Contacts of the helix formed by residues 1164 - 1179 (chain A) in PDB entry 2N1G
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 GLU1164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1162A ALA* 3.3 19.8 - - + +
1163A VAL* 1.4 80.8 + - - +
1165A PHE* 1.4 60.4 + - - +
1166A ASN* 4.3 9.4 - - + +
1167A ASP* 3.0 33.3 + - + +
1168A VAL* 3.0 14.2 + - - +
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Residues in contact with PHE1165 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1163A VAL 3.2 4.2 + - - -
1164A GLU* 1.4 67.3 - - - +
1166A ASN* 1.3 63.3 + - - +
1168A VAL* 3.8 24.9 - - + -
1169A LYS* 2.9 48.2 + - + +
1205A LYS* 4.7 6.3 - - + +
1208A LEU* 3.6 64.4 - - + -
1212A TYR* 4.3 21.5 - + + -
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Residues in contact with ASN1166 (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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1164A GLU* 3.1 8.7 - - + +
1165A PHE* 1.3 83.0 - - - +
1167A ASP* 1.3 54.3 + - - +
1169A LYS* 3.9 12.3 - - - +
1170A THR* 2.7 36.7 + - - -
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Residues in contact with ASP1167 (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 LEU 2.9 26.3 - - - +
1160A ALA* 4.9 0.3 - - - +
1161A GLY 4.9 0.4 + - - -
1162A ALA* 3.5 26.0 - - + +
1164A GLU* 3.0 15.8 + - + +
1166A ASN* 1.3 76.9 - - - +
1168A VAL* 1.4 54.7 + - - +
1170A THR* 3.2 5.8 + - - -
1171A LEU* 2.8 46.7 + - - +
242B ALA* 5.2 8.6 - - - +
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Residues in contact with VAL1168 (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 ASN 5.4 0.9 - - - -
1159A LEU* 3.7 34.8 - - + -
1162A ALA 4.4 0.2 - - - +
1163A VAL* 4.0 11.7 - - - +
1164A GLU 3.0 21.1 + - - +
1165A PHE* 3.6 25.6 - - + +
1167A ASP* 1.4 74.1 + - - +
1169A LYS* 1.3 57.4 - - - +
1171A LEU* 3.3 3.4 + - - +
1172A LEU* 2.9 51.8 + - + +
1205A LYS* 4.8 4.0 - - + -
1209A VAL* 3.7 29.4 - - + -
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Residues in contact with LYS1169 (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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1165A PHE* 2.9 37.0 + - + +
1166A ASN* 3.9 11.7 - - - +
1168A VAL* 1.3 76.4 - - - +
1170A THR* 1.3 83.0 + - - +
1173A ARG* 2.9 41.3 + - + +
1174A GLU* 5.6 0.6 + - - -
1212A TYR* 3.5 43.7 - - + +
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Residues in contact with THR1170 (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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1166A ASN* 2.7 23.3 + - - +
1167A ASP* 3.2 5.8 + - - -
1169A LYS* 1.3 94.4 + - - +
1171A LEU* 1.3 62.6 + - - +
1174A GLU* 3.0 44.4 - - - +
238B PHE* 5.0 0.9 - - - -
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Residues in contact with LEU1171 (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 LEU* 3.6 44.2 - - + +
1160A ALA* 3.7 13.9 - - + -
1167A ASP* 2.8 23.7 + - - +
1168A VAL 3.4 7.4 - - - +
1170A THR* 1.3 82.4 - - - +
1172A LEU* 1.3 64.0 + - - +
1173A ARG 3.3 0.9 + - - -
1175A TRP* 3.2 22.2 + - - +
238B PHE* 3.8 18.8 - - + +
239B PHE* 3.3 38.4 - - + -
242B ALA* 3.9 16.6 - - + -
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Residues in contact with LEU1172 (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 LEU* 4.5 4.5 - - + -
1168A VAL* 2.9 40.0 + - + +
1171A LEU* 1.3 73.3 - - - +
1173A ARG* 1.3 62.1 + - - +
1175A TRP* 3.9 8.7 - - + -
1176A ILE* 3.0 37.3 + - + +
1190A VAL* 4.3 2.7 - - + -
1209A VAL* 3.5 29.8 - - + +
1212A TYR* 3.9 19.3 - - + -
1213A MET* 3.9 33.0 - - + +
1216A LEU* 4.2 1.1 - - - -
239B PHE* 3.6 29.4 - - + -
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Residues in contact with ARG1173 (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 LYS* 2.9 23.5 + - + +
1171A LEU 3.3 0.4 + - - -
1172A LEU* 1.3 76.7 - - - +
1174A GLU* 1.3 71.0 + - - +
1176A ILE* 4.1 1.2 - - - +
1177A THR* 2.9 39.8 + - + +
1212A TYR* 2.9 33.0 + - - +
1216A LEU* 3.6 34.4 - - - +
1219A GLN* 5.9 0.8 + - - -
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Residues in contact with GLU1174 (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 LYS* 5.6 0.7 + - - -
1170A THR* 3.0 41.3 - - - +
1173A ARG* 1.3 86.9 - - + +
1175A TRP* 1.3 59.2 + - - +
1177A THR* 3.3 9.0 - - - +
1178A THR* 2.9 42.3 + - - +
1179A ILE 3.8 0.5 + - - -
238B PHE* 3.4 31.7 - - + -
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Residues in contact with TRP1175 (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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1171A LEU 3.2 17.4 + - - +
1172A LEU* 3.5 13.7 - - + +
1174A GLU* 1.3 79.4 - - - +
1176A ILE* 1.3 71.0 + - + +
1179A ILE* 3.1 30.5 + - + +
1182A PRO* 4.3 5.8 - - + +
1183A MET* 5.3 0.6 - - + +
1186A ASP* 3.4 36.5 + - + +
1187A ILE* 3.9 24.5 - - + -
1190A VAL* 4.1 23.1 - - + -
1213A MET* 4.9 1.6 - - + -
1217A MET* 3.6 25.1 - - + -
1225A TRP* 3.0 43.9 - + - -
1228A ALA* 5.7 0.2 - - + -
1232A ILE* 4.5 2.0 - - + -
238B PHE* 3.2 23.1 - + + -
239B PHE* 3.4 29.6 - + + -
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Residues in contact with ILE1176 (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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1172A LEU* 3.0 22.0 + - + +
1173A ARG 4.2 0.7 - - - +
1175A TRP* 1.3 91.3 - - + +
1177A THR* 1.3 61.6 + - + +
1213A MET* 3.3 39.3 - - + +
1216A LEU* 3.6 36.3 - - + +
1217A MET* 3.6 28.9 - - + +
1220A SER* 5.0 4.7 - - - +
1225A TRP* 3.0 44.5 + - + -
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Residues in contact with THR1177 (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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1173A ARG* 2.9 39.5 + - + +
1174A GLU* 3.3 10.6 - - - -
1176A ILE* 1.3 82.3 - - + +
1178A THR* 1.4 66.5 + - - +
1179A ILE 5.3 0.2 - - - -
1216A LEU* 4.9 9.9 - - + +
1219A GLN* 6.4 1.3 - - + -
1225A TRP* 5.4 0.2 - - - -
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Residues in contact with THR1178 (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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1174A GLU* 2.9 29.0 + - - +
1177A THR* 1.4 86.5 + - - +
1179A ILE* 1.4 70.2 + - + +
1180A SER* 3.2 9.9 + - - -
238B PHE* 5.9 2.0 - - + -
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Residues in contact with ILE1179 (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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1174A GLU 4.0 3.4 - - - +
1175A TRP* 3.1 36.2 + - + +
1178A THR* 1.4 79.4 - - + +
1180A SER* 1.3 63.8 - - - +
1181A ASP 3.3 20.9 - - - +
1182A PRO* 4.5 4.0 - - + -
1183A MET* 4.7 14.6 - - + -
1225A TRP* 3.0 34.9 + - + -
235B MET 5.9 1.1 - - - +
238B PHE* 3.6 41.5 - - + -
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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