Contacts of the helix formed by residues 232 - 246 (chain A) in PDB entry 2C1H
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 THR 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A ASN* 1.3 71.9 - - - +
233A GLU* 1.3 64.3 + - - -
234A GLU 3.2 1.6 - - - -
235A ALA* 3.2 18.6 + - - +
236A MET* 3.6 7.3 + - - +
260A ASP* 4.0 11.7 - - - +
261A ILE* 3.5 24.0 - - + -
264A ARG* 3.3 39.7 + - - +
28B GLU* 2.7 9.6 + - - -
29B ASN* 3.6 8.8 + - - -
263B TRP* 4.4 12.9 - - + -
309B ARG* 3.0 22.9 + - + +
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Residues in contact with GLU 233 (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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232A THR* 1.3 75.1 - - - +
234A GLU* 1.3 55.8 + - - +
236A MET* 3.1 26.0 + - - +
237A LYS* 3.3 7.8 + - - +
264A ARG* 2.8 35.3 + - - +
28B GLU* 2.6 25.6 + - + +
263B TRP* 4.9 3.6 - - - -
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Residues in contact with GLU 234 (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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227A MET* 3.2 20.1 - - + +
228A ASN 4.4 3.3 + - - -
231A ASN* 3.0 22.2 - - + +
232A THR 3.2 0.6 - - - -
233A GLU* 1.3 73.5 - - - +
235A ALA* 1.3 60.4 + - - +
237A LYS* 3.6 29.9 + - - +
238A GLU* 3.1 27.5 + - - +
13B PRO* 4.3 6.1 - - - +
16B LEU* 5.0 7.4 - - + +
17B ARG* 2.8 45.3 + - - +
26B VAL* 6.3 1.8 - - - -
28B GLU* 2.9 15.8 + - - +
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Residues in contact with ALA 235 (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 ALA* 4.0 8.9 - - + +
201A TYR* 3.4 25.6 - - - +
227A MET* 3.4 15.1 - - + +
232A THR 3.2 11.7 + - - +
234A GLU* 1.3 77.4 - - - +
236A MET* 1.3 63.7 + - + +
238A GLU* 3.6 1.8 - - - +
239A VAL* 3.0 35.2 + - + +
261A ILE* 3.8 19.7 - - + -
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Residues in contact with MET 236 (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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232A THR 4.0 4.0 - - - +
233A GLU* 3.1 12.2 + - - +
235A ALA* 1.3 89.1 - - + +
237A LYS* 1.3 62.5 + - - +
239A VAL* 5.0 0.7 - - + -
240A GLU* 3.4 20.4 + - - +
261A ILE* 4.2 2.9 - - + +
264A ARG* 3.5 62.4 - - + +
265A THR* 3.6 22.9 - - - +
268A ARG* 3.3 33.1 - - - +
269A PHE* 3.5 27.0 - - + -
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Residues in contact with LYS 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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233A GLU 3.3 7.9 + - - +
234A GLU* 3.7 29.5 + - - +
236A MET* 1.3 78.2 - - - +
238A GLU* 1.3 62.3 + - - +
240A GLU* 3.6 6.1 + - - +
241A LEU* 3.4 36.0 + - + +
13B PRO* 4.4 22.6 - - + +
16B LEU* 3.6 29.7 - - - +
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Residues in contact with GLU 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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172A MET* 4.3 6.1 - - - +
174A ASP* 4.4 1.7 - - - +
198A ALA 3.6 19.8 - - - +
227A MET* 4.1 9.6 - - - -
234A GLU* 3.1 22.2 + - + +
235A ALA* 3.6 8.1 - - - +
236A MET 3.4 0.2 - - - -
237A LYS* 1.3 76.5 - - + +
239A VAL* 1.3 65.1 + - - +
241A LEU* 3.6 8.5 + - - +
242A ASP* 3.5 23.7 + - - -
1329A MG 2.2 31.3 - - - -
13B PRO* 3.2 25.9 - - + +
17B ARG* 2.8 35.7 + - - +
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Residues in contact with VAL 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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198A ALA* 3.7 23.6 - - + -
199A ALA* 4.5 10.3 - - + -
235A ALA 3.0 22.1 + - - +
236A MET* 5.0 0.7 - - + -
238A GLU* 1.3 74.8 - - - +
240A GLU* 1.3 64.3 + - - +
242A ASP* 3.1 6.6 + - - +
243A ILE* 3.0 33.0 + - + +
250A VAL* 4.1 10.1 - - + -
252A VAL* 5.5 2.7 - - + -
261A ILE* 6.1 0.2 - - + -
265A THR* 3.9 28.7 - - + +
269A PHE* 3.7 30.7 - - + -
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Residues in contact with GLU 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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236A MET 3.4 17.4 + - - +
237A LYS* 3.9 5.0 - - - +
238A GLU 3.4 0.6 - - - -
239A VAL* 1.3 78.5 - - - +
241A LEU* 1.3 58.0 + - + +
243A ILE* 3.1 6.6 + - + +
244A VAL* 2.9 42.0 + - + +
268A ARG* 5.4 7.4 + - - -
269A PHE* 3.6 26.7 - - + -
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Residues in contact with LEU 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 LYS* 3.4 27.2 + - + +
238A GLU* 3.8 11.0 - - - +
240A GLU* 1.3 79.4 - - + +
242A ASP* 1.3 60.3 + - - +
244A VAL* 3.6 7.2 + - + +
245A GLU* 3.0 44.1 + - - +
11B HIS* 3.8 37.5 - - + +
13B PRO* 3.7 32.5 - - + -
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Residues in contact with ASP 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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175A GLY 5.6 1.7 + - - -
176A ARG* 3.7 7.1 + - - -
177A ILE* 3.7 14.3 - - + +
196A SER* 2.7 28.6 + - - +
198A ALA* 3.3 19.6 - - + -
238A GLU 3.5 8.9 + - - +
239A VAL 3.1 10.5 + - - +
241A LEU* 1.3 78.5 - - - +
243A ILE* 1.3 60.0 - - - +
245A GLU* 3.3 14.8 + - - +
246A GLY 3.0 8.8 + - - -
247A ALA* 3.0 33.3 + - + +
250A VAL* 4.4 5.2 - - + -
1329A MG 3.9 12.6 - - - -
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Residues in contact with ILE 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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239A VAL* 3.0 22.0 + - + +
240A GLU* 3.1 9.2 + - + +
242A ASP* 1.3 74.8 - - - +
244A VAL* 1.3 66.2 + - + +
246A GLY* 3.1 14.2 + - - -
247A ALA 4.2 9.8 + - - +
250A VAL* 4.0 15.5 - - + -
269A PHE* 3.6 46.4 - - + +
271A VAL* 4.2 29.4 - - + -
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Residues in contact with VAL 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 GLU* 2.9 34.1 + - + +
241A LEU* 3.9 7.9 - - + +
243A ILE* 1.3 77.4 - - + +
245A GLU* 1.3 63.2 + - + +
246A GLY* 3.4 1.2 + - - -
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Residues in contact with GLU 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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175A GLY* 3.4 30.5 + - - -
176A ARG 3.9 0.2 + - - -
177A ILE* 3.4 13.4 + - + +
178A GLY* 2.8 48.1 + - - +
181A ARG* 4.1 13.2 - - - +
241A LEU* 3.0 35.9 + - - +
242A ASP* 3.6 12.2 - - - +
243A ILE 3.2 0.6 - - - -
244A VAL* 1.3 78.7 - - + +
246A GLY* 1.3 55.4 + - - +
247A ALA 3.8 0.4 - - - -
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Residues in contact with GLY 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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177A ILE* 4.6 2.2 - - - -
181A ARG* 4.6 17.3 + - - -
194A ILE* 5.3 1.3 - - - +
242A ASP 3.0 1.8 + - - -
243A ILE 3.1 11.4 + - - -
244A VAL 3.2 1.5 - - - -
245A GLU* 1.3 79.7 - - - +
247A ALA* 1.3 67.5 + - - +
248A ASP* 3.4 12.1 + - - +
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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