238G LEU* 4.3 6.1 - - + +
1253G GLU* 2.9 28.2 + - - -
1254G VAL 4.3 0.2 - - - +
1255G MET* 3.0 41.4 + - - +
1256G GLU 3.3 0.8 - - - -
1257G ASP* 1.3 75.6 - - - +
1259G ASN* 1.3 74.0 + - - +
1261G ARG* 3.3 24.1 + - - +
1262G ILE* 3.2 42.5 + - + +
1346G ASP* 2.9 29.5 + - - -
1348G LEU* 4.8 1.8 - - - +
1349G LYS* 5.5 0.8 - - - +
1572G TYR* 3.0 36.4 + - - -
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Residues in contact with ASN1259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1255G MET 5.6 1.2 + - - -
1257G ASP 3.4 0.4 - - - -
1258G ARG* 1.3 83.5 + - - +
1260G GLN* 1.3 59.2 + - - +
1262G ILE* 3.2 8.7 + - - +
1263G LYS* 2.9 34.2 + - - +
1344G ASP* 3.4 35.8 + - - +
1345G GLY 3.8 12.7 - - - +
1346G ASP* 3.5 28.8 + - - +
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Residues in contact with GLN1260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1257G ASP* 3.5 34.3 + - + +
1258G ARG 3.2 0.6 - - - -
1259G ASN* 1.3 80.0 - - + +
1261G ARG* 1.3 57.7 + - + +
1263G LYS* 3.5 8.1 + - + +
1264G GLU* 2.9 31.3 + - - +
1275G PHE* 4.2 26.5 - - - -
1277G LEU* 4.5 12.9 - - + +
1341G ASN* 4.7 13.6 + - - +
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Residues in contact with ARG1261 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1236G LEU* 4.5 6.7 - - + +
1237G PRO* 2.8 51.1 + - + +
1238G LEU* 4.4 5.1 - - - +
1239G LEU* 3.7 34.8 - - - +
1253G GLU* 4.9 1.6 + - - -
1254G VAL* 3.5 21.4 + - - +
1256G GLU 3.3 18.8 + - - -
1257G ASP* 3.1 39.1 + - + +
1258G ARG* 3.3 19.1 + - - +
1259G ASN 3.3 0.4 - - - -
1260G GLN* 1.3 73.6 - - + +
1262G ILE* 1.3 67.1 + - + +
1264G GLU* 3.3 18.8 + - - +
1265G MET* 3.3 13.2 + - - +
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Residues in contact with ILE1262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1236G LEU* 3.8 28.3 - - + -
1238G LEU* 5.4 0.4 - - + -
1258G ARG* 3.2 55.6 - - + +
1259G ASN* 3.2 7.8 + - - +
1261G ARG* 1.3 77.7 - - + +
1263G LYS* 1.3 61.7 + - - +
1265G MET* 3.4 3.6 + - - +
1266G TYR* 3.2 51.4 + - + -
1346G ASP* 3.9 11.4 - - - +
1347G LEU* 4.2 5.8 - - + +
1348G LEU* 3.9 26.7 - - + +
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Residues in contact with LYS1263 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1259G ASN 2.9 18.3 + - - +
1260G GLN* 3.6 6.7 - - + +
1262G ILE* 1.3 75.3 - - - +
1264G GLU* 1.3 64.7 + - - +
1266G TYR 3.4 0.5 + - - -
1267G TRP* 3.0 20.6 + - - +
1275G PHE* 3.9 1.3 - - - -
1277G LEU* 3.8 20.0 - - + -
1338G ILE 4.0 10.8 - - - -
1339G PHE* 2.9 61.5 + - + +
1340G PRO 3.3 12.5 + - - -
1341G ASN* 4.7 6.1 - - - +
1343G VAL 3.4 12.2 + - - -
1344G ASP* 3.8 15.0 + - - +
1345G GLY 3.9 17.7 - - - +
1347G LEU* 4.4 12.6 - - + -
1412G TYR* 4.3 3.8 - - - -
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Residues in contact with GLU1264 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1260G GLN* 2.9 18.8 + - - +
1261G ARG* 3.3 10.3 + - - +
1263G LYS* 1.3 77.4 - - - +
1265G MET* 1.3 60.7 + - - +
1267G TRP* 3.5 3.1 - - - +
1268G LYS* 3.3 44.9 + - - +
1275G PHE* 3.1 40.2 - - + +
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Residues in contact with MET1265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1223G MET 5.3 0.2 - - - +
1225G GLU* 4.3 6.1 - - + -
1234G VAL* 4.2 21.7 - - + +
1235G SER 4.4 13.7 - - - +
1236G LEU* 3.7 36.3 - - + -
1237G PRO* 6.2 0.2 - - + -
1261G ARG 3.3 9.0 + - - +
1262G ILE 3.8 5.2 - - - +
1263G LYS 3.2 0.8 - - - -
1264G GLU* 1.3 76.4 - - - +
1266G TYR* 1.3 77.0 + - + +
1267G TRP 3.2 0.2 - - - -
1268G LYS* 3.4 5.2 + - - +
1269G LEU* 3.4 36.3 + - + +
1562G PRO* 3.3 35.7 - - + -
1569G PHE* 3.6 18.2 - - + -
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Residues in contact with TYR1266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1262G ILE* 3.2 33.1 + - + +
1263G LYS 3.8 1.1 - - - +
1265G MET* 1.3 87.4 - - + +
1267G TRP* 1.3 62.2 + - - +
1269G LEU* 3.0 10.3 + - + +
1270G TRP* 2.9 60.8 + + + +
1339G PHE* 4.0 4.3 - - + -
1347G LEU* 3.1 42.7 + - + -
1348G LEU* 3.0 35.1 - - + +
1561G ASN* 3.1 44.6 + - + -
1562G PRO* 4.0 14.0 - - + +
1563G ILE* 4.6 2.6 + - - +
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Residues in contact with TRP1267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1263G LYS 3.0 16.8 + - - +
1264G GLU 3.5 7.2 - - - +
1265G MET 3.2 0.2 - - - -
1266G TYR* 1.3 76.9 - - - +
1268G LYS* 1.3 62.6 + - + +
1271G ILE* 2.7 69.5 + - + +
1273G GLU* 3.3 29.5 + - + -
1274G PRO 3.2 23.5 + - - -
1275G PHE* 3.6 23.1 - + + -
1276G ASN 3.7 5.6 - - - -
1277G LEU* 3.8 17.3 - - + -
1279G PHE* 3.4 39.7 - + - -
1336G LYS* 4.3 10.3 - - + -
1339G PHE* 3.7 32.3 - + + -
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Residues in contact with LYS1268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1229G MET* 2.8 29.7 + - - +
1234G VAL* 4.0 30.8 - - + +
1264G GLU* 3.3 35.5 + - + +
1265G MET* 3.9 7.9 - - - +
1266G TYR 3.3 0.6 - - - -
1267G TRP* 1.3 83.1 - - + +
1269G LEU* 1.3 58.0 + - - +
1271G ILE 4.6 2.0 - - - -
1275G PHE* 6.2 2.5 - - + -
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Residues in contact with LEU1269 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1225G GLU* 4.4 5.6 - - + -
1227G ARG 3.8 22.9 - - - +
1228G THR* 3.8 23.3 - - + -
1229G MET* 3.5 11.5 - - - +
1234G VAL* 4.2 11.4 - - + -
1265G MET* 3.4 45.7 + - + +
1266G TYR* 3.0 11.9 + - + +
1268G LYS* 1.3 80.3 - - - +
1270G TRP* 1.3 63.5 + - + +
1332G ARG* 4.7 0.2 + - - -
1560G LEU* 3.0 46.9 - - + +
1561G ASN* 5.5 0.4 - - - +
1562G PRO* 4.2 14.1 - - + -
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Residues in contact with TRP1270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1229G MET* 4.5 2.2 - - - +
1266G TYR* 2.9 44.1 + + - +
1269G LEU* 1.3 84.4 - - + +
1271G ILE* 1.3 77.4 + - + +
1331G TRP* 3.4 27.1 - + - +
1332G ARG* 2.6 32.5 + - - +
1335G ILE* 3.4 36.6 - - + -
1339G PHE* 3.8 13.5 - + - -
1347G LEU* 3.6 20.9 - - + -
1350G LEU* 4.7 8.5 - - + -
1558G GLY 3.3 19.3 - - - -
1559G ASP* 3.0 30.8 + - - +
1560G LEU 3.9 5.1 - - - +
1561G ASN* 4.0 15.5 - - + +
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Residues in contact with ILE1271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1229G MET* 3.8 11.4 - - - +
1267G TRP* 2.7 77.9 + - + +
1268G LYS* 4.4 1.6 - - - +
1269G LEU 3.8 0.2 - - - -
1270G TRP* 1.3 91.2 - - + +
1272G ASP* 1.3 60.8 + - - +
1273G GLU* 3.2 32.4 + - + +
1332G ARG* 4.0 30.3 - - + +
1335G ILE* 4.6 9.4 - - + -
1336G LYS* 4.6 11.2 - - + +
1339G PHE* 4.9 5.2 - - + -
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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