Contacts of the helix formed by residues 1202 - 1209 (chain B) in PDB entry 3GIL
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 LEU1202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1150B PHE* 4.5 12.1 - - + -
1174B LEU 4.6 2.2 - - - +
1175B ILE* 3.2 38.2 + - + +
1178B LEU* 3.5 16.5 + - + +
1180B ILE* 4.3 7.0 - - + +
1183B VAL* 4.0 23.1 - - + -
1201B LYS* 1.3 74.4 - - - +
1203B VAL* 1.3 57.1 + - - +
1204B ASP 3.3 0.5 + - - -
1205B THR* 2.6 33.6 + - + +
1225B LEU* 3.6 39.5 - - + +
1228B LEU* 4.2 19.5 - - + -
1229B ALA* 3.7 8.0 - - - +
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Residues in contact with VAL1203 (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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1175B ILE* 2.8 35.5 + - + +
1176B ARG* 3.9 25.4 - - + +
1201B LYS* 4.2 4.9 - - + -
1202B LEU* 1.3 73.0 - - - +
1204B ASP* 1.3 80.4 + - - +
1206B LEU* 3.0 40.4 + - + +
1207B SER* 5.8 0.2 - - - -
1229B ALA* 4.6 0.4 - - - -
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Residues in contact with ASP1204 (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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1198B GLY 4.3 2.1 - - - +
1199B ILE* 3.7 19.5 - - + -
1200B ASN* 3.2 22.0 + - - +
1201B LYS* 3.2 28.8 + - - +
1202B LEU 3.2 0.4 - - - -
1203B VAL* 1.3 89.8 - - - +
1205B THR* 1.3 62.3 + - - +
1206B LEU 3.1 0.9 + - - -
1207B SER* 3.3 14.7 + - - -
1208B ILE* 3.6 14.8 - - + +
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Residues in contact with THR1205 (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* 4.7 3.4 - - + -
1194B LEU* 5.6 0.4 - - + -
1199B ILE* 4.1 29.8 - - + -
1201B LYS 4.6 0.2 - - - +
1202B LEU* 2.6 23.3 + - + +
1204B ASP* 1.3 76.6 - - - +
1206B LEU* 1.3 57.4 + - - +
1207B SER 3.0 6.4 + - - -
1208B ILE* 3.9 13.2 + - - +
1213B LEU* 4.8 12.4 - - + +
1225B LEU* 4.0 29.8 + - + -
1226B ILE* 4.5 21.8 - - - +
1229B ALA* 3.3 17.2 - - - +
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Residues in contact with LEU1206 (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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1175B ILE* 5.3 0.4 - - + -
1203B VAL* 3.0 35.4 + - + +
1204B ASP 4.1 0.2 - - - -
1205B THR* 1.3 75.2 - - - +
1207B SER* 1.3 64.1 + - - +
1208B ILE 4.0 0.4 - - - -
1226B ILE* 4.5 7.0 - - + +
1229B ALA* 3.9 33.4 - - + +
1230B ARG* 3.8 37.2 - - + +
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Residues in contact with SER1207 (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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1204B ASP* 3.3 8.1 + - - -
1205B THR 3.0 1.4 + - - -
1206B LEU* 1.3 84.7 + - - +
1208B ILE* 1.3 76.4 + - - +
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Residues in contact with ILE1208 (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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1197B LEU* 5.1 18.8 - - + +
1199B ILE* 3.7 28.5 - - + -
1204B ASP* 3.6 17.5 - - + +
1205B THR 3.9 9.0 + - - +
1206B LEU 4.0 0.4 - - - -
1207B SER* 1.3 94.2 - - - +
1209B GLU* 1.3 54.7 + - - +
1210B PHE* 2.7 20.6 + - - -
1212B LYS* 3.6 38.4 - - + -
1213B LEU* 4.2 19.0 - - + +
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Residues in contact with GLU1209 (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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1208B ILE* 1.3 69.6 - - - +
1210B PHE* 1.3 51.9 + - - +
1211B ASP* 2.6 6.7 + - + +
1212B LYS* 2.6 43.7 + - + +
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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