Contacts of the strand formed by residues 283 - 288 (chain A) in PDB entry 2OHM
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 ILE 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A VAL* 4.7 5.2 - - + -
207A GLU 3.7 9.9 - - - +
208A ILE* 4.4 10.8 - - + -
234A LEU* 4.7 6.3 - - + -
236A LEU* 6.0 1.1 - - + -
244A ALA* 5.7 2.0 - - + -
248A ILE* 4.0 20.2 - - + -
281A PRO* 4.9 0.7 - - + +
282A VAL* 1.3 79.9 - - - +
284A SER* 1.3 63.9 + - - +
285A LEU* 4.0 22.9 - - + +
298A ILE 3.8 0.9 - - - +
299A THR* 3.2 2.8 - - - -
300A ILE* 2.9 48.0 + - + +
305A TYR* 4.0 18.6 - - + +
324A ILE* 3.3 34.1 - - + -
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Residues in contact with SER 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ARG 3.9 0.2 - - - +
206A VAL* 3.3 5.2 - - - -
207A GLU* 2.9 53.4 + - - +
210A GLY 6.2 0.2 - - - -
282A VAL* 4.3 3.3 - - - +
283A ILE* 1.3 69.9 - - - +
285A LEU* 1.3 66.5 + - - +
286A TYR* 4.0 5.6 - - - -
297A ARG* 3.5 17.6 + - - -
298A ILE 3.2 6.3 - - - -
299A THR* 2.9 32.4 + - - +
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ILE* 4.4 19.5 - - + -
205A ARG 3.5 3.8 - - - -
206A VAL* 4.2 16.8 - - + -
234A LEU* 5.2 11.9 - - + -
236A LEU* 5.5 7.0 - - + -
283A ILE* 4.0 18.6 - - + +
284A SER* 1.3 81.7 - - - +
286A TYR* 1.3 61.3 + - - +
287A LEU* 3.8 7.3 + - + +
297A ARG* 3.4 0.5 - - - -
298A ILE* 3.0 40.4 + - + +
331A THR* 5.9 1.3 - - + -
333A MET* 4.4 22.9 - - + -
337A ILE* 3.8 32.5 - - + -
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Residues in contact with TYR 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ILE* 3.4 7.6 - - - +
204A VAL* 2.8 33.4 + - + -
205A ARG* 2.6 53.3 + - + -
207A GLU* 2.4 41.9 + - + -
284A SER* 4.4 6.1 - - - -
285A LEU* 1.3 72.4 - - - +
287A LEU* 1.3 60.5 + - - +
295A SER* 3.7 17.9 - - - +
296A PHE 3.3 7.2 - - - +
297A ARG* 2.9 40.6 + - + +
374A PHE* 3.9 32.9 - + + -
376A THR* 4.8 1.8 - - - -
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A THR* 3.6 17.3 - - + +
201A VAL* 4.6 7.4 - - + -
202A ILE 3.7 4.7 - - - +
203A ILE* 3.6 32.3 - - + +
204A VAL* 4.2 2.5 - - - -
285A LEU* 4.4 14.1 - - + +
286A TYR* 1.3 75.5 - - - +
288A MET* 1.3 68.2 + - - +
289A GLY 3.2 2.4 + - - -
295A SER* 3.5 3.7 - - - -
296A PHE* 2.9 46.2 + - + +
298A ILE* 4.2 12.3 - - + -
333A MET* 4.6 12.8 - - + -
354A PHE* 3.8 34.3 - - + -
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Residues in contact with MET 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A THR* 2.4 35.5 + - - +
192A PRO* 4.1 21.5 - - + -
202A ILE* 3.0 42.6 + - + +
204A VAL* 3.5 14.2 - - + +
287A LEU* 1.3 72.1 - - - +
289A GLY* 1.3 68.5 + - - +
296A PHE* 3.9 0.7 - - - -
379A MET* 3.5 53.2 - - + +
380A GLU* 3.7 28.0 - - + +
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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