Contacts of the helix formed by residues 236 - 247 (chain A) in PDB entry 2O2C
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 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 ASN* 3.1 29.2 + - + +
235A VAL* 1.3 78.7 - - - +
237A GLY* 1.3 63.5 + - - +
238A THR* 2.9 34.4 + - - +
239A HIS* 3.0 18.9 + - + +
240A ILE 4.3 1.0 + - - -
269A ASN* 5.1 1.0 - - - +
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Residues in contact with GLY 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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235A VAL 3.1 7.1 + - - -
236A ASP* 1.3 73.9 + - - +
238A THR* 1.3 61.1 + - - +
239A HIS 3.3 0.2 - - - -
240A ILE* 3.4 14.5 - - - +
241A ALA* 3.1 25.3 + - - +
269A ASN* 5.9 0.4 - - - -
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Residues in contact with THR 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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236A ASP* 3.3 22.8 + - - +
237A GLY* 1.3 76.8 - - - +
239A HIS* 1.3 59.6 + - - +
241A ALA* 4.1 5.6 - - - -
242A GLU* 2.9 45.2 + - + +
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Residues in contact with HIS 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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231A PHE 3.3 20.2 + - - -
232A VAL* 4.4 4.5 - - + -
233A SER* 3.1 38.2 + - - -
234A ASN* 3.2 31.0 - - + +
236A ASP* 3.0 14.3 + - + +
238A THR* 1.3 82.7 - - - +
240A ILE* 1.3 61.1 + - - +
242A GLU* 4.2 3.2 - - - +
243A VAL* 3.4 28.3 + - + +
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Residues in contact with ILE 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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201A VAL* 5.3 0.2 - - + -
203A ILE* 5.5 1.3 - - + -
232A VAL* 3.6 34.9 - - + +
236A ASP 4.3 1.0 + - - -
237A GLY* 3.4 17.6 + - - +
239A HIS* 1.3 75.9 - - - +
241A ALA* 1.3 65.3 + - + +
243A VAL* 3.4 4.4 + - + -
244A LEU* 2.9 60.0 + - + +
254A PHE* 5.2 4.3 - - + -
269A ASN* 4.1 22.4 + - - +
272A SER* 4.6 17.5 - - - +
273A ALA* 4.6 17.3 - - + +
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Residues in contact with ALA 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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237A GLY 3.1 20.3 + - - +
238A THR* 3.6 9.0 - - - +
239A HIS 3.3 0.2 - - - -
240A ILE* 1.3 79.3 - - + +
242A GLU* 1.3 62.5 + - + +
244A LEU* 3.3 11.1 + - - +
245A LYS* 3.2 33.9 + - - +
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Residues in contact with GLU 242 (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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238A THR* 2.9 34.0 + - + +
239A HIS* 4.2 4.0 - - - +
241A ALA* 1.3 74.2 - - + +
243A VAL* 1.3 58.7 + - + +
245A LYS* 3.5 28.1 + - - +
246A SER* 2.7 32.6 + - - -
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Residues in contact with VAL 243 (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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201A VAL* 3.9 25.1 - - + -
230A HIS* 3.9 32.8 - - + +
231A PHE 4.5 10.1 - - - +
232A VAL* 3.7 15.9 - - + -
239A HIS* 3.4 19.4 + - + +
240A ILE* 3.4 8.2 + - + +
241A ALA 3.3 0.4 - - - -
242A GLU* 1.3 75.9 - - + +
244A LEU* 1.3 61.0 + - + +
245A LYS 3.1 0.4 - - - -
246A SER* 3.0 20.5 + - - -
247A ILE* 3.2 20.7 + - + +
254A PHE* 5.6 0.9 - - + -
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Residues in contact with LEU 244 (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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240A ILE* 2.9 49.7 + - + +
241A ALA* 3.3 9.2 + - - +
243A VAL* 1.3 76.7 - - + +
245A LYS* 1.3 60.3 + - - +
247A ILE* 3.7 27.7 - - + +
249A ILE* 4.1 16.4 - - + -
254A PHE* 4.7 6.3 - - + -
272A SER* 5.1 2.7 - - - +
273A ALA* 5.4 0.7 - - - -
276A ALA* 3.8 32.3 - - + -
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Residues in contact with LYS 245 (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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241A ALA* 3.2 22.1 + - - +
242A GLU* 3.6 34.3 - - - +
243A VAL 3.1 0.4 - - - -
244A LEU* 1.3 76.5 - - + +
246A SER* 1.3 60.8 + - - +
247A ILE 3.5 1.9 + - - +
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Residues in contact with SER 246 (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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199A HIS* 3.6 15.9 + - - -
230A HIS* 4.1 19.4 - - - -
242A GLU* 2.7 21.5 + - - -
243A VAL* 3.0 9.8 + - - -
245A LYS* 1.3 78.7 - - - +
247A ILE* 1.3 58.6 + - - +
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Residues in contact with ILE 247 (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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199A HIS* 4.0 11.0 - - + -
201A VAL* 4.3 4.0 - - + -
230A HIS* 3.6 31.0 - - + +
243A VAL* 3.3 23.8 - - + +
244A LEU* 3.7 28.8 - - + +
245A LYS 3.5 2.5 - - - +
246A SER* 1.3 81.9 - - - +
248A ASP* 1.3 59.6 - - - +
249A ILE* 3.8 13.7 + - + +
252A THR* 3.5 29.8 - - + +
254A PHE* 4.0 19.1 - - + -
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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