Contacts of the helix formed by residues 1216 - 1234 (chain C) in PDB entry 3B13
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 ARG1216 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1210C PHE* 4.3 27.3 - - - -
1211C TYR* 3.1 28.7 + - + +
1214C ASN* 3.5 27.9 + - + +
1215C ASN* 1.3 75.5 - - - +
1217C GLU* 1.3 58.9 + - - +
1218C GLU* 3.4 1.8 - - + -
1219C MET* 3.5 17.7 + - + +
1220C TYR* 3.0 29.2 + - - +
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Residues in contact with GLU1217 (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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1215C ASN 3.8 4.8 + - - +
1216C ARG* 1.3 70.7 - - - +
1218C GLU* 1.3 68.1 + - - +
1220C TYR* 3.3 8.5 + - + +
1221C ILE* 2.9 30.1 + - + +
1250C LEU* 3.5 28.6 - - + +
1261C GLN* 3.0 37.8 + - + +
1262C VAL* 3.0 31.9 - - - +
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Residues in contact with GLU1218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1216C ARG 3.4 0.4 - - - -
1217C GLU* 1.3 80.6 - - - +
1219C MET* 1.3 63.4 + - + +
1221C ILE* 3.5 3.5 + - - +
1222C ARG* 2.9 48.4 + - - +
1260C SER* 5.3 1.0 - - - +
1261C GLN* 4.0 35.2 + - + +
1263C MET 6.0 1.3 - - - +
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Residues in contact with MET1219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1211C TYR* 3.6 52.0 - - + +
1216C ARG* 3.5 18.7 + - + +
1217C GLU 3.3 0.8 - - - -
1218C GLU* 1.3 79.5 - - + +
1220C TYR* 1.3 67.0 + - - +
1222C ARG* 3.1 31.9 + - - +
1223C TYR* 2.9 47.4 + - + +
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Residues in contact with TYR1220 (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 LEU* 3.2 45.9 - - + +
1211C TYR* 3.8 12.0 - - + +
1212C LYS* 3.7 39.4 + - + +
1216C ARG 3.0 19.1 + - - +
1217C GLU* 3.5 10.3 - - + +
1219C MET* 1.3 75.5 - - - +
1221C ILE* 1.3 65.3 + - + +
1223C TYR 3.1 2.9 + - - -
1224C LEU* 2.9 49.8 + - + +
1246C LEU* 3.4 37.2 + - - +
1250C LEU* 4.7 14.1 - - + -
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Residues in contact with ILE1221 (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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1217C GLU* 2.9 23.9 + - - +
1218C GLU* 3.8 3.8 - - - +
1220C TYR* 1.3 70.6 - - + +
1222C ARG* 1.3 66.2 + - - +
1224C LEU* 3.2 13.4 + - + +
1225C TYR* 3.0 51.4 + - + -
1247C HIS* 3.8 23.1 - - + +
1250C LEU* 4.2 16.8 - - + -
1261C GLN 3.5 23.8 - - - +
1262C VAL* 3.6 21.5 - - - +
1263C MET 4.6 1.3 - - - +
1264C GLN* 4.4 16.8 - - + -
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Residues in contact with ARG1222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1218C GLU* 2.9 36.7 + - - +
1219C MET* 3.1 38.8 + - - +
1221C ILE* 1.3 76.4 - - - +
1223C TYR* 1.3 64.6 + - + +
1225C TYR* 3.3 6.5 + - - +
1226C LYS* 3.0 53.0 + - - +
1264C GLN* 5.8 3.6 - - - -
1265C THR* 4.4 29.1 + - + +
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Residues in contact with TYR1223 (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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1204C THR* 3.7 34.8 - - + +
1207C LEU* 3.6 37.5 - - + +
1208C LEU* 3.6 24.6 - - + +
1211C TYR* 4.1 13.9 + + + -
1219C MET* 2.9 37.6 + - + +
1220C TYR 3.6 1.3 - - - +
1222C ARG* 1.3 90.2 - - + +
1224C LEU* 1.3 67.1 + - - +
1225C TYR 3.0 1.1 - - - -
1226C LYS* 3.5 23.2 - - + +
1227C LEU* 2.9 25.5 + - - +
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Residues in contact with LEU1224 (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 LEU* 3.6 13.1 - - + +
1220C TYR* 2.9 37.0 + - + +
1221C ILE* 3.3 18.8 - - + +
1223C TYR* 1.3 72.4 - - - +
1225C TYR* 1.3 65.1 + - + +
1227C LEU* 3.7 5.8 - - + +
1228C ARG* 2.9 26.7 + - - +
1243C THR* 3.7 17.4 + - - +
1244C LEU* 5.1 2.7 - - + +
1246C LEU* 3.2 40.6 - - + -
1247C HIS* 3.5 39.3 - - + +
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Residues in contact with TYR1225 (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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1221C ILE* 3.0 33.6 + - + +
1222C ARG* 3.6 8.1 - - - +
1223C TYR 3.0 0.6 - - - -
1224C LEU* 1.3 84.4 - - + +
1226C LYS* 1.3 65.3 + - - +
1228C ARG* 3.2 41.2 + - - +
1229C ASP* 3.0 31.2 + - - +
1244C LEU* 3.8 18.0 - - + +
1247C HIS* 2.9 37.8 + + - -
1264C GLN* 3.7 41.7 - - + +
1267C GLN* 4.1 6.0 + - - -
1280C LEU* 3.5 19.0 - - + +
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Residues in contact with LYS1226 (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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1204C THR* 3.9 18.2 - - + +
1222C ARG* 3.0 45.9 + - - +
1223C TYR* 3.5 32.5 - - + +
1225C TYR* 1.3 74.6 - - - +
1227C LEU* 1.3 63.9 + - - +
1229C ASP* 3.1 10.7 + - - +
1230C LEU* 2.9 26.5 + - + +
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Residues in contact with LEU1227 (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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1201C MET* 4.0 25.8 - - + -
1204C THR* 4.0 11.9 - - + +
1205C VAL* 3.6 28.7 - - + -
1208C LEU* 4.6 11.0 - - + -
1223C TYR 2.9 16.4 + - - +
1224C LEU* 3.7 5.8 - - + +
1226C LYS* 1.3 74.2 - - - +
1228C ARG* 1.3 67.1 + - - +
1230C LEU* 3.1 7.0 + - + +
1231C HIS* 2.9 44.3 + - + +
1243C THR* 3.6 10.3 - - + -
1478C ILE* 3.6 31.6 - - + +
1479C LEU* 4.4 0.9 - - + -
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Residues in contact with ARG1228 (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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1224C LEU 2.9 16.9 + - - +
1225C TYR* 3.2 41.0 + - - +
1227C LEU* 1.3 74.3 - - - +
1229C ASP* 1.3 94.8 + - - +
1231C HIS* 3.0 9.7 + - - +
1232C LEU* 3.0 33.1 + - + +
1240C ALA* 4.1 13.9 - - + +
1243C THR* 3.8 14.9 + - - +
1244C LEU* 4.2 16.8 - - + +
1264C GLN* 5.3 4.2 + - - +
1283C THR* 5.9 1.0 - - - +
1287C TYR* 3.4 29.0 + - + +
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Residues in contact with ASP1229 (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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1225C TYR* 3.0 20.3 + - - +
1226C LYS* 3.5 9.2 - - - +
1228C ARG* 1.3 108.9 + - - +
1230C LEU* 1.3 58.2 + - + +
1232C LEU* 3.4 8.5 + - - +
1233C ASP* 3.0 37.8 + - - +
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Residues in contact with LEU1230 (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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1197C LYS* 4.5 12.3 - - + -
1200C ARG* 3.8 40.2 - - + +
1201C MET* 3.4 60.0 - - + +
1204C THR* 3.9 15.0 - - + +
1226C LYS* 2.9 17.0 + - + +
1227C LEU* 3.1 10.7 + - + +
1229C ASP* 1.3 77.7 - - + +
1231C HIS* 1.3 60.8 + - - +
1233C ASP* 3.3 29.0 - - - +
1234C CYS* 3.5 6.6 + - - -
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Residues in contact with HIS1231 (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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1201C MET* 3.4 30.4 - - + +
1227C LEU* 2.9 32.4 + - + +
1228C ARG 3.4 5.6 - - - +
1230C LEU* 1.3 74.6 - - - +
1232C LEU* 1.3 58.3 + - - +
1233C ASP 3.1 0.2 - - - -
1234C CYS* 3.2 2.8 + - - -
1235C ASP 3.0 8.1 + - - -
1236C ASN* 2.7 57.3 + - + +
1239C GLU* 3.4 33.1 - - + +
1240C ALA* 3.7 9.0 - - + -
1243C THR* 3.5 8.9 - - + +
1478C ILE 2.8 26.7 + - - -
1479C LEU* 4.5 7.6 - - + -
1480C ARG* 5.3 1.1 - - + -
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Residues in contact with LEU1232 (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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1228C ARG* 3.0 33.5 + - + +
1229C ASP* 3.9 8.1 - - - +
1231C HIS* 1.3 73.6 - - - +
1233C ASP* 1.3 68.7 + - - +
1235C ASP* 3.1 17.4 + - - +
1236C ASN 4.6 1.1 - - - +
1237C TYR* 3.5 37.3 + - + -
1240C ALA* 3.9 17.0 - - + -
1287C TYR* 3.6 27.4 - - + +
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Residues in contact with ASP1233 (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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1197C LYS* 3.8 30.6 + - - +
1200C ARG* 4.9 3.1 + - - -
1229C ASP* 3.0 24.6 + - - +
1230C LEU* 3.3 27.3 - - - +
1232C LEU* 1.3 80.1 - - - +
1234C CYS* 1.3 57.9 + - - +
1235C ASP* 3.1 8.0 + - - +
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Residues in contact with CYS1234 (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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1197C LYS* 3.7 30.7 - - - +
1201C MET* 3.9 13.7 - - - -
1230C LEU 3.5 12.8 + - - -
1231C HIS 3.2 2.9 + - - +
1233C ASP* 1.3 76.4 - - - +
1235C ASP* 1.3 67.9 + - - +
1236C ASN* 3.5 26.7 - - - +
1366C LYS* 4.4 14.4 + - - +
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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
------------------------------------------------------------
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