Contacts of the strand formed by residues 287 - 292 (chain E) in PDB entry 2OHI
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 ASP 287 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B PRO* 3.5 6.6 - - - +
180B GLN* 3.3 27.9 + - - +
257E GLU 2.9 16.8 + - - +
258E ARG* 2.7 42.8 + - - +
259E VAL 2.8 25.5 + - - -
285E GLY 4.2 0.2 + - - -
286E VAL* 1.3 73.7 - - - +
288E VAL* 1.3 70.0 + - - +
289E ARG* 2.9 28.9 + - - -
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Residues in contact with VAL 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TRP* 4.1 9.0 - - + -
179B PRO* 3.8 18.9 - - + +
258E ARG* 5.0 0.4 - - - -
259E VAL* 3.2 12.1 - - + +
261E VAL* 4.7 5.8 - - + -
278E ALA* 4.1 17.5 - - + -
281E ALA* 3.7 27.8 - - + -
282E MET* 3.9 24.5 - - + +
286E VAL* 4.0 5.8 - - + +
287E ASP* 1.3 86.5 + - - +
289E ARG* 1.3 86.1 + - - +
290E VAL* 4.0 16.2 - - + -
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Residues in contact with ARG 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TRP* 4.8 2.7 - - - -
178B CYS* 5.9 6.0 - - - +
179B PRO* 5.8 2.5 - - - -
180B GLN* 5.2 4.6 + - - -
187B PRO* 6.0 4.6 - - - +
189E TYR* 5.8 1.6 + - - -
258E ARG* 4.4 11.9 - - - +
259E VAL 3.0 6.6 + - - +
260E THR* 3.4 13.6 - - - +
261E VAL* 2.7 32.6 + - - +
287E ASP* 2.9 34.9 + - - -
288E VAL* 1.3 79.6 + - - +
290E VAL* 1.3 61.7 + - - +
291E TYR* 3.9 13.2 - - + -
304E ASP* 3.4 35.8 + - - +
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Residues in contact with VAL 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TRP* 3.5 62.2 - - + +
21B ASP* 4.6 1.1 - - - +
23B ARG* 3.9 14.0 + - - -
261E VAL* 3.2 18.8 - - + +
263E TYR* 4.1 22.2 - - + -
274E ALA* 5.0 4.9 - - + +
275E HIS* 5.0 2.9 - - - +
278E ALA* 3.8 19.3 - - + -
288E VAL* 4.0 5.2 - - + -
289E ARG* 1.3 81.2 - - - +
291E TYR* 1.3 65.6 + - - +
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Residues in contact with TYR 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ASP* 5.6 0.4 - - - -
23B ARG* 4.8 1.8 - - - -
31B GLN* 4.8 12.3 - - - -
260E THR* 3.8 19.5 - - + -
261E VAL 2.8 9.8 + - - +
262E ILE* 4.5 5.2 - - + -
263E TYR* 3.2 33.3 + - - -
289E ARG* 3.9 18.1 - - + +
290E VAL* 1.3 78.4 - - - +
292E CYS* 1.3 60.3 + - - +
293E LEU 4.2 0.2 - - - -
296E ASP* 3.4 26.2 - - + +
300E GLU* 3.9 25.4 + - + +
301E ILE* 3.8 34.3 - - + -
303E LYS* 5.2 2.4 + - - -
304E ASP* 2.3 42.7 + - + -
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Residues in contact with CYS 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ASP* 4.6 7.2 - - + +
23B ARG* 5.3 2.2 - - - +
263E TYR* 3.3 40.2 - - + +
264E ASP* 4.1 9.9 - - - -
265E THR* 5.4 2.2 - - - -
271E ARG* 4.8 5.6 - - - -
291E TYR* 1.3 75.6 - - - +
293E LEU* 1.3 61.2 + - - +
294E HIS* 3.1 17.7 - - - -
295E GLU* 2.9 19.8 + - + -
296E ASP* 2.8 40.0 + - - +
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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
------------------------------------------------------------
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