Contacts of the helix formed by residues 1168 - 1183 (chain A) in PDB entry 5A31
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 LEU1168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1136A SER* 5.0 6.7 - - - +
1163A PRO* 3.5 29.1 - - + +
1165A HIS* 4.2 12.8 - - + -
1167A GLU* 1.3 81.8 - - - +
1169A ALA* 1.3 63.8 + - - +
1170A ASN* 3.0 8.7 + - - +
1171A GLU* 3.3 36.1 - - + +
1172A TYR 3.5 2.3 + - - -
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Residues in contact with ALA1169 (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 PRO* 4.0 17.6 - - + +
1166A ALA* 4.7 16.6 - - - +
1167A GLU* 3.2 4.4 - - - +
1168A LEU* 1.3 77.4 - - - +
1170A ASN* 1.3 57.9 + - - +
1172A TYR* 3.2 6.2 + - + +
1173A ALA* 3.0 26.2 + - - +
1201A HIS* 4.5 20.2 - - + +
1204A THR* 4.5 7.1 - - + +
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Residues in contact with ASN1170 (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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1133A SER* 3.2 40.2 + - - -
1136A SER* 4.3 9.6 - - - +
1137A PHE* 3.7 7.8 - - - +
1168A LEU* 4.4 5.4 - - - +
1169A ALA* 1.3 78.7 - - - +
1171A GLU* 1.3 61.4 + - - +
1173A ALA* 3.2 12.8 + - - +
1174A GLY 3.2 9.4 + - - -
1201A HIS* 4.0 18.7 + - + +
1203A MET* 3.3 35.0 - - - +
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Residues in contact with GLU1171 (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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1102A ILE* 3.3 42.2 - - + +
1136A SER* 3.2 39.5 + - - +
1137A PHE* 4.2 0.4 - - - +
1139A ASN* 4.9 4.5 - - - +
1140A GLY* 3.1 20.1 - - - +
1163A PRO* 5.2 5.0 - - - +
1168A LEU* 3.3 33.9 + - + +
1170A ASN* 1.3 80.8 - - - +
1172A TYR* 1.3 67.1 + - - +
1174A GLY 3.4 0.7 + - - -
1175A PHE 3.0 15.6 + - - -
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Residues in contact with TYR1172 (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 ILE 3.0 18.5 + - - -
1159A VAL* 3.8 0.2 - - - -
1161A ASN 3.6 15.7 - - - -
1162A LYS* 3.5 34.4 + - + -
1163A PRO* 3.8 27.1 - - + -
1168A LEU 3.5 0.8 + - - -
1169A ALA* 3.2 12.5 + - + +
1170A ASN 3.2 0.4 - - - -
1171A GLU* 1.3 89.5 - - - +
1173A ALA* 1.3 53.3 + - - +
1175A PHE* 2.9 29.3 + + - +
1176A LEU* 2.8 56.0 + - + +
1196A TYR* 3.0 34.4 + + - -
1204A THR* 4.8 10.1 - - + -
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Residues in contact with ALA1173 (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 PHE* 3.7 5.1 - - + -
1169A ALA 3.0 6.5 + - - +
1170A ASN 3.2 10.5 - - - +
1172A TYR* 1.3 74.4 - - - +
1174A GLY* 1.3 67.5 - - - +
1176A LEU* 3.4 8.0 - - - +
1177A MET* 3.2 21.3 + - - +
1201A HIS* 5.2 0.2 - - + -
1203A MET* 3.6 15.9 - - + +
1204A THR* 3.5 45.5 - - + +
1207A GLY* 3.9 3.6 - - - -
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Residues in contact with GLY1174 (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 PHE* 3.3 39.7 - - - -
1141A VAL* 3.4 13.0 - - - +
1170A ASN 3.2 7.5 + - - -
1171A GLU 3.6 2.2 - - - -
1172A TYR 3.2 0.4 - - - -
1173A ALA* 1.3 79.6 - - - +
1175A PHE* 1.3 61.6 + - - -
1177A MET* 3.1 15.9 + - - +
1178A ALA 3.1 9.2 + - - -
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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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1100A LEU* 3.3 28.7 - - + -
1102A ILE* 4.1 15.0 - - + -
1140A GLY 3.4 14.9 - - - +
1144A GLY* 3.5 16.2 - - - -
1147A ILE* 3.6 12.3 - - + -
1157A TRP* 4.0 20.6 - + - -
1158A ILE* 4.5 6.7 - - - -
1161A ASN* 3.9 25.4 - - + -
1171A GLU 3.0 11.7 + - - +
1172A TYR* 2.9 33.9 + + - +
1174A GLY* 1.3 71.1 - - - +
1176A LEU* 1.3 68.6 + - + +
1178A ALA* 3.0 19.4 + - - +
1179A LEU* 3.2 40.9 + - + +
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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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1158A ILE* 4.0 12.8 - - + -
1172A TYR* 2.8 56.4 + - + +
1173A ALA* 3.4 14.1 - - - +
1175A PHE* 1.3 79.4 - - + +
1177A MET* 1.3 58.8 + - - +
1179A LEU* 3.3 16.4 + - - +
1180A GLY 3.5 7.1 + - - -
1185A LEU* 3.7 25.4 - - + +
1188A LEU* 4.4 5.6 - - + -
1196A TYR* 4.6 9.4 - - + -
1204A THR* 5.9 4.5 - - + +
1207A GLY 4.8 0.7 - - - -
1208A LEU* 3.7 35.9 - - + +
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Residues in contact with MET1177 (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 PHE* 3.5 19.7 - - + -
1141A VAL* 3.9 4.0 - - + -
1173A ALA 3.2 2.0 + - - +
1174A GLY 3.1 12.1 + - - +
1176A LEU* 1.3 75.9 - - - +
1178A ALA* 1.3 68.9 + - - +
1179A LEU 3.1 1.8 - - - -
1180A GLY* 3.1 10.7 + - - -
1181A LEU* 3.3 39.0 + - + +
1207A GLY* 3.2 32.5 - - - +
1210A LEU* 3.9 30.1 - - + -
1211A GLY* 3.8 4.8 - - - -
1605A ALA* 3.8 15.5 - - + +
1608A HIS* 3.7 27.4 - - + -
1609A LEU* 5.0 3.4 - - + -
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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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1141A VAL* 3.5 35.7 - - + +
1144A GLY* 3.6 20.4 - - - -
1145A LEU* 3.8 6.6 - - + +
1174A GLY 3.1 4.2 + - - -
1175A PHE 3.1 13.5 - - - +
1177A MET* 1.3 79.6 - - - +
1179A LEU* 1.3 61.2 + - - +
1181A LEU* 3.2 16.8 + - - +
1182A ASN* 3.2 22.1 + - - +
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Residues in contact with LEU1179 (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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1144A GLY 4.4 2.0 - - - +
1147A ILE* 3.6 25.8 - - + -
1153A ILE* 4.1 5.6 - - + -
1158A ILE* 4.2 19.3 - - + -
1175A PHE* 3.2 60.1 + - + +
1176A LEU* 3.6 10.3 - - - +
1177A MET 3.1 0.8 - - - -
1178A ALA* 1.3 80.7 - - - +
1180A GLY* 1.3 56.8 + - - +
1182A ASN* 3.3 11.8 - - - +
1183A GLY 3.0 23.4 + - - -
1184A HIS* 3.1 29.7 + - + -
1185A LEU* 3.4 18.3 + - + +
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Residues in contact with GLY1180 (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 LEU 3.5 4.8 + - - -
1177A MET 3.1 4.2 + - - -
1179A LEU* 1.3 81.1 - - - +
1181A LEU* 1.3 60.7 + - - +
1183A GLY* 3.4 8.2 + - - -
1185A LEU* 3.6 12.0 - - - +
1211A GLY* 3.1 32.8 - - - -
1214A ALA* 3.6 3.8 - - - +
1215A ALA* 3.3 22.8 + - - -
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Residues in contact with LEU1181 (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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1090A PHE* 5.1 1.7 - - - -
1141A VAL* 4.5 3.1 - - + -
1145A LEU* 4.4 4.9 - - + -
1177A MET* 3.3 44.6 + - + +
1178A ALA* 3.2 14.5 + - - +
1180A GLY* 1.3 76.7 - - - +
1182A ASN* 1.3 61.4 + - - +
1183A GLY* 3.5 0.5 + - - -
1210A LEU 4.2 7.4 - - - +
1214A ALA* 3.5 26.7 - - + +
1608A HIS* 4.2 11.2 - - + +
1609A LEU* 4.4 11.9 - - + -
1611A VAL* 3.3 38.9 - - + +
1612A LEU* 4.0 17.7 - - + +
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Residues in contact with ASN1182 (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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1090A PHE* 3.3 28.6 - - + -
1144A GLY 3.7 9.7 + - - +
1145A LEU* 4.9 0.9 - - + +
1147A ILE* 2.9 42.4 + - - +
1149A PRO* 3.4 28.1 - - - +
1178A ALA 3.4 9.6 - - - +
1179A LEU* 3.3 18.6 - - - +
1181A LEU* 1.3 79.5 - - - +
1183A GLY* 1.3 56.9 + - - +
1184A HIS* 4.0 11.4 + - - +
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Residues in contact with GLY1183 (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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1179A LEU 3.0 4.8 + - - -
1180A GLY 3.4 7.5 + - - -
1181A LEU 3.3 3.8 - - - -
1182A ASN* 1.3 76.8 - - - +
1184A HIS* 1.3 61.4 + - - +
1185A LEU 3.3 3.3 + - - -
1186A THR* 3.1 26.3 + - - +
1187A LYS* 4.3 3.5 + - - -
1215A ALA* 4.9 9.0 - - - -
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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