Contacts of the helix formed by residues 1096 - 1100 (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 LEU1096 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ALA* 5.9 0.4 - - - -
209B THR 5.6 0.2 - - - +
210B ASN* 5.6 0.2 - - - -
211B THR* 4.0 15.0 - - - +
1046B ALA* 3.7 37.5 - - + +
1049B ALA* 4.2 8.8 - - + +
1050B LYS* 4.1 15.3 - - + -
1091B LEU* 2.7 24.9 + - + +
1094B ASN* 3.6 26.9 - - + +
1095B GLN* 1.3 74.0 - - - +
1097B ARG* 1.3 64.4 + - - +
1098B ASP* 3.3 6.3 - - - -
1099B ARG* 3.0 60.7 + - - +
1100B VAL* 4.1 2.3 + - - +
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Residues in contact with ARG1097 (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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1088B HIS* 3.0 23.1 + - - +
1091B LEU* 3.3 27.1 + - - -
1092B MET* 3.6 30.5 - - + +
1095B GLN* 3.6 2.2 - - - -
1096B LEU* 1.3 78.0 - - - +
1098B ASP* 1.3 57.0 + - - +
1099B ARG 3.3 0.3 + - - -
1100B VAL* 2.9 53.4 + - - +
1102B LEU* 3.4 18.6 - - - +
1121B GLY 2.9 26.9 + - - -
1123B GLU* 2.8 28.5 + - - -
1234B TRP* 3.6 41.4 - - + +
1237B HIS* 4.0 3.6 - - - -
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Residues in contact with ASP1098 (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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1095B GLN 3.9 9.8 - - - +
1096B LEU 3.8 6.1 - - - -
1097B ARG* 1.3 73.8 + - - +
1099B ARG* 1.3 78.5 + - - +
1100B VAL 3.3 0.7 - - - -
1233B GLN 4.5 2.7 - - - +
1234B TRP* 3.5 29.6 - - + +
1236B ASN 4.0 10.1 - - - +
1237B HIS* 2.9 28.1 + - - +
1238B GLU 4.8 1.7 + - - -
1241B HIS* 5.3 1.0 - - - -
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Residues in contact with ARG1099 (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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34B CYS 5.7 2.2 + - - -
35B SER 4.4 5.1 + - - -
36B ALA* 3.9 14.6 + - - +
38B ASN* 2.9 35.7 + - - +
211B THR* 5.5 0.2 + - - -
1049B ALA* 4.3 21.7 + - + +
1050B LYS* 4.7 15.2 + - - +
1053B ALA 3.4 2.0 - - - +
1054B ASP 3.8 3.1 - - - +
1095B GLN 4.7 4.8 + - - -
1096B LEU* 3.0 45.0 + - - +
1098B ASP* 1.3 93.3 + - - +
1100B VAL* 1.3 63.8 + - + +
1237B HIS* 4.7 2.1 - - - +
1241B HIS* 2.8 40.2 + - + +
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Residues in contact with VAL1100 (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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1049B ALA* 4.2 16.6 - - + -
1053B ALA* 3.4 23.3 - - + +
1054B ASP 3.3 7.2 - - - +
1056B ILE* 4.0 25.6 - - + -
1091B LEU* 3.5 32.1 - - + -
1096B LEU 4.5 4.0 - - - +
1097B ARG* 2.9 28.9 + - - +
1098B ASP 3.3 0.4 - - - -
1099B ARG* 1.3 85.7 - - - +
1101B LEU* 1.3 63.2 + - - +
1102B LEU* 3.9 10.1 - - + -
1237B HIS* 3.0 12.9 - - - -
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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