Contacts of the helix formed by residues 1187 - 1198 (chain B) in PDB entry 3GIJ
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 GLY1187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1181B ALA* 5.8 1.1 - - - -
1186B ILE* 1.3 73.4 - - - +
1188B ASN* 1.3 59.7 + - - -
1191B ALA* 2.8 35.8 + - - +
1812H A 2.9 34.3 + - - -
1813H G 4.0 11.4 - - - -
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Residues in contact with ASN1188 (chain B).
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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1187B GLY* 1.3 73.3 - - - -
1189B ILE* 1.3 64.9 + - + +
1191B ALA* 4.3 6.2 - - - +
1192B GLU* 3.1 33.6 + - + +
1812H A 3.8 2.8 + - - +
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Residues in contact with ILE1189 (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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1187B GLY 3.2 0.6 - - - -
1188B ASN* 1.3 84.0 - - + +
1190B THR* 1.3 59.1 + - - +
1192B GLU* 3.4 4.4 + - - +
1193B LYS* 3.0 51.7 + - + +
1811H T 3.4 40.4 - - + +
1812H A 3.3 18.4 + - - +
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Residues in contact with THR1190 (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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1186B ILE* 3.8 28.5 - - + -
1187B GLY 4.0 2.5 - - - -
1189B ILE* 1.3 69.3 - - - +
1191B ALA* 1.3 59.7 + - - +
1193B LYS* 3.0 16.2 + - - +
1194B LEU* 2.9 39.7 + - + +
1217B ILE* 3.7 29.7 - - + +
1221B LYS* 3.4 21.2 - - + +
1811H T 3.5 4.0 + - - -
1812H A 2.8 27.4 + - - -
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Residues in contact with ALA1191 (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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1180B ILE* 4.8 3.9 - - + +
1181B ALA* 3.7 30.1 - - + +
1186B ILE* 3.8 11.3 - - + +
1187B GLY 2.8 24.2 + - - +
1188B ASN* 4.3 4.9 - - - +
1190B THR* 1.3 72.1 - - - +
1192B GLU* 1.3 58.3 + - + +
1194B LEU* 3.2 8.6 + - - +
1195B LYS* 3.0 37.0 + - + +
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Residues in contact with GLU1192 (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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1188B ASN* 3.1 22.6 + - + +
1189B ILE* 3.7 4.9 - - + +
1191B ALA* 1.3 74.3 - - + +
1193B LYS* 1.3 63.2 + - - +
1195B LYS* 3.5 21.9 + - + +
1196B LYS* 2.8 61.1 + - - +
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Residues in contact with LYS1193 (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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1189B ILE* 3.0 41.3 + - + +
1190B THR* 3.0 16.9 + - - +
1192B GLU* 1.3 77.2 - - + +
1194B LEU* 1.3 62.2 + - - +
1196B LYS* 3.6 12.0 + - - +
1197B LEU* 3.4 24.9 + - - +
1216B MET* 3.6 46.1 + - + +
1217B ILE* 4.2 10.6 - - + +
1811H T 3.7 21.2 + - - -
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Residues in contact with LEU1194 (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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1180B ILE* 3.4 35.9 - - + -
1186B ILE* 4.2 2.9 - - + -
1190B THR* 2.9 34.5 + - + +
1191B ALA* 3.5 7.0 - - - +
1193B LYS* 1.3 77.7 - - - +
1195B LYS* 1.3 56.3 + - - +
1197B LEU* 3.0 7.5 + - + +
1198B GLY 2.9 7.1 + - - -
1199B ILE* 2.7 53.4 + - + +
1213B LEU* 3.6 31.2 - - + -
1217B ILE* 4.0 13.2 - - + -
1225B LEU* 3.9 13.2 - - + -
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Residues in contact with LYS1195 (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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1180B ILE* 5.5 3.6 - - + -
1191B ALA* 3.0 26.5 + - + +
1192B GLU* 4.0 24.2 + - + +
1193B LYS 3.4 0.2 - - - -
1194B LEU* 1.3 74.5 - - - +
1196B LYS* 1.3 63.2 + - - +
1197B LEU 3.1 0.2 - - - -
1198B GLY* 3.1 14.5 + - - +
1199B ILE 3.8 6.7 - - - +
1200B ASN* 3.4 29.5 + - - +
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Residues in contact with LYS1196 (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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1192B GLU* 2.8 48.7 + - - +
1193B LYS* 3.7 11.7 - - - +
1194B LEU 3.3 0.2 - - - -
1195B LYS* 1.3 77.5 - - - +
1197B LEU* 1.3 61.7 + - + +
1198B GLY 3.5 0.2 + - - -
1216B MET* 6.5 0.4 - - - -
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Residues in contact with LEU1197 (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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1193B LYS 3.4 15.0 + - - +
1194B LEU* 3.0 15.1 + - + +
1196B LYS* 1.3 80.0 - - + +
1198B GLY* 1.3 57.0 + - - +
1199B ILE* 3.3 8.1 + - + -
1208B ILE* 3.8 22.4 - - + +
1212B LYS* 3.9 49.9 - - + +
1213B LEU* 4.0 24.9 - - + -
1216B MET* 4.1 30.3 - - + -
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Residues in contact with GLY1198 (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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1194B LEU 2.9 3.1 + - - -
1195B LYS 3.1 12.8 + - - -
1196B LYS 3.2 0.4 - - - -
1197B LEU* 1.3 78.7 - - - +
1199B ILE* 1.3 62.5 + - - +
1200B ASN* 3.2 19.2 + - - +
1204B ASP* 4.1 5.3 - - - +
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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