Contacts of the helix formed by residues 1207 - 1216 (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 GLU1207 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1205C ARG 5.3 2.2 - - - +
1206C SER* 1.3 76.8 - - - +
1208C ARG* 1.3 57.1 + - - +
1209C LYS* 2.8 46.5 + - + +
1210C LYS* 3.1 24.2 + - + +
1211C TRP* 3.2 13.1 + - - -
1501D VAL* 5.0 0.4 - - - -
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Residues in contact with ARG1208 (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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1206C SER 4.1 0.2 + - - -
1207C GLU* 1.3 73.5 - - - +
1209C LYS* 1.3 59.8 + - + +
1211C TRP* 4.2 1.3 - - - -
1212C ILE* 2.9 44.5 + - + +
1497D ILE* 3.6 41.1 - - + +
1498D GLU* 4.1 32.4 - - - +
1501D VAL* 4.0 24.6 - - + +
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Residues in contact with LYS1209 (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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1207C GLU* 2.8 28.8 + - + +
1208C ARG* 1.3 79.7 - - + +
1210C LYS* 1.3 75.6 - - + +
1212C ILE* 3.3 4.2 + - - +
1213C HIS* 3.2 31.0 + - + -
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Residues in contact with LYS1210 (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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1184C ILE* 4.2 20.9 - - + -
1201C VAL* 6.5 0.2 - - + -
1206C SER* 4.0 16.6 - - - +
1207C GLU* 3.1 24.8 + - + +
1209C LYS* 1.3 86.9 - - + +
1211C TRP* 1.3 65.3 + - - +
1213C HIS* 3.0 12.3 + - - +
1214C CYS* 2.9 26.0 + - - -
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Residues in contact with TRP1211 (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* 5.1 0.7 - - + -
1039C LEU* 3.5 30.5 - - + -
1201C VAL* 3.4 48.5 - - + -
1202C GLY 5.3 0.9 - - - -
1204C GLN 5.1 0.4 - - - -
1206C SER* 3.3 26.7 + - - -
1207C GLU 3.2 12.3 + - - +
1208C ARG 4.2 0.7 - - - +
1210C LYS* 1.3 78.3 - - - +
1212C ILE* 1.3 63.8 + - + +
1214C CYS* 3.0 9.4 + - + +
1215C PHE* 3.0 51.9 + + + -
1501D VAL* 3.8 30.5 - - + +
1504D LEU* 3.9 31.3 - - + +
1505D ASN* 3.2 26.2 + - - -
1508D GLN* 4.1 11.9 - - + -
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Residues in contact with ILE1212 (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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1208C ARG* 2.9 33.3 + - + +
1209C LYS* 3.6 4.5 - - - +
1210C LYS 3.2 0.8 - - - -
1211C TRP* 1.3 77.7 - - + +
1213C HIS* 1.3 67.9 + - + +
1215C PHE* 3.1 7.1 + - + +
1216C GLU* 2.8 46.7 + - - +
1258C TRP* 3.4 34.0 - - + -
1497D ILE* 3.8 25.6 - - + -
1501D VAL* 5.8 0.4 - - + -
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Residues in contact with HIS1213 (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* 2.8 23.4 + - - -
1209C LYS* 3.2 19.3 + - + -
1210C LYS* 3.0 12.9 + - - +
1212C ILE* 1.3 83.4 - - + +
1214C CYS* 1.3 58.1 + - - +
1216C GLU* 3.3 24.2 + - + +
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Residues in contact with CYS1214 (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* 3.3 9.0 + - - +
1037C LEU* 3.9 22.2 - - + +
1184C ILE* 3.7 32.3 - - - -
1199C PHE* 5.2 11.0 - - + -
1201C VAL* 3.9 17.0 - - - -
1210C LYS 2.9 15.8 + - - +
1211C TRP* 3.0 16.4 + - + +
1213C HIS* 1.3 79.3 - - - +
1215C PHE* 1.3 58.1 + - - +
1218C VAL* 2.9 24.3 - - - +
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Residues in contact with PHE1215 (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* 3.2 30.7 - - + -
1039C LEU* 3.8 17.5 - - + -
1211C TRP* 3.0 36.8 + + + +
1212C ILE* 3.1 7.6 + - + +
1214C CYS* 1.3 75.2 - - - +
1216C GLU* 1.3 64.0 + - - +
1217C GLY 3.2 3.3 + - - -
1218C VAL* 3.9 15.1 + - + +
1221C ILE* 4.9 2.9 - - + -
1253C ILE* 4.5 2.7 - - + -
1258C TRP* 3.9 20.4 - + + -
1259C PHE* 3.6 41.6 - + + -
1262C THR* 4.8 4.7 + - - -
1497D ILE* 6.4 0.7 - - + -
1500D LEU* 4.2 7.6 - - + -
1501D VAL* 6.0 1.8 - - + -
1504D LEU* 3.4 33.4 - - + -
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Residues in contact with GLU1216 (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* 2.5 27.3 + - - +
1212C ILE* 2.8 37.1 + - - +
1213C HIS* 3.3 28.5 - - + +
1214C CYS 3.3 1.2 - - - -
1215C PHE* 1.3 74.2 - - - +
1217C GLY* 1.3 66.8 + - - +
1218C VAL 3.1 0.3 + - - -
1258C TRP* 3.9 18.0 - - - -
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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