Contacts of the helix formed by residues 1172 - 1178 (chain B) in PDB entry 1AIS
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 LEU1172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A GLU* 2.8 17.0 + - - +
133A GLN* 4.9 13.0 - - + +
1156B ALA 5.7 0.4 - - - +
1160B TYR* 3.8 46.2 - - + +
1170B ARG 3.3 3.0 + - - -
1171B THR* 1.3 69.0 - - - +
1173B ASP* 1.3 63.1 + - - +
1175B ILE* 4.0 8.5 - - + +
1176B ALA* 3.1 24.9 + - - +
1183B LYS* 4.1 28.5 - - + +
1186B ILE* 3.4 33.7 - - + -
1187B GLY* 5.5 5.4 - - - -
1190B TYR* 6.4 0.4 - - + -
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Residues in contact with ASP1173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLU* 4.4 2.7 + - - +
1171B THR* 2.8 14.1 + - - +
1172B LEU* 1.3 78.2 - - - +
1174B GLU* 1.3 57.9 + - - +
1176B ALA* 3.0 13.3 + - - +
1177B ASP* 2.7 25.9 + - - +
1183B LYS* 3.6 24.4 + - - +
1276B ARG* 4.6 24.3 - - - +
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Residues in contact with GLU1174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123B LEU* 3.5 20.4 - - + +
1170B ARG* 3.2 49.6 + - + +
1171B THR* 2.8 18.9 + - - +
1173B ASP* 1.3 80.0 - - - +
1175B ILE* 1.3 57.4 + - - +
1177B ASP* 3.7 8.1 - - - +
1178B ILE* 3.4 25.0 - - + +
1214B LYS* 4.1 10.2 - - - +
1276B ARG* 4.0 30.3 + - - +
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Residues in contact with ILE1175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119B ILE* 5.0 2.5 - - + -
1123B LEU* 3.7 18.6 - - + -
1156B ALA* 3.6 21.3 - - + +
1159B VAL* 3.6 29.8 - - + +
1160B TYR* 3.6 44.0 - - + -
1163B CYS* 4.9 0.4 - - - -
1170B ARG* 3.9 25.6 - - + +
1171B THR 3.4 1.8 + - - +
1172B LEU* 3.8 9.6 + - + +
1173B ASP 3.2 0.4 - - - -
1174B GLU* 1.3 76.1 - - - +
1176B ALA* 1.3 64.4 + - - +
1177B ASP 3.5 0.2 - - - -
1178B ILE* 3.8 6.2 - - + +
1179B ALA* 3.2 22.3 + - + +
1186B ILE* 4.8 3.1 - - + +
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Residues in contact with ALA1176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1172B LEU 3.1 20.1 + - - +
1173B ASP 3.0 5.4 + - - +
1175B ILE* 1.3 79.1 - - - +
1177B ASP* 1.3 60.3 + - - +
1179B ALA 4.0 0.9 - - - -
1180B ARG 3.5 3.8 + - - -
1181B VAL* 3.2 34.7 + - - +
1182B ASP* 4.8 0.4 - - - -
1183B LYS* 3.3 30.7 - - + +
1186B ILE* 3.8 22.2 - - + +
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Residues in contact with ASP1177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1173B ASP* 2.7 27.7 - - - +
1174B GLU* 3.7 7.3 - - - +
1176B ALA* 1.3 72.8 - - - +
1178B ILE* 1.3 80.6 + - - +
1179B ALA 3.0 5.4 - - - -
1180B ARG* 3.0 22.3 + - - +
1181B VAL 4.9 1.6 - - - -
1183B LYS* 5.4 0.2 - - - +
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Residues in contact with ILE1178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118B ARG* 5.7 0.9 - - - +
1119B ILE* 3.6 46.2 - - + +
1122B GLN* 3.1 51.3 + - + +
1123B LEU* 4.1 20.4 - - + -
1174B GLU* 3.4 18.6 - - + +
1175B ILE* 3.8 8.5 - - - +
1177B ASP* 1.3 88.1 + - - +
1179B ALA* 1.3 61.4 + - + +
1180B ARG* 3.3 9.5 + - - +
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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