Contacts of the helix formed by residues 286 - 294 (chain B) in PDB entry 2OB1
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 MET 286 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B LEU* 3.2 47.7 - - + +
81B ARG* 3.7 9.2 - - - +
84B GLY* 4.8 3.1 - - - -
231B TYR* 3.7 16.4 - - + -
285B ASP* 1.3 70.5 - - - +
287B TRP* 1.3 60.3 + - - +
288B GLU 3.3 0.2 - - - -
289B ILE* 3.4 19.8 + - + +
290B PHE* 2.8 27.2 + - - +
318B GLN* 2.9 35.2 + - - +
321B TYR* 3.0 30.9 + - + +
323B LEU* 3.8 31.4 - - + -
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Residues in contact with TRP 287 (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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285B ASP* 3.1 8.7 + - - +
286B MET* 1.3 78.2 - - - +
288B GLU* 1.3 70.2 + - + +
290B PHE* 3.2 34.9 + + + +
291B ASN* 3.0 55.3 + - - +
311B LEU* 3.8 34.8 - - + -
312B GLU* 6.0 0.2 - - - -
314B LEU* 4.3 8.7 - - + -
315B LYS* 3.5 69.9 - - + +
318B GLN* 3.5 12.3 + - + +
319B THR* 3.7 16.2 - - + -
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Residues in contact with GLU 288 (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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268B LYS* 3.5 25.6 + - - -
284B ASN* 3.2 25.4 - - + +
285B ASP* 2.8 48.7 + - - +
287B TRP* 1.3 80.4 - - + +
289B ILE* 1.3 57.3 + - - +
291B ASN* 3.3 6.9 + - - +
292B ALA* 2.7 35.6 + - + +
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Residues in contact with ILE 289 (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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80B LEU* 4.7 8.1 - - + +
84B GLY* 4.5 9.4 - - - -
284B ASN* 3.8 26.0 - - + +
285B ASP 3.1 15.1 + - - +
286B MET* 3.5 36.8 - - + +
288B GLU* 1.3 75.5 - - - +
290B PHE* 1.3 57.0 + - - +
292B ALA* 4.7 1.1 - - + -
293B GLN* 2.7 76.5 + - + +
294B ILE* 3.7 5.0 + - + -
323B LEU* 4.2 17.0 - - + -
325B LYS* 6.1 0.9 - - - +
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Residues in contact with PHE 290 (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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76B TYR* 4.0 27.1 - + - -
79B TYR* 5.9 0.7 - + - -
80B LEU* 3.8 26.5 - - + -
286B MET 2.8 17.8 + - - +
287B TRP* 3.3 45.3 - + + +
289B ILE* 1.3 73.5 - - - +
291B ASN* 1.3 63.5 + - - +
294B ILE* 3.4 30.7 + - + +
299B ARG* 2.6 61.8 + - + -
302B LEU* 5.9 0.7 - - + -
308B LEU* 5.3 0.7 - - + -
311B LEU* 4.0 19.3 - - + -
314B LEU* 4.6 2.9 - - + -
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Residues in contact with ASN 291 (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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287B TRP* 3.0 55.6 + - - +
288B GLU* 3.9 5.0 - - - +
290B PHE* 1.3 85.9 - - - +
292B ALA* 1.3 60.4 + - - +
294B ILE 4.9 1.7 - - - +
299B ARG* 3.2 22.0 + - - +
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Residues in contact with ALA 292 (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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284B ASN* 6.6 0.2 - - - -
288B GLU* 2.7 24.8 + - + +
289B ILE* 4.2 1.3 - - + +
291B ASN* 1.3 75.8 - - - +
293B GLN* 1.3 69.2 + - + +
294B ILE 3.7 0.8 - - - -
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Residues in contact with GLN 293 (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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30B LEU* 3.8 14.2 - - + +
83B VAL 5.0 0.2 - - - +
84B GLY* 4.3 8.7 - - - +
87B ALA* 4.3 19.7 - - - +
284B ASN* 5.2 2.2 - - - +
289B ILE* 2.7 57.1 + - + +
292B ALA* 1.3 83.8 - - + +
294B ILE* 1.3 64.7 + - + +
295B PRO* 3.2 12.6 - - - +
323B LEU* 5.3 1.7 - - - +
325B LYS* 4.6 15.0 - - - +
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Residues in contact with ILE 294 (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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30B LEU* 3.7 11.0 - - + -
79B TYR* 3.6 15.0 - - + +
80B LEU* 3.6 24.9 - - + -
83B VAL* 3.6 31.6 - - + -
289B ILE* 4.6 2.7 - - + +
290B PHE* 3.4 25.6 + - + +
291B ASN 4.9 1.9 - - - +
292B ALA 5.3 0.6 - - - -
293B GLN* 1.3 87.2 - - + +
295B PRO* 1.3 60.2 - - - +
298B GLU* 3.5 27.1 - - + -
299B ARG* 3.0 36.8 + - + +
302B LEU* 5.6 1.1 - - + -
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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