Contacts of the helix formed by residues 1164 - 1180 (chain A) in PDB entry 4M76
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 SER1164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1108A ILE* 3.8 9.6 - - - +
1109A LEU* 3.8 23.6 - - - +
1162A VAL* 3.8 9.5 - - - +
1163A ASN* 1.3 84.4 + - - +
1165A LEU* 1.3 58.3 + - - +
1166A PRO 3.6 0.7 - - - -
1167A GLY* 3.7 5.0 + - - +
1168A SER* 3.1 28.1 + - - -
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Residues in contact with LEU1165 (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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1104A VAL* 3.9 15.3 - - + -
1108A ILE* 3.7 19.7 - - + -
1151A LEU* 4.1 21.8 - - + +
1154A ALA 4.1 4.7 - - - +
1155A LYS* 3.8 37.0 - - + +
1158A CYS* 3.8 20.4 - - + +
1159A GLU* 4.4 2.5 - - + +
1162A VAL* 3.5 18.2 + - + +
1163A ASN 3.1 2.0 - - - -
1164A SER* 1.3 75.1 + - - +
1166A PRO* 1.3 72.0 - - + +
1167A GLY 3.2 1.3 - - - -
1168A SER* 2.7 21.2 + - - +
1169A ILE* 3.0 25.5 + - + +
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Residues in contact with PRO1166 (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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1155A LYS* 5.2 12.6 - - + +
1159A GLU* 4.6 24.5 - - + +
1162A VAL 4.5 2.0 - - - +
1163A ASN* 3.3 17.0 - - - +
1165A LEU* 1.3 95.7 - - + +
1167A GLY* 1.3 56.3 + - - +
1169A ILE* 3.7 10.9 - - + +
1170A THR* 3.0 32.7 + - - -
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Residues in contact with GLY1167 (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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1163A ASN 5.0 0.6 + - - -
1164A SER* 3.7 6.6 + - - +
1165A LEU 3.2 0.8 - - - -
1166A PRO* 1.3 79.8 - - - +
1168A SER* 1.3 58.8 + - - +
1170A THR* 3.5 5.9 + - - -
1171A LYS* 3.1 30.7 + - - +
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Residues in contact with SER1168 (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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1108A ILE* 3.3 31.1 - - - +
1112A GLN* 3.2 36.9 + - - +
1118A PHE* 5.2 0.2 - - - -
1151A LEU* 4.3 6.9 - - - +
1164A SER 3.1 12.8 + - - -
1165A LEU* 2.7 22.9 + - - +
1167A GLY* 1.3 73.3 - - - +
1169A ILE* 1.3 59.4 + - - +
1171A LYS* 3.4 1.7 + - - -
1172A ALA* 3.0 27.2 + - - +
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Residues in contact with ILE1169 (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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1148A LEU* 3.9 17.0 - - + -
1151A LEU* 4.4 9.2 - - + +
1152A GLN* 4.2 18.6 - - + +
1155A LYS* 3.9 38.6 - - + -
1165A LEU* 3.0 33.5 + - + +
1166A PRO* 3.7 6.5 - - + +
1167A GLY 3.3 0.2 - - - -
1168A SER* 1.3 83.0 + - - +
1170A THR* 1.3 60.0 + - - +
1172A ALA* 3.3 2.6 + - - +
1173A GLY 3.0 23.7 + - - -
1199A MET* 3.2 31.0 - - + +
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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 PRO 3.0 16.8 + - - -
1167A GLY* 3.8 6.3 - - - -
1168A SER 3.3 0.2 - - - -
1169A ILE* 1.3 80.1 - - - +
1171A LYS* 1.3 57.4 + - - +
1173A GLY 3.2 1.4 + - - -
1174A ASP* 2.8 51.0 + - - +
1199A MET* 5.0 0.9 - - - -
1201A ARG* 3.6 12.7 + - - +
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Residues in contact with LYS1171 (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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1112A GLN* 3.9 12.1 - - - +
1114A PRO* 2.5 32.8 + - - +
1115A ASP* 3.9 6.3 - - - +
1116A GLY* 3.7 19.5 - - - +
1167A GLY 3.1 18.4 + - - +
1168A SER* 3.7 6.1 - - - +
1170A THR* 1.3 77.4 - - - +
1172A ALA* 1.3 60.2 + - - +
1174A ASP* 3.3 16.7 + - + +
1175A PHE 3.3 16.6 + - - -
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Residues in contact with ALA1172 (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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1112A GLN* 4.0 0.4 - - - +
1116A GLY* 4.0 14.4 - - - +
1118A PHE* 4.2 9.9 - - + -
1144A THR* 3.8 18.1 - - + +
1148A LEU* 3.8 24.2 - - + -
1168A SER 3.0 17.0 + - - +
1169A ILE 3.7 4.0 - - - +
1171A LYS* 1.3 75.9 - - - +
1173A GLY* 1.3 62.5 + - - +
1175A PHE* 3.4 4.6 + - - +
1176A LEU* 3.3 26.3 + - - +
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Residues in contact with GLY1173 (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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1148A LEU* 4.3 3.4 - - - -
1169A ILE 3.0 10.9 + - - -
1170A THR 3.6 4.3 - - - -
1172A ALA* 1.3 74.8 - - - +
1174A ASP* 1.3 59.1 + - - +
1176A LEU* 3.6 4.0 + - - -
1177A GLU* 3.1 31.4 + - - +
1196A LEU* 3.9 4.3 - - - +
1199A MET* 3.6 28.4 - - - +
1201A ARG* 3.5 9.4 + - - -
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Residues in contact with ASP1174 (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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1115A ASP 5.9 0.2 - - - +
1170A THR* 2.8 39.5 + - - +
1171A LYS* 3.5 18.4 - - + +
1172A ALA 3.2 0.2 - - - -
1173A GLY* 1.3 78.1 - - - +
1175A PHE* 1.3 61.9 + - - +
1177A GLU* 3.7 1.4 + - - +
1178A ALA* 3.2 24.9 + - - +
1201A ARG* 2.6 34.9 + - - +
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Residues in contact with PHE1175 (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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1115A ASP* 3.5 31.6 + - + +
1116A GLY* 4.8 3.1 - - - -
1117A VAL* 3.5 34.3 - - + -
1139A LYS* 4.6 9.4 - - - -
1140A ASP* 4.0 11.4 - - + -
1141A MET* 3.5 41.1 - - + -
1144A THR* 4.5 7.4 - - + -
1171A LYS 3.3 4.8 + - - +
1172A ALA* 3.8 7.9 - - - +
1173A GLY 3.3 0.4 - - - -
1174A ASP* 1.3 77.2 - - - +
1176A LEU* 1.3 70.7 + - + +
1178A ALA* 3.4 3.0 + - - -
1179A ASN* 3.1 49.3 + - - +
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Residues in contact with LEU1176 (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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1141A MET* 3.7 49.1 - - + +
1144A THR* 4.4 3.1 - - + -
1145A ALA* 4.2 16.4 - - + +
1148A LEU* 3.7 29.2 - - + -
1172A ALA 3.3 11.8 + - - +
1173A GLY 3.9 4.0 - - - +
1175A PHE* 1.3 82.0 - - + +
1177A GLU* 1.3 57.8 + - - +
1179A ASN 3.2 1.4 + - - -
1180A TYR* 2.8 35.5 + - - +
1192A ALA* 4.4 9.4 - - + +
1195A ALA* 3.8 19.1 - - + -
1196A LEU* 4.0 15.5 - - + -
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Residues in contact with GLU1177 (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 GLY 3.1 13.3 + - - +
1174A ASP 4.2 1.6 - - - +
1176A LEU* 1.3 80.1 - - - +
1178A ALA* 1.3 60.8 + - - +
1179A ASN 3.5 0.2 + - - -
1180A TYR* 4.0 6.1 + - - -
1181A MET* 5.2 1.7 + - - +
1196A LEU* 4.0 13.9 - - + +
1201A ARG* 2.6 53.5 + - - +
1206A LEU* 3.6 33.6 - - + +
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Residues in contact with ALA1178 (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 ASP 3.2 19.3 + - - +
1175A PHE* 3.8 6.1 - - - +
1176A LEU 3.2 1.0 - - - -
1177A GLU* 1.3 77.1 - - - +
1179A ASN* 1.3 70.4 + - - +
1180A TYR 3.7 0.2 - - - -
1181A MET 5.5 0.7 - - - -
1182A ASN* 4.5 5.7 + - - -
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Residues in contact with ASN1179 (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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1139A LYS* 4.9 10.5 + - - +
1141A MET* 3.8 18.3 - - + +
1175A PHE* 3.1 47.0 + - - +
1176A LEU 3.2 4.6 + - - -
1178A ALA* 1.3 90.0 - - - +
1180A TYR* 1.3 62.3 + - - +
1181A MET 3.4 2.9 - - - +
1182A ASN* 3.5 28.5 + - + +
1183A LEU* 3.7 14.9 + - - +
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Residues in contact with TYR1180 (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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1141A MET* 4.2 0.7 - - + -
1176A LEU 2.8 15.2 + - - +
1177A GLU 4.0 1.9 + - - +
1178A ALA 3.7 1.2 - - - -
1179A ASN* 1.3 76.2 - - - +
1181A MET* 1.3 64.7 + - - +
1182A ASN 3.3 0.9 + - - -
1183A LEU* 3.3 36.2 + - + +
1189A VAL* 2.6 36.9 + - + +
1192A ALA* 3.8 11.7 - - + -
1193A GLY* 3.4 27.9 - - - -
1196A LEU* 3.7 17.7 - - + -
1202A LEU* 4.5 2.7 - - + -
1206A LEU* 3.4 50.9 - - + -
1209A LYS* 3.7 23.5 - - + -
1210A PHE* 3.4 14.3 - - - +
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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