Contacts of the helix formed by residues 1168 - 1176 (chain A) in PDB entry 4IGI
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 ASP1168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1139A GLU 4.6 0.4 + - - -
1140A PRO* 4.5 17.1 - - + +
1166A ASN 3.4 2.1 + - - -
1167A ALA* 1.3 72.7 - - - +
1169A ILE* 1.3 67.6 + - - +
1170A SER* 3.1 16.2 + - - -
1171A GLU* 2.9 54.1 + - - +
1172A MET* 3.0 26.1 + - - +
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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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1167A ALA 3.5 6.0 + - - +
1168A ASP* 1.3 73.4 - - - +
1170A SER* 1.3 64.3 + - - +
1172A MET* 3.3 7.3 + - - +
1173A GLN* 3.0 45.6 + - + +
1182A ALA* 5.3 0.2 - - - +
1184A ALA* 4.1 26.7 - - + -
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Residues in contact with SER1170 (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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1168A ASP* 3.1 10.8 + - - -
1169A ILE* 1.3 82.0 - - - +
1171A GLU* 1.3 57.4 + - - +
1173A GLN* 3.2 14.0 + - - +
1174A THR* 2.9 39.1 + - - -
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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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1139A GLU 4.5 1.0 - - - +
1140A PRO* 3.6 9.3 - - - +
1141A SER* 2.9 44.1 + - - +
1143A ASP 4.9 1.7 - - - +
1145A VAL* 4.0 20.9 + - + +
1168A ASP* 2.9 35.3 + - - +
1170A SER* 1.3 75.4 - - - +
1172A MET* 1.3 69.1 + - + +
1174A THR* 3.2 7.5 + - - -
1175A ILE* 3.0 34.3 + - + +
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Residues in contact with MET1172 (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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1105A THR* 5.3 1.8 - - + -
1135A VAL* 4.9 4.0 - - + +
1137A THR* 3.5 33.2 - - + -
1139A GLU 5.8 0.4 - - - +
1161A GLY* 3.9 24.0 - - - +
1162A ILE 3.8 5.8 - - - -
1163A GLY* 3.7 30.3 - - - +
1167A ALA* 4.7 2.5 - - + -
1168A ASP 3.0 18.4 + - - +
1169A ILE* 3.8 8.1 - - - +
1170A SER 3.2 0.2 - - - -
1171A GLU* 1.3 87.3 - - + +
1173A GLN* 1.3 61.8 + - - +
1175A ILE* 3.5 23.6 + - + +
1176A SER* 2.7 28.9 + - - -
1182A ALA* 3.8 6.3 - - + -
1183A VAL 4.7 2.9 - - - +
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Residues in contact with GLN1173 (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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1153A LYS* 4.7 0.9 + - - -
1169A ILE* 3.0 36.8 + - + +
1170A SER* 3.5 14.1 + - - +
1172A MET* 1.3 77.5 - - - +
1174A THR* 1.3 61.1 + - - +
1176A SER* 3.3 18.7 + - - +
1179A PRO* 3.9 48.4 + - + +
1182A ALA* 3.8 13.2 - - + +
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Residues in contact with THR1174 (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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1145A VAL* 4.4 7.4 - - + -
1146A ARG* 4.3 18.8 - - + -
1149A SER* 3.3 25.2 - - - +
1153A LYS* 2.8 31.2 + - - +
1170A SER* 2.9 26.2 + - - -
1171A GLU* 3.5 8.0 - - - -
1173A GLN* 1.3 74.7 - - - +
1175A ILE* 1.3 57.0 - - - +
1219A PRO* 5.5 6.7 - - + +
1220A SER 5.5 4.5 + - - +
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Residues in contact with ILE1175 (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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1105A THR* 3.7 30.1 - - + -
1109A LEU* 3.8 31.0 - - + -
1135A VAL* 4.3 13.0 - - + -
1145A VAL* 4.1 20.9 - - + -
1149A SER* 4.0 11.0 - - - +
1153A LYS* 3.9 5.5 - - - +
1159A PRO* 3.3 31.5 - - + +
1161A GLY* 4.9 4.9 - - - -
1171A GLU* 3.0 20.2 + - + +
1172A MET* 3.8 22.4 - - + +
1174A THR* 1.3 74.4 - - - +
1176A SER* 1.3 65.7 + - - +
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Residues in contact with SER1176 (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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1153A LYS* 3.1 18.4 + - - -
1159A PRO* 3.3 12.8 - - - -
1161A GLY 2.9 21.1 + - - +
1172A MET 2.7 22.2 + - - -
1173A GLN 3.4 10.2 - - - +
1174A THR 3.3 0.6 - - - -
1175A ILE* 1.3 77.3 - - - +
1177A PHE* 1.3 66.9 + - - +
1178A ILE* 3.2 20.0 + - - -
1181A PHE* 4.2 1.8 - - - -
1182A ALA* 3.5 17.8 + - - +
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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