Contacts of the helix formed by residues 236 - 241 (chain A) in PDB entry 2OT7
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 ALA 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A CYS* 3.2 9.7 + - - -
235A GLU* 1.3 78.8 - - - +
237A PHE* 1.3 56.2 + - - -
238A LEU* 3.2 4.3 - - - -
239A ARG* 2.9 32.5 + - + +
240A HIS* 4.1 1.7 + - - -
304A VAL* 3.7 20.9 - - + +
305A LEU 3.6 31.2 - - - +
306A CYS* 3.7 4.8 - - - +
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Residues in contact with PHE 237 (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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220A GLU 5.4 0.9 - - - -
223A ALA* 3.6 33.2 - - + -
224A LYS* 4.2 10.3 - - + -
227A PHE* 4.1 21.3 - + + -
230A SER* 3.7 24.9 - - - +
231A ALA* 3.7 32.8 - - + -
234A CYS 3.2 13.8 + - - +
235A GLU 3.3 8.2 + - - -
236A ALA* 1.3 72.1 - - - +
238A LEU* 1.3 77.5 + - + +
240A HIS* 3.0 42.7 + - + +
241A LYS 4.2 0.7 + - - -
242A MET* 5.3 0.5 + - - +
243A THR* 3.6 23.3 + - - -
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Residues in contact with LEU 238 (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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187A TRP* 3.5 30.3 - - + +
188A HIS* 4.3 3.5 - - - +
219A LEU* 5.0 6.1 - - + +
220A GLU* 4.3 13.7 - - + +
223A ALA* 4.0 19.5 - - + -
236A ALA* 3.2 1.7 - - - -
237A PHE* 1.3 98.6 - - + +
239A ARG* 1.3 56.6 + - + +
241A LYS* 3.1 19.3 + - - +
243A THR* 3.6 37.2 - - + -
245A ILE* 5.5 1.1 - - + -
275A TYR* 3.7 39.9 - - + +
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Residues in contact with ARG 239 (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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188A HIS* 5.6 2.0 - - - -
189A THR* 3.5 18.2 + - - +
190A GLU 2.9 29.7 + - - -
191A ASP* 4.1 12.1 - - - +
192A MET 4.6 0.9 - - - -
193A ASP* 2.9 30.1 + - - +
236A ALA* 2.9 20.9 + - + +
238A LEU* 1.3 73.5 - - + +
240A HIS* 1.3 64.3 + - - +
241A LYS* 3.1 18.6 + - - +
273A TYR* 6.1 0.4 - - - -
303A ALA* 4.1 9.7 - - - +
304A VAL 2.8 30.3 + - - +
305A LEU* 4.0 9.9 - - - +
306A CYS* 4.0 24.7 - - + +
312A MET* 6.0 2.1 - - - +
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Residues in contact with HIS 240 (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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230A SER* 5.6 1.1 - - - -
234A CYS* 3.6 5.0 - - + -
236A ALA 4.2 1.3 - - - -
237A PHE* 3.0 34.4 + - + +
239A ARG* 1.3 80.8 - - - +
241A LYS* 1.3 67.7 + - - +
242A MET* 3.4 14.9 + - + +
306A CYS* 3.9 9.9 - - - -
308A CYS* 3.3 13.3 - - - -
309A ARG* 3.8 37.8 + - - +
312A MET* 6.2 0.7 - - - -
502A ZN 2.0 37.0 - - - -
12C GLY* 3.8 0.7 - - - -
13C GLY* 3.3 20.6 + - - -
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Residues in contact with LYS 241 (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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84A GLN* 4.4 4.0 + - - -
86A ASN* 4.2 5.4 + - - -
186A ALA* 3.3 25.4 - - + +
187A TRP 4.7 0.7 - - - -
188A HIS* 3.4 48.3 + - + +
189A THR 4.6 4.1 + - - -
190A GLU* 5.4 2.0 + - - -
191A ASP* 4.4 15.0 + - - +
238A LEU 3.1 9.6 + - - +
239A ARG* 3.1 15.3 - - - +
240A HIS* 1.3 79.7 - - - +
242A MET* 1.3 57.5 + - - +
243A THR 4.6 0.2 - - - +
9C MLZ 4.4 19.4 - - - +
10C SER* 3.0 30.5 + - - +
11C THR 3.5 17.8 - - - +
12C GLY* 3.7 11.9 - - - +
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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