Contacts of the helix formed by residues 1175 - 1191 (chain A) in PDB entry 3Q71
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 ASP1175 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800A AR6 2.5 30.4 + - - +
1141A LYS* 2.8 23.6 + - - -
1171A LEU 5.2 0.2 - - - -
1172A HIS* 2.8 29.4 + - + +
1173A PRO 3.3 0.2 - - - -
1174A SER* 1.3 75.1 + - - +
1176A HIS* 1.3 61.9 + - - +
1177A GLU* 3.8 1.9 + - - +
1178A ASN* 3.0 34.4 + - + -
1179A ILE* 3.0 25.5 + - - +
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Residues in contact with HIS1176 (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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1020A LYS* 5.2 4.5 - - - -
1173A PRO 3.7 21.1 + - - -
1174A SER* 2.9 23.3 + - - -
1175A ASP* 1.3 73.0 - - - +
1177A GLU* 1.3 62.5 + - - +
1179A ILE* 3.7 11.1 - - - +
1180A GLN* 3.0 25.5 + - - +
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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
----------------------------------------------------------
1141A LYS* 3.0 41.6 + - + +
1175A ASP* 3.2 0.6 + - - +
1176A HIS* 1.3 78.5 - - + +
1178A ASN* 1.3 57.0 + - - +
1180A GLN* 3.3 7.0 + - - +
1181A ALA* 3.0 27.7 + - - +
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Residues in contact with ASN1178 (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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800A AR6 3.3 3.4 + - - -
1131A ALA* 3.3 16.3 - - - +
1134A THR* 3.2 24.5 + - - +
1141A LYS* 3.5 28.0 - - - +
1171A LEU* 4.0 13.0 - - + -
1175A ASP* 3.0 34.8 + - + +
1177A GLU* 1.3 74.6 - - - +
1179A ILE* 1.3 68.1 + - - +
1181A ALA* 3.2 2.1 + - - -
1182A PHE* 2.9 48.2 + - - +
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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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993A LEU* 4.1 20.6 - - + -
1020A LYS* 3.9 27.6 - - + +
1171A LEU* 3.9 26.1 - - + +
1172A HIS 3.9 8.7 - - - +
1173A PRO 3.8 21.8 - - - +
1175A ASP 3.0 14.5 + - - +
1176A HIS* 3.7 13.7 - - - +
1177A GLU 3.3 0.2 - - - -
1178A ASN* 1.3 74.8 - - - +
1180A GLN* 1.3 54.7 + - - +
1182A PHE* 4.1 0.9 - - - +
1183A SER* 2.7 44.8 + - - +
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Residues in contact with GLN1180 (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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1176A HIS 3.0 17.6 + - - +
1177A GLU* 3.6 6.3 - - - +
1179A ILE* 1.3 75.6 - - - +
1181A ALA* 1.3 60.3 - - - +
1183A SER* 3.2 6.6 + - - -
1184A ASP* 2.8 70.2 + - - +
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Residues in contact with ALA1181 (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 LYS* 3.6 33.2 - - + +
1142A ASN* 3.8 14.3 - - + +
1145A ALA* 3.8 5.9 - - + +
1177A GLU 3.0 17.6 + - - +
1178A ASN* 3.7 6.7 - - - +
1180A GLN* 1.3 76.9 - - - +
1182A PHE* 1.3 63.9 + - + +
1184A ASP* 3.5 7.4 + - - +
1185A GLU* 3.1 23.7 + - - +
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Residues in contact with PHE1182 (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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1018A LEU* 3.7 17.0 - - + -
1129A PHE 6.0 0.4 - - - -
1130A PRO 5.9 0.9 - - - -
1131A ALA* 4.3 5.8 - - + -
1144A PHE* 4.0 18.4 - + - -
1145A ALA* 3.9 19.7 - - + -
1148A ILE* 3.8 27.6 - - + -
1149A ILE* 4.3 9.9 - - + -
1169A PHE* 3.6 44.2 - + + -
1171A LEU* 3.6 27.8 - - + -
1178A ASN* 2.9 41.5 + - - +
1181A ALA* 1.3 77.5 - - + +
1183A SER* 1.3 63.3 + - - +
1185A GLU* 3.3 2.8 + - - +
1186A PHE* 3.0 28.4 + - - -
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Residues in contact with SER1183 (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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993A LEU* 5.0 1.6 - - - +
994A TYR 4.1 7.5 + - - -
995A PHE* 3.6 20.2 - - - +
996A GLN 5.5 0.9 - - - -
1018A LEU* 3.9 20.2 - - - +
1179A ILE* 2.7 32.2 + - - +
1180A GLN* 3.6 8.5 - - - -
1182A PHE* 1.3 76.7 - - - +
1184A ASP* 1.3 65.2 + - - +
1186A PHE* 3.2 3.9 + - - +
1187A ALA* 2.9 21.4 + - - +
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Residues in contact with ASP1184 (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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1180A GLN* 2.8 56.3 + - - +
1181A ALA* 3.7 7.0 - - - +
1183A SER* 1.3 73.7 - - - +
1185A GLU* 1.3 62.0 + - - +
1187A ALA* 3.4 8.3 + - - +
1188A ARG* 3.1 40.0 + - - +
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Residues in contact with GLU1185 (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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1142A ASN 5.4 0.3 - - - +
1145A ALA* 4.5 4.7 - - + -
1146A GLU* 3.6 38.7 - - - +
1149A ILE* 3.4 34.2 - - + +
1150A SER* 5.1 0.7 + - - -
1181A ALA 3.1 16.6 + - - +
1182A PHE 3.8 0.9 - - - +
1183A SER 3.2 0.4 - - - -
1184A ASP* 1.3 74.5 - - - +
1186A PHE* 1.3 67.1 + - - +
1188A ARG* 3.3 27.2 + - - +
1189A ARG* 3.0 44.2 + - + +
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Residues in contact with PHE1186 (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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995A PHE* 3.6 21.1 - + + -
1006A GLY 3.8 11.7 - - - -
1007A SER 3.8 9.2 - - - -
1008A LEU* 3.5 36.5 - - + +
1016A MET* 3.7 30.5 - - + -
1018A LEU* 3.3 38.4 - - + -
1149A ILE* 3.9 15.0 - - + -
1169A PHE* 3.9 24.5 - + - -
1182A PHE 3.0 21.8 + - - +
1183A SER 3.2 7.2 + - - +
1185A GLU* 1.3 75.5 - - - +
1187A ALA* 1.3 62.9 + - - +
1189A ARG* 3.3 2.8 + - - +
1190A ALA* 2.9 25.3 + - - +
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Residues in contact with ALA1187 (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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995A PHE* 3.5 13.3 - - + -
996A GLN 3.3 25.8 - - - +
997A SER* 5.4 0.4 - - - +
998A MET* 4.1 19.6 + - + +
1183A SER 2.9 13.3 + - - +
1184A ASP* 3.5 12.1 - - - +
1185A GLU 3.3 0.2 - - - -
1186A PHE* 1.3 77.1 - - - +
1188A ARG* 1.3 62.2 + - - +
1190A ALA* 3.3 2.3 + - - +
1191A ASN* 3.1 23.6 + - - +
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Residues in contact with ARG1188 (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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998A MET* 3.9 26.1 - - + +
1146A GLU* 5.8 0.8 + - - -
1184A ASP* 3.1 28.5 + - - +
1185A GLU* 3.5 34.4 + - - +
1187A ALA* 1.3 81.5 - - - +
1189A ARG* 1.3 63.2 + - - +
1191A ASN* 3.4 14.6 + - - +
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Residues in contact with ARG1189 (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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1008A LEU* 3.7 24.9 - - + -
1149A ILE* 4.1 8.4 - - + +
1150A SER* 2.9 40.4 + - - +
1153A PHE* 3.8 43.6 - - + +
1185A GLU* 3.0 36.7 + - - +
1186A PHE 3.7 4.0 - - - +
1188A ARG* 1.3 77.1 - - + +
1190A ALA* 1.3 61.2 + - - +
1191A ASN 3.4 5.4 + - - +
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Residues in contact with ALA1190 (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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995A PHE* 3.5 28.9 - - + -
1004A GLU* 4.7 9.4 - - - +
1008A LEU* 4.1 11.8 - - + +
1186A PHE 2.9 17.2 + - - +
1187A ALA 3.8 2.0 - - - +
1188A ARG 3.3 0.2 - - - -
1189A ARG* 1.3 76.0 - - - +
1191A ASN* 1.3 62.3 + - - +
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Residues in contact with ASN1191 (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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998A MET* 3.7 37.6 - - + +
1187A ALA 3.1 16.0 + - - +
1188A ARG 3.7 8.4 - - - +
1189A ARG 3.3 7.8 - - - +
1190A ALA* 1.3 83.1 - - - +
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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