Contacts of the helix formed by residues 1209 - 1226 (chain C) 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 ASP1209 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1208C VAL* 1.3 84.1 - - - +
1210C PRO* 1.4 82.5 - - - +
1211C ILE* 3.3 18.5 + - + +
1212C THR* 2.7 29.6 + - - +
1253C GLY* 3.0 25.3 - - - -
1254C VAL 4.8 0.3 + - - -
1255C SER* 3.2 10.1 + - - -
1256C ALA* 2.9 29.3 + - + +
1277C GLU* 4.0 29.2 + - + +
1334C ASP* 4.5 2.9 - - - +
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Residues in contact with PRO1210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112C ASN* 6.4 0.2 - - - +
1208C VAL 3.9 5.3 - - - +
1209C ASP* 1.4 92.2 - - - +
1211C ILE* 1.3 56.8 + - - +
1213C LEU* 2.9 37.1 + - + +
1214C PHE* 3.2 19.7 + - + -
1255C SER* 4.1 15.5 - - - +
1334C ASP* 3.7 19.1 - - - +
1336C GLN* 5.1 3.8 - - - +
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Residues in contact with ILE1211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1209C ASP* 3.0 12.7 + - - +
1210C PRO* 1.3 77.9 - - - +
1212C THR* 1.3 66.2 + - - +
1214C PHE* 3.3 16.0 + - + +
1215C VAL* 3.1 22.6 + - - +
1252C GLY* 3.7 17.9 - - - -
1253C GLY 3.7 18.2 - - - +
1283C MET* 3.7 18.8 - - + -
1332C TYR* 3.4 38.1 - - + +
1333C ASP* 3.5 32.5 - - - +
1334C ASP* 4.2 10.5 + - + +
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Residues in contact with THR1212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1208C VAL* 3.2 27.1 - - + +
1209C ASP 2.7 15.6 + - - -
1211C ILE* 1.3 75.1 - - - +
1213C LEU* 1.3 54.6 + - - -
1215C VAL* 3.7 1.5 - - + +
1216C LEU* 2.8 36.8 + - + +
1277C GLU* 4.2 2.4 + - - -
1283C MET* 3.1 43.6 - - + +
1286C TRP* 3.6 35.4 - - + -
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Residues in contact with LEU1213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193C TRP* 4.2 11.7 - - + -
1195C ALA* 3.5 32.3 - - + +
1200C ILE* 4.3 16.4 - - + -
1204C ILE* 4.3 8.3 - - + -
1205C ILE* 3.9 32.3 - - + +
1208C VAL* 3.8 22.2 - - + +
1209C ASP 3.6 0.6 + - - -
1210C PRO* 2.9 20.2 + - + +
1212C THR* 1.3 75.6 - - - +
1214C PHE* 1.3 66.6 + - - +
1216C LEU* 3.9 4.4 - - + +
1217C VAL* 3.0 29.6 + - - +
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Residues in contact with PHE1214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027C VAL* 3.5 21.0 - - + +
1189C ILE* 3.8 22.4 - - + -
1193C TRP* 4.0 25.4 - + - -
1210C PRO* 3.2 18.6 + - + -
1211C ILE* 3.3 19.3 + - + +
1213C LEU* 1.3 77.5 - - + +
1215C VAL* 1.3 58.1 + - - +
1217C VAL 3.2 0.3 + - - -
1218C SER* 2.8 30.9 + - - -
1333C ASP 4.6 0.2 - - - -
1334C ASP* 3.6 27.1 - - + -
1380C GLN* 3.9 13.2 - - - -
1381C GLY* 3.9 28.9 - - - -
1382C ALA* 3.7 16.6 - - + +
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Residues in contact with VAL1215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1211C ILE 3.1 17.2 + - - +
1212C THR* 3.7 5.6 - - + +
1214C PHE* 1.3 76.3 - - - +
1216C LEU* 1.3 67.4 + - - +
1218C SER* 3.3 6.0 + - - -
1219C VAL* 2.9 35.0 + - + +
1247C SER* 5.4 3.1 - - - +
1283C MET* 4.1 10.8 - - + -
1287C VAL* 3.6 25.6 - - + -
1332C TYR* 3.2 56.8 - - + -
1382C ALA* 4.2 3.6 - - + -
1384C ILE* 4.5 4.9 - - + +
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Residues in contact with LEU1216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1200C ILE* 4.0 13.7 - - + -
1204C ILE* 4.1 18.2 - - + -
1212C THR* 2.8 35.3 + - + +
1213C LEU* 3.9 6.5 - - + +
1215C VAL* 1.3 76.0 - - - +
1217C VAL* 1.3 62.6 + - - +
1219C VAL* 3.4 3.6 + - - +
1220C VAL* 3.2 26.8 + - - +
1286C TRP* 4.2 0.7 - - + -
1287C VAL* 3.9 36.1 - - + +
1290C LEU* 3.6 27.1 - - + -
1291C LEU* 4.4 8.0 - - + +
1698C PHE* 4.0 24.7 - - + -
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Residues in contact with VAL1217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027C VAL* 4.0 14.4 - - + -
1193C TRP* 3.8 17.3 - - + -
1195C ALA* 4.6 0.9 - - + -
1198C TYR* 3.5 52.7 - - + -
1200C ILE* 3.7 20.2 - - + -
1213C LEU 3.0 21.8 + - - +
1214C PHE 3.7 3.1 - - - +
1216C LEU* 1.3 75.5 - - - +
1218C SER* 1.3 58.8 + - - +
1220C VAL* 3.6 7.2 - - + +
1221C GLU* 3.0 29.6 + - + +
1698C PHE* 5.7 1.6 - - + -
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Residues in contact with SER1218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025C ALA* 3.6 23.7 - - - +
1026C GLU* 4.2 2.9 - - - -
1027C VAL* 3.6 15.1 + - - +
1214C PHE 2.8 20.7 + - - -
1215C VAL* 3.8 4.3 + - - -
1217C VAL* 1.3 74.1 - - - +
1219C VAL* 1.3 55.5 + - - +
1220C VAL 3.2 1.6 - - - -
1221C GLU* 3.5 6.0 - - - +
1222C ALA* 2.6 37.2 + - - +
1382C ALA* 3.9 10.4 - - - +
1383C GLY 4.6 0.2 + - - -
1384C ILE* 3.3 14.9 - - - +
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Residues in contact with VAL1219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1215C VAL* 2.9 28.7 + - + +
1216C LEU 3.8 4.0 - - - +
1218C SER* 1.3 74.8 - - - +
1220C VAL* 1.3 61.4 + - - +
1222C ALA* 3.9 0.5 - - - +
1223C PHE* 3.0 56.9 + - + -
1245C ASN* 6.0 0.2 - - - +
1287C VAL* 3.8 39.0 - - + -
1291C LEU* 4.1 11.4 - - + -
1292C ILE* 4.6 0.2 - - + -
1328C ILE* 3.9 13.2 - - + -
1384C ILE* 2.9 23.3 - - + +
1386C ILE* 6.5 0.2 - - + -
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Residues in contact with VAL1220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1198C TYR* 6.5 0.2 - - + -
1216C LEU 3.2 7.7 + - - +
1217C VAL* 3.6 10.8 - - + +
1218C SER 3.2 0.2 - - - -
1219C VAL* 1.3 76.2 - - - +
1221C GLU* 1.3 66.8 + - + +
1223C PHE* 3.1 8.6 + - - +
1224C ILE* 3.0 34.3 + - + +
1291C LEU* 3.7 16.4 - - + -
1697C LEU* 3.4 34.5 - - + +
1698C PHE* 3.5 38.8 - - + +
1699C VAL 5.3 0.2 - - - +
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Residues in contact with GLU1221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025C ALA* 3.5 22.8 - - + +
1026C GLU 4.1 5.5 + - - +
1027C VAL* 6.4 0.2 - - - -
1032C SER* 3.4 21.9 - - - -
1033C ALA* 4.8 0.7 + - - +
1034C ARG* 3.1 36.0 + - - +
1055C TRP* 5.6 0.5 - - - -
1198C TYR* 3.4 35.0 + - + -
1217C VAL* 3.0 22.2 + - + +
1218C SER* 4.3 1.2 - - - -
1220C VAL* 1.3 78.0 - - + +
1222C ALA* 1.3 57.1 + - - +
1224C ILE* 3.5 12.7 - - + +
1225C ALA* 3.1 24.6 + - - +
1688C PHE* 5.0 4.6 - - + -
1697C LEU* 5.1 9.2 - - + +
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Residues in contact with ALA1222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023C GLY* 3.8 4.0 - - - -
1024C PHE* 3.8 26.0 - - - +
1025C ALA* 3.4 4.9 - - - +
1218C SER 2.6 21.6 + - - +
1219C VAL 3.9 2.7 - - - +
1220C VAL 3.1 0.2 + - - -
1221C GLU* 1.3 70.4 - - - +
1223C PHE* 1.3 66.4 + - - +
1225C ALA* 3.1 12.3 + - - +
1226C SER* 3.3 13.7 + - - -
1384C ILE* 3.9 21.8 - - + -
1386C ILE* 4.2 12.9 - - + +
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Residues in contact with PHE1223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1219C VAL* 3.0 42.5 + - + +
1220C VAL* 3.1 6.5 + - - +
1222C ALA* 1.3 75.7 - - - +
1224C ILE* 1.3 63.8 + - + +
1226C SER* 3.0 11.2 + - - -
1228C ILE* 3.0 57.2 + - + +
1231C PRO* 4.9 15.3 - - + -
1234C MET* 3.8 35.7 - - + -
1291C LEU* 5.7 2.0 - - + -
1292C ILE* 3.6 34.8 - - + -
1328C ILE* 3.9 7.9 - - + -
1386C ILE* 3.4 24.7 - - + -
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Residues in contact with ILE1224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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990C LEU* 4.1 22.5 - - + +
992C PHE* 4.1 1.4 - - - -
1034C ARG* 6.1 1.6 - - - +
1220C VAL* 3.0 28.1 + - + +
1221C GLU* 3.5 13.2 - - + +
1223C PHE* 1.3 75.7 - - + +
1225C ALA* 1.3 57.9 + - - +
1227C GLY* 3.1 17.5 + - - +
1228C ILE 4.4 7.2 - - - +
1229C THR* 5.4 1.8 - - - +
1684C ALA* 4.3 6.8 - - + +
1687C PHE* 3.3 39.5 - - + -
1688C PHE* 4.1 30.1 - - + -
1697C LEU* 3.9 14.8 - - + -
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Residues in contact with ALA1225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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990C LEU* 5.6 4.9 - - - +
992C PHE* 3.6 12.0 - - - -
1022C THR 4.2 1.1 - - - -
1023C GLY* 4.1 0.7 - - - -
1024C PHE* 3.4 34.8 - - + +
1034C ARG* 6.4 0.2 - - - +
1221C GLU 3.1 9.5 + - - +
1222C ALA 3.1 8.7 + - - +
1224C ILE* 1.3 75.8 - - - +
1226C SER* 1.3 57.7 + - - +
1227C GLY 3.4 0.2 - - - -
1399C PRO* 3.9 1.0 - - - +
1401C TYR* 2.8 36.8 + - + +
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Residues in contact with SER1226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1022C THR* 2.7 46.5 - - - +
1023C GLY* 3.8 1.1 - - - -
1222C ALA 3.3 9.1 + - - -
1223C PHE* 3.0 11.1 + - - -
1225C ALA* 1.3 79.7 - - - +
1227C GLY* 1.3 60.1 + - - +
1228C ILE* 3.2 18.2 + - - +
1386C ILE* 4.6 4.1 - - - +
1398C VAL* 3.4 10.2 - - - +
1399C PRO* 3.1 21.7 - - - +
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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
------------------------------------------------------------
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