Contacts of the strand formed by residues 293 - 296 (chain C) in PDB entry 2OQH
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 GLY 293 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265C ASP 2.9 13.3 + - - -
266C VAL* 3.3 8.5 - - - -
267C ILE* 3.0 21.5 + - - -
287C CYS* 4.2 1.0 - - - -
291C GLY 4.2 0.8 + - - -
292C LEU* 1.3 79.4 - - - +
294C MSE 1.3 59.5 + - - +
318C VAL* 5.1 2.5 - - - -
321C ARG* 3.9 22.2 - - - -
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Residues in contact with MSE 294 (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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266C VAL* 4.0 2.0 - - - +
267C ILE 3.3 12.8 - - - +
269C GLY* 3.7 15.3 - - - -
280C THR* 3.8 24.7 - - + +
283C LEU* 3.6 34.8 - - + -
284C ALA* 3.5 31.6 - - - -
287C CYS* 4.0 13.2 - - + -
292C LEU 3.9 0.2 + - - -
293C GLY* 1.3 76.4 - - - +
295C ASN* 1.3 68.3 + - - +
296C LEU* 4.6 0.9 - - + -
318C VAL* 3.6 36.0 + - + +
319C LEU* 3.6 21.5 - - + +
321C ARG* 3.5 16.6 - - - +
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Residues in contact with ASN 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C ARG* 3.4 9.3 - - - +
221C TYR* 3.1 26.1 + - + +
266C VAL* 4.6 2.0 - - + +
267C ILE 3.3 4.8 + - - -
268C HIS* 3.4 19.9 + - + +
269C GLY* 2.7 25.3 + - - -
294C MSE 1.3 76.5 - - - +
296C LEU* 1.3 69.0 + - - +
319C LEU* 3.6 11.4 - - - +
321C ARG* 3.8 19.3 + - - +
322C ALA 2.9 22.8 + - - +
323C ILE* 3.3 26.7 + - - +
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Residues in contact with LEU 296 (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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268C HIS* 3.6 6.4 + - - -
269C GLY* 3.5 25.8 - - - -
270C ASP* 4.0 5.4 - - - +
280C THR* 4.5 11.9 - - + -
294C MSE 4.6 0.9 - - + -
295C ASN* 1.3 86.1 + - - +
297C HIS* 1.3 63.8 + - - +
309C HIS* 3.7 36.1 - - + +
312C VAL* 4.9 2.5 - - + -
313C VAL* 3.5 27.6 - - + -
319C LEU* 4.1 22.2 - - + -
323C ILE* 4.0 15.3 - - + -
324C ASP* 3.1 29.6 + - - +
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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