Contacts of the helix formed by residues 1187 - 1198 (chain A) in PDB entry 1DSZ
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 CYS1187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1122A ZN 2.3 37.0 - - - -
1170A THR 4.7 1.3 - - - -
1171A CYS* 3.8 11.2 - - - -
1172A HIS 5.2 0.9 - - - -
1177A CYS* 3.9 16.4 - - + -
1179A ILE* 4.1 4.4 - - + +
1183A THR 4.5 1.0 + - - -
1184A ARG 4.0 5.2 + - - +
1185A ASN 3.3 1.2 - - - -
1186A ARG* 1.3 82.5 - - + +
1188A GLN* 1.3 60.7 + - - +
1189A TYR* 3.8 9.9 - - - -
1190A CYS* 3.3 15.3 - - + -
1191A ARG* 3.0 26.7 + - - +
1311B ARG 3.0 6.3 - - - -
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Residues in contact with GLN1188 (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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1158A PHE* 3.4 16.5 - - + -
1169A TYR* 3.4 46.7 + - + -
1184A ARG 5.4 0.4 - - - +
1185A ASN* 5.1 1.8 - - - +
1187A CYS* 1.3 69.3 - - - +
1189A TYR* 1.3 66.1 + - - +
1191A ARG* 4.3 1.8 - - - -
1192A LEU* 3.0 22.2 + - - +
1310B GLN 5.1 0.5 - - - +
1311B ARG* 2.6 43.9 + - + +
1538D T 3.4 19.6 + - - -
1539D T 2.9 29.9 + - - +
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Residues in contact with TYR1189 (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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1169A TYR* 3.3 35.9 - + + +
1170A THR* 3.7 23.7 + - - -
1171A CYS* 3.7 18.4 - - + +
1175A LYS* 3.3 36.5 - - + +
1187A CYS* 3.3 5.3 - - - -
1188A GLN* 1.3 79.1 - - - +
1190A CYS* 1.3 65.1 + - - +
1192A LEU* 3.3 2.9 + - - +
1193A GLN* 2.9 56.7 + - + +
1311B ARG 4.5 0.8 + - - -
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Residues in contact with CYS1190 (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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1122A ZN 2.4 34.3 - - - -
1171A CYS* 3.9 0.7 - - - -
1175A LYS* 3.6 22.9 - - - -
1176A ASN 4.3 0.2 - - - -
1177A CYS* 3.4 33.2 - - + +
1179A ILE* 4.0 10.4 - - + +
1187A CYS* 3.3 4.6 - - - -
1189A TYR* 1.3 82.9 - - - +
1191A ARG* 1.3 61.1 + - - +
1193A GLN* 3.6 11.4 - - - +
1194A LYS* 2.9 30.1 + - - +
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Residues in contact with ARG1191 (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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1137A VAL* 4.1 6.1 - - + +
1154A GLY 3.2 26.1 - - - -
1155A CYS* 3.3 16.4 - - - +
1158A PHE* 3.5 39.1 - - + +
1179A ILE* 3.8 22.1 - - + +
1184A ARG* 3.4 41.0 - - - +
1185A ASN* 3.0 21.6 + - - -
1187A CYS 3.0 18.5 + - - +
1188A GLN* 3.7 5.2 - - - +
1189A TYR 3.2 0.2 - - - -
1190A CYS* 1.3 77.3 - - - +
1192A LEU* 1.3 62.9 + - - +
1194A LYS* 3.3 4.0 + - - +
1195A CYS* 3.0 22.8 + - - -
1539D T 4.5 3.0 + - - -
1540D G 2.8 29.7 + - - -
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Residues in contact with LEU1192 (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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1158A PHE* 3.5 11.8 - - + -
1159A PHE* 3.8 27.8 - - + -
1162A SER* 3.9 24.2 - - - +
1163A ILE* 5.1 2.7 - - + -
1167A MET 4.7 9.2 - - - +
1169A TYR* 4.0 22.7 - - + +
1188A GLN 3.0 16.3 + - - +
1189A TYR* 3.8 3.4 - - - +
1191A ARG* 1.3 74.8 - - - +
1193A GLN* 1.3 60.2 + - - +
1195A CYS* 2.7 23.9 + - - +
1196A PHE* 3.0 38.3 + - + -
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Residues in contact with GLN1193 (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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1175A LYS* 3.5 23.7 + - - +
1176A ASN* 5.4 0.5 - - - -
1189A TYR* 2.9 48.8 + - + +
1190A CYS* 3.6 14.1 - - - +
1192A LEU* 1.3 77.6 - - - +
1194A LYS* 1.3 61.4 + - - +
1196A PHE* 3.4 9.9 + - - +
1197A GLU* 3.0 24.0 + - + +
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Residues in contact with LYS1194 (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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1136A PHE 3.9 12.4 + - - -
1137A VAL* 3.0 39.4 + - + +
1139A GLN* 4.4 8.7 + - - +
1179A ILE* 3.5 27.4 + - + +
1190A CYS 2.9 17.1 + - - +
1191A ARG 3.8 4.3 - - - +
1193A GLN* 1.3 76.4 + - - +
1195A CYS* 1.3 66.5 + - - +
1197A GLU* 4.0 7.9 - - + -
1198A VAL* 2.9 36.3 + - + +
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Residues in contact with CYS1195 (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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1137A VAL* 4.0 22.2 - - - +
1155A CYS* 4.5 5.8 - - - -
1158A PHE* 4.3 18.6 - - - -
1159A PHE* 3.6 27.1 - - + -
1191A ARG* 3.0 21.7 + - - -
1192A LEU* 2.7 17.0 + - - +
1194A LYS* 1.3 74.0 - - - +
1196A PHE* 1.3 59.4 + - - +
1198A VAL* 3.3 5.7 - - - +
1200A MET* 2.8 49.1 + - - +
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Residues in contact with PHE1196 (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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1159A PHE* 3.7 20.9 - + - -
1163A ILE* 4.0 20.6 - - + -
1192A LEU* 3.0 45.3 + - + -
1193A GLN* 3.8 7.9 - - - +
1195A CYS* 1.3 76.4 - - - +
1197A GLU* 1.3 59.8 + - - +
1199A GLY* 2.8 23.0 + - - -
1200A MET 3.7 16.6 + - - +
1202A LYS* 4.0 25.8 - - + -
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Residues in contact with GLU1197 (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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1193A GLN* 3.0 18.8 + - + +
1194A LYS* 3.2 11.2 + - + +
1196A PHE* 1.3 78.2 - - - +
1198A VAL* 1.3 61.8 + - + +
1199A GLY* 3.3 1.4 + - - -
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Residues in contact with VAL1198 (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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1136A PHE* 3.4 45.1 - - + +
1137A VAL* 3.6 22.7 - - + -
1149A VAL* 3.5 17.4 - - + +
1194A LYS* 2.9 37.9 + - + +
1195A CYS 3.3 10.5 - - - +
1197A GLU* 1.3 77.8 - - + +
1199A GLY* 1.3 57.2 + - - +
1200A MET 4.6 1.3 - - - +
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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