Contacts of the helix formed by residues 226 - 239 (chain A) in PDB entry 2HCR
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 CYS 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A ALA* 3.7 13.9 - - - -
224A ASP 3.1 8.6 - - - -
225A THR* 1.3 78.1 - - - +
227A GLY* 1.3 58.0 + - - +
228A THR 3.4 2.0 - - - -
229A ILE* 3.7 17.7 - - + -
230A CYS* 3.0 39.2 + - - +
248A LEU* 5.5 0.2 - - - -
253A PHE* 3.4 39.3 - - - -
257A ALA* 3.8 12.8 - - + +
260A ARG* 4.3 1.3 - - + -
261A ILE* 4.0 7.9 - - + -
1004A SO4 2.9 13.8 + - - -
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Residues in contact with GLY 227 (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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225A THR* 3.1 6.7 + - - -
226A CYS* 1.3 76.0 - - - +
228A THR* 1.3 64.4 + - - +
230A CYS* 4.0 1.6 - - - +
231A HIS* 2.9 42.0 + - - -
260A ARG* 3.4 23.7 - - - +
1004A SO4 3.5 5.1 + - - -
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Residues in contact with THR 228 (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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170A PRO* 3.7 36.3 - - + +
171A ASP* 4.7 9.9 - - + +
194A LYS* 6.2 0.2 - - - +
205A MET* 3.9 13.4 - - + +
220A ASP* 5.8 0.9 - - - +
227A GLY* 1.3 74.7 - - - +
229A ILE* 1.3 58.1 + - - +
231A HIS* 3.8 1.0 - - - -
232A ALA* 2.9 31.2 + - - +
1004A SO4 3.2 23.5 + - - -
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Residues in contact with ILE 229 (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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170A PRO* 3.6 29.2 - - + -
218A LEU* 3.6 25.7 - - + +
220A ASP* 4.5 2.5 - - + +
222A MET 5.7 0.2 - - - +
223A ALA* 4.7 6.7 - - + -
226A CYS* 3.4 35.3 - - + +
228A THR* 1.3 79.0 - - - +
230A CYS* 1.3 62.8 + - - +
232A ALA* 4.3 3.6 - - - -
233A ALA* 3.1 20.4 + - - +
246A ALA* 4.0 15.9 - - + -
248A LEU* 3.7 27.8 - - + -
261A ILE* 5.7 0.7 - - + -
266A PHE* 3.2 22.4 - - + -
269A VAL* 6.4 0.7 - - + -
1004A SO4 5.1 1.3 + - - +
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Residues in contact with CYS 230 (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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226A CYS* 3.0 28.2 + - - +
227A GLY* 4.1 3.6 - - - +
229A ILE* 1.3 77.2 - - - +
231A HIS* 1.3 67.5 + - + +
233A ALA* 3.4 3.9 + - - +
234A ASP* 3.3 27.0 + - - +
260A ARG* 3.7 40.4 - - + +
261A ILE* 4.1 2.7 - - - -
264A ALA* 3.9 8.2 - - + +
266A PHE* 3.7 25.6 - - - -
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Residues in contact with HIS 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LYS* 4.9 17.1 + - - -
205A MET* 3.7 23.9 - - + +
227A GLY* 2.9 35.2 + - - +
228A THR* 5.1 0.4 - - - -
230A CYS* 1.3 74.2 - - + +
232A ALA* 1.3 64.4 + - - +
234A ASP* 3.2 17.1 + - - +
235A LYS* 3.1 21.8 + - - +
260A ARG* 6.0 2.6 + - - -
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Residues in contact with ALA 232 (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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170A PRO* 4.5 6.5 - - + -
192A ILE* 3.5 31.6 - - + +
205A MET* 3.7 7.3 - - - -
218A LEU* 3.9 19.1 - - + -
228A THR 2.9 18.8 + - - +
229A ILE* 3.7 7.9 - - - +
231A HIS* 1.3 77.8 - - - +
233A ALA* 1.3 55.3 + - - +
235A LYS 3.3 1.2 + - - -
236A LEU* 2.9 32.4 + - - +
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Residues in contact with ALA 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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218A LEU* 3.9 6.0 - - + +
229A ILE 3.1 10.0 + - - +
230A CYS* 3.6 7.2 - - - +
231A HIS 3.2 0.2 - - - -
232A ALA* 1.3 74.1 - - - +
234A ASP* 1.3 60.5 + - - +
236A LEU* 3.4 7.0 + - - +
237A LEU* 3.0 30.8 + - - +
244A VAL* 4.0 14.1 - - + +
264A ALA* 5.3 2.2 - - + -
265A CYS* 4.0 10.3 - - - -
266A PHE* 3.5 35.4 - - + -
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Residues in contact with ASP 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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230A CYS 3.3 13.6 + - - +
231A HIS* 3.2 20.1 + - - +
233A ALA* 1.3 76.0 - - - +
235A LYS* 1.3 58.7 - - - +
237A LEU* 3.1 10.4 + - - +
238A SER* 2.9 32.2 + - - +
264A ALA* 5.5 4.2 - - - +
265A CYS* 4.9 11.1 + - - +
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Residues in contact with LYS 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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192A ILE* 4.4 8.7 - - + -
205A MET* 3.3 42.2 + - + -
206A VAL* 4.4 0.8 - - - +
207A LEU* 3.6 41.4 + - + +
231A HIS 3.1 9.3 + - - +
232A ALA* 3.6 9.9 - - - +
233A ALA 3.3 0.2 - - - -
234A ASP* 1.3 78.7 - - - +
236A LEU* 1.3 57.0 + - - +
238A SER* 3.4 11.5 + - - -
239A ALA* 3.1 28.7 + - + +
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Residues in contact with LEU 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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168A VAL* 3.7 17.0 - - + -
192A ILE* 3.9 4.3 - - + -
207A LEU* 3.6 24.0 - - + -
211A VAL* 3.7 24.0 - - + -
216A ALA* 4.0 10.3 - - + -
218A LEU* 3.6 36.3 - - + -
232A ALA 2.9 19.5 + - - +
233A ALA* 3.7 5.8 - - - +
234A ASP 3.3 0.2 - - - -
235A LYS* 1.3 78.0 - - - +
237A LEU* 1.3 57.3 + - - +
239A ALA* 3.5 7.1 + - - +
240A GLY 3.6 0.2 + - - -
241A ALA* 3.1 34.9 + - + +
244A VAL* 3.7 18.8 - - + -
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Residues in contact with LEU 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 ALA 3.0 9.1 + - - +
234A ASP* 3.1 11.0 + - - +
236A LEU* 1.3 74.8 - - - +
238A SER* 1.3 60.6 + - - +
240A GLY* 3.1 19.2 + - - -
241A ALA* 3.6 22.2 - - + +
242A THR 4.5 8.1 - - - +
243A ARG* 5.4 2.2 - - - -
244A VAL* 5.0 6.3 - - + +
265A CYS* 3.6 39.5 - - + -
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Residues in contact with SER 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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212A LYS* 6.0 0.2 + - - -
234A ASP* 2.9 18.3 + - - +
235A LYS* 3.7 12.4 - - - -
237A LEU* 1.3 75.7 - - - +
239A ALA* 1.3 58.4 + - - +
240A GLY* 3.2 1.9 + - - -
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Residues in contact with ALA 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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207A LEU* 3.9 11.7 - - + -
211A VAL* 3.5 23.5 - - + +
212A LYS* 3.5 27.1 + - - +
235A LYS* 3.1 21.6 + - + +
236A LEU 3.8 0.9 - - - +
237A LEU 3.1 0.6 - - - -
238A SER* 1.3 77.1 - - - +
240A GLY* 1.3 59.5 + - - +
241A ALA 3.5 1.3 + - - -
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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