Contacts of the helix formed by residues 1282 - 1286 (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 PRO1282 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1230C TYR* 3.7 3.3 - - - -
1280C LYS 3.5 10.1 - - - +
1281C SER* 1.3 84.6 - - - +
1283C LEU* 1.3 63.8 + - - +
1284C THR* 3.1 21.3 + - - +
1285C ILE* 3.2 34.8 + - + +
1294C ASN* 3.3 29.4 - - - +
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Residues in contact with LEU1283 (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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1230C TYR* 3.7 32.0 - - + -
1274C PHE* 4.9 3.6 - - + -
1278C ILE* 4.2 7.5 - - + +
1281C SER 3.7 1.6 + - - -
1282C PRO* 1.3 67.1 - - - +
1284C THR* 1.3 56.2 + - - +
1285C ILE 2.9 6.3 - - - -
1286C CYS* 2.8 20.4 + - + -
1287C TYR* 3.0 28.0 + - + -
1290C TYR* 3.6 31.4 - - + -
1294C ASN* 2.9 11.7 + - - +
1299C ALA* 3.8 22.2 - - + +
1302C TYR* 3.6 29.6 - - + -
1303C ILE* 4.1 15.5 - - + -
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Residues in contact with THR1284 (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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1282C PRO* 3.4 22.7 - - - +
1283C LEU* 1.3 74.5 - - - +
1285C ILE* 1.3 60.7 + - - +
1286C CYS 3.1 0.4 - - - -
1287C TYR 3.4 12.8 - - - +
1288C PRO* 3.3 34.3 - - - +
1290C TYR* 3.3 32.2 - - + +
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Residues in contact with ILE1285 (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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1144C ARG* 3.6 38.4 - - - +
1230C TYR* 4.0 3.8 - - + +
1231C ASP* 3.9 28.5 - - + +
1232C LEU 5.2 3.4 - - - +
1241C ASN* 4.5 3.5 - - - +
1281C SER* 4.1 12.3 - - - +
1282C PRO* 3.2 30.5 + - + +
1283C LEU 2.9 0.8 + - - -
1284C THR* 1.3 79.0 - - - +
1286C CYS* 1.3 61.1 + - - +
1288C PRO* 4.9 2.3 - - - +
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Residues in contact with CYS1286 (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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1230C TYR* 3.1 34.5 - - + +
1241C ASN* 3.5 17.1 - - - +
1243C MET* 3.5 39.0 - - - -
1244C HIS* 3.2 23.2 - - - -
1283C LEU* 2.8 9.7 + - + +
1285C ILE* 1.3 81.9 - - - +
1287C TYR* 1.3 74.5 + - + +
1288C PRO* 3.4 8.6 - - - +
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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