Contacts of the strand formed by residues 1194 - 1200 (chain C) in PDB entry 2OM2
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 LEU1194 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1031C ALA 4.6 0.2 - - - -
1032C ARG* 3.3 50.3 - - + +
1034C VAL* 4.5 5.8 - - + -
1190C THR* 3.1 9.8 - - - +
1191C PHE 2.9 33.4 + - - +
1192C LYS 3.6 8.3 - - - +
1193C ASP* 1.3 88.1 - - - +
1195C HIS* 1.3 63.8 + - - +
1196C PHE* 3.6 32.4 + - + -
1340C THR* 4.1 6.7 - - + +
1343C ILE* 5.1 2.9 - - + -
1344C ILE* 4.1 26.5 - - + -
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Residues in contact with HIS1195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031C ALA* 3.7 37.8 - - + +
1032C ARG 3.3 10.1 + - - +
1033C GLU* 3.4 19.2 - - + +
1034C VAL 2.9 24.6 + - - -
1189C PHE 3.8 2.9 - - - -
1190C THR* 3.4 27.6 + - + -
1193C ASP 5.6 1.5 - - - -
1194C LEU* 1.3 73.0 + - - +
1196C PHE* 1.3 63.2 + - - +
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Residues in contact with PHE1196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034C VAL* 3.7 27.8 - - + -
1036C LEU* 3.7 27.4 - - + -
1188C HIS* 3.3 10.9 - - - +
1189C PHE* 2.8 69.7 + + + +
1191C PHE* 3.7 19.7 - + + -
1194C LEU* 3.6 42.2 - - + -
1195C HIS* 1.3 72.6 - - - +
1197C LYS* 1.3 60.4 + - - +
1198C MET 4.0 0.4 - - - -
1336C PHE* 4.2 6.3 - + - -
1340C THR* 3.7 23.3 - - + -
1343C ILE* 4.3 10.8 - - + -
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Residues in contact with LYS1197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033C GLU* 4.2 33.0 + - + +
1034C VAL 2.8 16.0 + - - +
1035C LYS* 3.6 7.0 - - + -
1036C LEU* 2.7 35.4 + - - +
1186C GLU* 3.3 27.1 - - - +
1187C THR 4.0 2.2 - - - -
1188C HIS* 3.7 22.2 - - + -
1196C PHE* 1.3 73.3 - - - +
1198C MET* 1.3 54.3 + - - +
1199C PHE* 3.5 21.5 - - + -
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Residues in contact with MET1198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036C LEU* 3.3 20.4 - - + +
1038C LEU* 3.7 45.1 - - + -
1049C ILE* 4.2 10.8 - - + -
1050C VAL* 4.2 12.1 - - + +
1053C MET* 3.6 33.2 - - + -
1186C GLU* 3.4 5.4 - - - +
1187C THR* 3.1 43.5 + - + +
1189C PHE* 4.6 7.2 - - + -
1196C PHE 4.0 0.6 - - - -
1197C LYS* 1.3 72.3 - - - +
1199C PHE* 1.3 62.3 + - - +
1222C ILE* 4.4 3.6 - - + -
1336C PHE* 3.8 25.4 - - + -
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Residues in contact with PHE1199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035C LYS* 4.1 28.0 - - + -
1036C LEU 2.7 15.6 + - - +
1037C LEU* 4.2 15.9 - - + -
1038C LEU* 2.9 31.0 + - - +
1184C ILE* 4.3 20.2 - - + -
1185C VAL 3.7 3.6 - - - +
1186C GLU* 2.8 35.0 - - + -
1197C LYS* 3.5 39.9 - - + -
1198C MET* 1.3 78.5 - - - +
1200C ASP* 1.3 63.5 + - - +
1214C CYS* 5.2 12.3 - - + -
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Residues in contact with ASP1200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801C MG 2.6 26.9 - - - -
1038C LEU* 4.1 9.8 - - + +
1046C LYS* 3.2 34.4 - - - +
1047C SER* 4.2 4.5 + - - -
1050C VAL* 4.1 17.9 - - + +
1181C THR* 5.5 1.6 - - - +
1184C ILE* 4.6 1.6 - - - -
1185C VAL* 3.0 43.6 + - + +
1199C PHE* 1.3 78.1 - - - +
1201C VAL* 1.3 63.1 + - - +
1202C GLY* 3.0 13.4 + - - -
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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