Contacts of the helix formed by residues 1196 - 1214 (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 SER1196 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1197C LYS* 1.3 62.2 + - - +
1199C ASN* 2.8 33.0 + - - +
1200C ARG* 2.9 30.5 + - - +
1381C GLN* 2.9 24.7 - - - +
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Residues in contact with LYS1197 (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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1196C SER* 1.3 75.9 - - - +
1198C ASP* 1.3 63.9 + - - +
1200C ARG* 3.9 21.7 - - - +
1201C MET* 2.9 37.7 + - + +
1230C LEU* 4.5 14.1 - - + +
1233C ASP* 3.8 37.0 + - + +
1234C CYS* 3.7 30.9 - - - +
1381C GLN* 3.6 3.4 + - - +
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Residues in contact with ASP1198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1196C SER 3.4 0.6 - - - -
1197C LYS* 1.3 77.7 - - - +
1199C ASN* 1.3 58.7 + - - +
1201C MET* 3.8 3.9 - - - +
1202C SER* 2.9 28.9 + - - -
1363C TYR* 4.2 15.9 + - - +
1374C PHE* 6.1 0.2 - - - -
1378C LEU* 4.3 13.7 - - - +
1381C GLN* 3.8 27.4 + - + +
1382C PHE* 5.9 2.4 - - + -
1481C TRP* 4.1 33.0 - - + -
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Residues in contact with ASN1199 (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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1196C SER* 2.8 18.6 + - - +
1198C ASP* 1.3 75.3 - - - +
1200C ARG* 1.3 59.1 + - + +
1202C SER* 3.0 7.6 + - - -
1203C CYS* 2.9 37.2 + - - -
1381C GLN* 3.1 41.2 + - - +
1382C PHE* 4.7 11.1 - - - -
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Residues in contact with ARG1200 (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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1196C SER* 2.9 36.5 + - - +
1197C LYS* 3.9 23.3 - - - +
1199C ASN* 1.3 71.6 - - - +
1201C MET* 1.3 57.3 + - - +
1203C CYS* 3.4 7.1 + - - +
1204C THR* 2.8 33.6 + - - +
1230C LEU* 3.8 36.3 - - + +
1233C ASP* 4.9 3.0 + - - -
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Residues in contact with MET1201 (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* 2.9 24.9 + - + +
1198C ASP* 3.8 5.2 - - - +
1200C ARG* 1.3 73.0 - - - +
1202C SER* 1.3 67.4 + - - +
1204C THR* 3.8 2.1 - - - -
1205C VAL* 2.9 29.8 + - - +
1227C LEU* 4.0 9.2 - - + -
1230C LEU* 3.4 46.0 - - + +
1231C HIS* 3.4 35.0 - - - +
1234C CYS* 3.9 17.5 - - - -
1236C ASN* 4.1 5.8 - - - +
1479C LEU* 4.5 5.8 - - + -
1480C ARG 6.2 0.2 - - - -
1481C TRP* 4.1 25.4 - - + -
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Residues in contact with SER1202 (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 ASP 2.9 19.5 + - - -
1199C ASN* 3.0 8.5 + - - -
1201C MET* 1.3 77.6 - - - +
1203C CYS* 1.3 64.2 + - - +
1205C VAL* 3.7 3.9 - - - +
1206C ASN* 2.9 29.7 + - - +
1355C PHE* 3.9 30.0 - - - -
1356C LEU* 5.5 1.6 - - - +
1479C LEU* 6.1 0.9 - - - -
1481C TRP* 4.2 16.6 + - - -
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Residues in contact with CYS1203 (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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1199C ASN* 2.9 21.2 + - - -
1200C ARG* 3.6 10.5 - - - +
1202C SER* 1.3 70.8 - - - +
1204C THR* 1.3 65.6 + - - +
1206C ASN* 2.9 22.5 + - - +
1207C LEU* 2.9 29.3 + - + +
1355C PHE* 5.9 0.2 - - - -
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Residues in contact with THR1204 (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 ARG* 2.8 25.8 + - - +
1201C MET* 3.8 6.5 - - - -
1203C CYS* 1.3 76.5 - - - +
1205C VAL* 1.3 57.5 + - - +
1207C LEU* 3.5 0.6 + - - -
1208C LEU* 2.9 27.8 + - + +
1223C TYR* 3.7 28.4 - - + +
1226C LYS* 3.9 30.2 - - + +
1227C LEU* 4.0 20.0 - - + +
1230C LEU* 3.9 9.1 - - - +
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Residues in contact with VAL1205 (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 2.9 22.2 + - - +
1202C SER* 3.8 4.3 - - - +
1204C THR* 1.3 72.6 - - - +
1206C ASN* 1.3 63.8 + - - +
1208C LEU* 3.2 11.4 - - + +
1209C ASN* 2.9 48.3 + - - +
1227C LEU* 3.6 23.8 - - + -
1478C ILE* 4.9 3.8 - - + -
1479C LEU* 3.6 39.9 - - + -
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Residues in contact with ASN1206 (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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1202C SER* 2.9 25.7 + - - +
1203C CYS* 2.9 14.1 + - - +
1205C VAL* 1.3 82.4 - - - +
1207C LEU* 1.3 59.7 + - + +
1209C ASN* 3.4 8.0 + - - +
1210C PHE* 2.9 27.0 + - - +
1355C PHE* 3.8 40.2 - - - +
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Residues in contact with LEU1207 (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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1203C CYS* 2.9 39.0 + - + +
1204C THR* 5.0 0.2 - - - -
1206C ASN* 1.3 76.3 - - + +
1208C LEU* 1.3 66.2 + - - +
1210C PHE* 3.3 11.8 + - + +
1211C TYR* 2.9 47.0 + - + +
1223C TYR* 3.6 37.9 - - + +
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Residues in contact with LEU1208 (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* 2.9 16.5 + - + +
1205C VAL* 3.2 16.8 - - + +
1207C LEU* 1.3 74.5 - - - +
1209C ASN* 1.3 68.6 + - - +
1211C TYR* 2.9 19.2 + - - +
1212C LYS 2.9 10.6 + - - -
1220C TYR* 3.2 51.3 - - + +
1223C TYR* 3.6 14.9 - - + -
1224C LEU* 3.6 13.0 - - + +
1227C LEU* 4.6 19.3 - - + -
1246C LEU* 4.2 23.6 - - + -
1478C ILE* 5.4 2.5 - - + -
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Residues in contact with ASN1209 (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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1205C VAL* 2.9 38.6 + - - +
1206C ASN* 3.6 9.9 - - - +
1208C LEU* 1.3 74.5 - - - +
1210C PHE* 1.3 64.7 + - - +
1212C LYS* 3.1 13.9 + - - +
1213C ASP* 2.9 36.9 + - - +
1220C TYR* 5.8 0.2 - - - -
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Residues in contact with PHE1210 (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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1206C ASN 2.9 15.7 + - - +
1207C LEU* 3.4 14.4 - - + +
1209C ASN* 1.3 75.7 - - - +
1211C TYR* 1.3 86.9 + + - +
1213C ASP* 3.4 4.7 + - - +
1214C ASN* 2.9 63.6 + - + +
1216C ARG* 4.3 22.2 - - - -
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Residues in contact with TYR1211 (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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1207C LEU* 2.9 56.8 + - + +
1208C LEU* 3.5 8.1 - - - +
1210C PHE* 1.3 94.6 - + - +
1212C LYS* 1.3 61.3 + - - +
1214C ASN* 4.6 2.2 - - - -
1215C ASN 2.8 26.2 + - - -
1216C ARG* 3.1 33.1 + - - +
1219C MET* 3.6 58.6 - - + +
1220C TYR* 3.8 19.1 - - - +
1223C TYR* 4.1 14.7 + + - -
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Residues in contact with LYS1212 (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 2.9 7.7 + - - +
1209C ASN* 3.1 18.1 + - - +
1211C TYR* 1.3 75.8 - - - +
1213C ASP* 1.3 71.5 + - - +
1215C ASN* 3.1 20.5 + - - +
1220C TYR* 3.7 36.1 + - + +
1246C LEU* 6.3 0.6 - - - +
1249C TRP* 6.2 1.8 - - - -
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Residues in contact with ASP1213 (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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1209C ASN* 2.9 28.7 + - - +
1210C PHE* 3.7 5.7 - - - +
1212C LYS* 1.3 85.7 - - - +
1214C ASN* 1.3 66.5 + - - +
1215C ASN* 3.4 11.9 + - - -
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Residues in contact with ASN1214 (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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1210C PHE* 2.9 57.3 + - + +
1211C TYR* 3.4 2.5 - - - +
1212C LYS 3.1 0.2 - - - -
1213C ASP* 1.3 81.2 + - - +
1215C ASN* 1.3 73.0 + - - +
1216C ARG* 3.2 30.3 + - - +
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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