Contacts of the helix formed by residues 1196 - 1214 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1197A LYS* 1.3 64.6 + - - -
1198A ASP 3.2 0.2 - - - -
1199A ASN* 3.0 21.7 + - - +
1200A ARG* 2.8 34.3 + - - +
1380A THR* 6.2 0.2 - - - +
1381A GLN* 2.4 37.8 + - - +
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Residues in contact with LYS1197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196A SER* 1.3 79.4 - - - +
1198A ASP* 1.3 63.9 + - - +
1200A ARG* 3.3 34.1 - - - +
1201A MET* 2.9 35.1 + - + +
1230A LEU* 3.9 14.5 - - + +
1233A ASP* 3.2 37.0 + - - +
1234A CYS* 4.6 22.7 - - - -
1381A GLN* 4.0 7.1 + - - +
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Residues in contact with ASP1198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196A SER 3.2 0.6 - - - -
1197A LYS* 1.3 77.8 - - - +
1199A ASN* 1.3 66.4 + - - +
1201A MET* 3.1 8.5 + - - +
1202A SER* 2.9 20.0 + - - -
1347A TYR* 5.1 0.3 + - - -
1363A TYR* 3.7 27.9 + - - -
1378A LEU* 4.2 6.8 - - - +
1381A GLN* 3.5 36.1 + - + +
1382A PHE* 5.3 3.3 - - + -
1481A TRP* 3.7 30.0 - - + -
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Residues in contact with ASN1199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196A SER* 3.0 32.7 + - - +
1198A ASP* 1.3 74.7 - - - +
1200A ARG* 1.3 53.0 + - - +
1202A SER* 3.0 11.4 + - - -
1203A CYS* 2.8 42.4 + - - -
1355A PHE* 5.3 7.4 - - + -
1356A LEU* 4.8 5.9 - - - +
1381A GLN* 3.6 21.6 + - - +
1382A PHE* 3.6 25.4 - - - -
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Residues in contact with ARG1200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196A SER 2.8 20.8 + - - +
1197A LYS* 3.3 39.1 - - - +
1199A ASN* 1.3 73.5 - - - +
1201A MET* 1.3 56.8 + - - +
1203A CYS* 3.3 9.3 + - - +
1204A THR* 2.8 34.7 + - - +
1226A LYS* 5.6 6.1 - - - +
1230A LEU* 3.8 29.0 - - + +
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Residues in contact with MET1201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197A LYS* 2.9 25.5 + - + +
1198A ASP* 3.1 9.4 + - - +
1200A ARG* 1.3 70.9 - - - +
1202A SER* 1.3 64.5 + - - +
1204A THR* 3.2 3.4 + - - -
1205A VAL* 2.9 29.8 + - - +
1227A LEU* 4.2 6.3 - - + -
1230A LEU* 3.6 55.2 - - + +
1231A HIS* 3.8 26.0 - - - +
1234A CYS* 4.0 20.4 - - - -
1236A ASN* 4.8 4.7 - - - +
1479A LEU* 4.0 15.0 - - + -
1481A TRP* 4.0 15.7 - - + -
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Residues in contact with SER1202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1198A ASP 2.9 10.7 + - - -
1199A ASN* 3.0 12.1 + - - -
1201A MET* 1.3 78.9 - - - +
1203A CYS* 1.3 57.1 + - - +
1205A VAL* 3.3 5.6 + - - +
1206A ASN* 2.9 36.1 + - - -
1355A PHE* 3.8 30.4 - - - -
1356A LEU* 5.5 2.3 - - - +
1479A LEU* 5.2 2.6 - - - +
1481A TRP* 3.6 25.7 + - - -
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Residues in contact with CYS1203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199A ASN* 2.8 25.9 + - - -
1200A ARG* 3.7 9.0 - - - +
1201A MET 3.3 0.2 - - - -
1202A SER* 1.3 71.5 - - - +
1204A THR* 1.3 64.4 + - - +
1206A ASN* 3.1 9.0 + - - +
1207A LEU* 2.9 38.9 + - + +
1355A PHE* 5.4 11.4 - - - -
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Residues in contact with THR1204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1200A ARG* 2.8 23.8 + - - +
1201A MET* 3.6 7.2 - - - -
1202A SER 3.2 0.2 - - - -
1203A CYS* 1.3 78.1 - - - +
1205A VAL* 1.3 57.0 + - - +
1207A LEU 3.4 0.5 + - - -
1208A LEU* 2.9 26.3 + - + +
1223A TYR* 3.7 32.6 - - + +
1226A LYS* 4.2 13.5 - - + -
1227A LEU* 3.9 33.9 - - + +
1230A LEU* 3.6 12.3 - - - +
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Residues in contact with VAL1205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1201A MET 2.9 19.8 + - - +
1202A SER* 3.8 4.0 - - - +
1204A THR* 1.3 73.0 - - - +
1206A ASN* 1.3 63.4 + - - +
1208A LEU* 3.2 9.6 + - + +
1209A ASN* 2.9 43.8 + - - +
1227A LEU* 3.7 28.7 - - + -
1478A ILE* 4.4 13.9 - - + -
1479A LEU* 3.9 33.2 - - + -
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Residues in contact with ASN1206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1202A SER* 2.9 26.1 + - - +
1203A CYS* 3.1 8.2 + - - +
1205A VAL* 1.3 79.0 - - - +
1207A LEU* 1.3 61.1 + - + +
1209A ASN* 3.3 14.5 + - - +
1210A PHE* 2.9 25.2 + - - +
1355A PHE* 3.8 42.3 - - - +
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Residues in contact with LEU1207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1203A CYS* 2.9 38.8 + - + +
1204A THR* 4.9 0.2 - - - -
1206A ASN* 1.3 77.5 - - + +
1208A LEU* 1.3 65.1 + - - +
1210A PHE* 3.0 11.1 + - + +
1211A TYR* 2.9 46.4 + - + +
1223A TYR* 3.4 42.4 - - + +
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Residues in contact with LEU1208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1204A THR* 2.9 16.0 + - + +
1205A VAL* 3.3 12.3 - - + +
1207A LEU* 1.3 75.4 - - - +
1209A ASN* 1.3 62.2 + - - +
1211A TYR* 3.2 2.8 + - - -
1212A LYS 2.9 24.1 + - - -
1220A TYR* 3.0 58.9 - - + +
1223A TYR* 3.7 10.9 - - + +
1224A LEU* 3.6 33.9 - - + +
1227A LEU* 4.6 18.2 - - + -
1246A LEU* 4.1 14.1 - - + -
1478A ILE* 4.7 7.4 - - + -
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Residues in contact with ASN1209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1205A VAL* 2.9 38.7 + - - +
1206A ASN* 3.5 15.2 + - - +
1207A LEU 3.2 0.4 - - - -
1208A LEU* 1.3 78.5 - - - +
1210A PHE* 1.3 65.8 + - - +
1212A LYS* 3.5 13.1 - - - +
1213A ASP* 2.8 37.9 + - - +
1220A TYR* 5.9 0.3 - - - -
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Residues in contact with PHE1210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1206A ASN 2.9 13.8 + - - +
1207A LEU* 3.0 14.8 + - + +
1209A ASN* 1.3 77.4 - - - +
1211A TYR* 1.3 95.7 + + - +
1213A ASP* 3.2 5.1 + - - -
1214A ASN* 2.8 60.0 + - - +
1216A ARG* 3.5 27.8 - - - -
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Residues in contact with TYR1211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1207A LEU* 2.9 50.3 + - + +
1208A LEU* 3.8 2.0 - - - +
1210A PHE* 1.3 99.9 - + - +
1212A LYS* 1.3 65.8 + - - +
1214A ASN* 4.4 3.1 - - - +
1215A ASN* 3.1 2.9 + - - -
1216A ARG* 3.0 51.1 + - - +
1219A MET* 3.4 42.3 - - + -
1220A TYR* 3.6 21.5 - - - +
1223A TYR* 3.9 30.1 + + - -
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Residues in contact with LYS1212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1208A LEU 2.9 14.1 + - - +
1209A ASN* 3.5 17.7 - - - +
1211A TYR* 1.3 75.9 - - - +
1213A ASP* 1.3 66.8 + - - +
1215A ASN* 2.8 30.4 + - - +
1220A TYR* 3.5 35.8 - - + +
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Residues in contact with ASP1213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1209A ASN* 2.8 31.4 + - - +
1210A PHE* 3.7 5.5 - - - +
1212A LYS* 1.3 87.3 + - - +
1214A ASN* 1.3 62.5 + - - +
1215A ASN* 3.6 9.9 + - - +
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Residues in contact with ASN1214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210A PHE* 2.8 54.2 + - + +
1211A TYR* 4.5 0.7 - - - -
1212A LYS 3.1 0.4 - - - -
1213A ASP* 1.3 78.7 - - - +
1215A ASN* 1.3 71.7 + - - +
1216A ARG* 3.1 29.9 + - + +
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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