Contacts of the helix formed by residues 1192 - 1197 (chain B) in PDB entry 1OFD
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 SER1192 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861B GLU* 3.5 24.5 + - - -
869B ARG* 5.0 0.5 + - - -
1185B LEU* 3.6 16.0 - - - +
1190B TYR 3.4 1.6 - - - -
1191B ARG* 1.3 82.6 - - - +
1193B LEU* 1.3 63.1 + - - +
1194B ASP* 2.9 27.2 + - - +
1195B ASP* 3.0 30.3 + - - +
1196B ILE* 3.8 1.6 + - - +
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Residues in contact with LEU1193 (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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861B GLU* 2.8 17.9 + - - +
866B ILE* 4.1 15.5 - - + -
869B ARG* 3.8 31.0 - - - +
1114B VAL* 4.4 5.8 - - + -
1115B VAL* 4.6 6.1 - - + -
1118B ALA* 4.1 12.6 - - + -
1125B TYR* 4.1 21.3 - - + +
1181B VAL* 3.9 31.9 - - + -
1185B LEU* 3.8 8.4 - - + +
1192B SER* 1.3 71.0 - - - +
1194B ASP* 1.3 63.3 + - - +
1196B ILE* 3.0 38.2 + - + +
1197B ILE* 3.2 19.9 + - + +
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Residues in contact with ASP1194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869B ARG* 3.7 21.0 + - - +
1192B SER* 2.9 15.2 + - - +
1193B LEU* 1.3 77.7 - - - +
1195B ASP* 1.3 61.3 + - - +
1197B ILE* 4.2 5.6 + - - -
1232B ARG* 2.9 24.1 + - - -
1235B LEU* 3.6 31.8 - - - +
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Residues in contact with ASP1195 (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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1190B TYR* 3.7 25.9 - - + -
1191B ARG* 3.7 14.0 + - - +
1192B SER* 3.0 36.1 + - - +
1194B ASP* 1.3 84.4 - - - +
1196B ILE* 1.3 58.9 + - - +
1199B ARG* 3.9 13.2 + - - +
1232B ARG* 3.5 20.1 + - - +
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Residues in contact with ILE1196 (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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1115B VAL* 3.9 26.0 - - + -
1118B ALA* 4.3 8.3 - - + -
1119B LEU* 3.5 25.8 - - + +
1185B LEU* 4.0 19.7 - - + -
1188B LEU* 4.4 8.3 - - + -
1190B TYR* 3.6 39.0 - - + -
1192B SER 4.2 0.2 - - - +
1193B LEU* 3.0 34.6 + - + +
1195B ASP* 1.3 83.3 - - - +
1197B ILE* 1.3 67.7 + - - +
1198B GLY 3.2 0.7 + - - -
1199B ARG* 3.0 22.5 + - - +
1202B LEU* 4.6 5.6 - - + -
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Residues in contact with ILE1197 (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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869B ARG* 3.5 29.4 - - - +
1118B ALA* 3.3 20.9 - - + +
1121B GLY 3.6 23.6 - - - +
1122B ALA 3.7 10.1 - - - +
1123B GLU* 3.9 22.9 - - + -
1125B TYR* 4.1 4.0 - - - +
1193B LEU 3.2 20.5 + - - +
1194B ASP* 4.3 5.4 - - - +
1196B ILE* 1.3 74.4 - - - +
1198B GLY* 1.3 57.3 + - - +
1232B ARG* 2.5 41.6 + - - +
1234B TRP* 3.5 16.7 - - + -
1235B LEU* 4.5 8.5 - - + -
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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