Contacts of the strand formed by residues 1033 - 1039 (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 GLU1033 (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* 6.2 1.3 - - + -
1032C ARG* 1.3 88.6 + - - +
1034C VAL* 1.3 66.8 + - - +
1035C LYS* 4.2 1.5 + - + +
1188C HIS* 6.0 0.7 - - - -
1195C HIS* 3.4 21.8 - - + +
1197C LYS* 4.2 34.8 + - + +
1219C THR* 4.4 2.8 + - - -
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Residues in contact with VAL1034 (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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1032C ARG* 4.0 28.3 - - - +
1033C GLU* 1.3 81.5 - - - +
1035C LYS* 1.3 55.4 + - - +
1036C LEU* 3.6 19.2 + - + -
1194C LEU* 4.5 12.1 - - + -
1195C HIS 2.9 11.0 + - - +
1196C PHE* 3.7 29.9 - - + -
1197C LYS* 2.8 36.0 + - - +
1219C THR* 3.2 29.2 - - + +
1343C ILE* 4.3 7.9 - - + -
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Residues in contact with LYS1035 (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 1.0 - - + -
1034C VAL* 1.3 71.4 - - - +
1036C LEU* 1.3 60.1 + - - +
1197C LYS* 3.6 8.5 - - + -
1199C PHE* 4.1 32.5 - - + -
1213C HIS 2.8 26.0 + - - -
1214C CYS* 3.3 20.4 + - - +
1216C GLU* 2.5 36.0 + - - +
1217C GLY 3.6 8.1 - - - +
1218C VAL* 3.3 19.6 - - + -
1219C THR* 2.7 36.0 + - - +
1220C ALA 3.2 8.1 + - - +
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Residues in contact with LEU1036 (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* 3.6 17.9 + - + -
1035C LYS* 1.3 79.7 - - - +
1037C LEU* 1.3 60.0 + - - +
1038C LEU 4.0 0.4 + - - -
1196C PHE* 3.7 28.7 - - + -
1197C LYS 2.7 14.2 + - - +
1198C MET* 3.3 25.2 - - + +
1199C PHE* 2.7 31.3 + - - +
1220C ALA* 3.4 24.5 - - + +
1222C ILE* 4.0 17.5 - - + -
1265C ILE* 5.6 0.7 - - + -
1336C PHE* 3.9 22.0 - - + -
1339C VAL* 5.8 0.9 - - + -
1343C ILE* 4.2 10.3 - - + -
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Residues in contact with LEU1037 (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* 4.2 1.4 + - - -
1036C LEU* 1.3 72.4 - - - +
1038C LEU* 1.3 76.2 + - - +
1039C LEU* 4.0 13.5 - - + -
1199C PHE* 3.9 22.0 - - + +
1201C VAL* 4.6 10.5 - - + -
1211C TRP* 5.1 0.2 - - + -
1214C CYS* 3.9 23.6 - - + +
1215C PHE* 3.2 43.7 - - + -
1218C VAL* 4.2 15.7 - - + -
1220C ALA 2.9 11.9 + - - +
1221C ILE* 3.2 14.7 - - + +
1222C ILE 2.8 24.4 + - - -
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Residues in contact with LEU1038 (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 4.9 0.9 - - - +
1037C LEU* 1.3 81.1 - - - +
1039C LEU* 1.3 69.9 + - - +
1046C LYS* 4.1 19.2 - - + +
1049C ILE* 4.4 14.8 - - + -
1050C VAL* 3.4 33.0 - - + -
1198C MET* 3.7 31.0 - - + -
1199C PHE 2.9 15.9 + - - +
1200C ASP* 4.1 17.7 - - + +
1201C VAL 4.6 1.9 + - - -
1222C ILE* 3.4 41.3 - - + +
1224C CYS* 4.9 4.0 - - - -
1508D GLN* 4.6 1.0 + - - +
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Residues in contact with LEU1039 (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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1037C LEU* 4.0 14.6 - - + -
1038C LEU* 1.3 81.7 - - - +
1040C GLY* 1.3 60.4 + - - +
1046C LYS* 3.2 13.8 - - - +
1201C VAL* 5.4 0.2 - - + -
1211C TRP* 3.5 30.1 - - + -
1215C PHE* 3.8 20.4 - - + -
1221C ILE* 3.7 24.0 - - + -
1222C ILE 3.1 6.5 + - - +
1223C PHE* 4.1 15.7 - - + -
1224C CYS 2.9 23.3 + - - -
1253C ILE* 4.1 23.8 - - + -
1504D LEU* 4.1 7.0 - - + -
1508D GLN* 3.3 16.4 - - - +
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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