Contacts of the helix formed by residues 225 - 237 (chain B) in PDB entry 2CNW
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 GLU 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193B GLN* 4.3 0.2 + - - -
222B THR* 4.8 0.4 - - - -
223B GLY 3.0 1.6 + - - -
224B GLN* 1.3 80.2 - - + +
226B ALA* 1.3 64.4 + - - +
227B LEU 3.4 0.4 - - - -
228B SER* 3.2 24.8 + - - -
229B VAL* 2.9 30.5 + - + +
41E ALA 4.5 9.9 - - - +
43E ASP* 4.6 5.8 + - - +
231E VAL* 4.2 20.0 - - + +
260E THR* 2.8 32.8 + - - +
261E ALA* 3.6 29.2 - - + +
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Residues in contact with ALA 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B LEU* 4.9 8.2 - - + +
222B THR* 4.0 13.0 - - + +
223B GLY 3.0 17.0 + - - +
224B GLN 3.1 1.3 - - - +
225B GLU* 1.3 74.9 - - - +
227B LEU* 1.3 58.6 + - - +
229B VAL* 3.2 4.7 + - - +
230B ALA* 2.8 32.5 + - - +
255B ALA* 3.5 38.8 - - + +
258B SER* 4.1 6.3 - - - +
259B ALA* 5.0 1.0 - - - +
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Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ASN* 4.0 21.8 - - - +
46B GLU* 5.0 12.3 - - + +
47B VAL* 3.6 29.4 - - + -
224B GLN 4.0 1.6 + - - -
225B GLU 3.4 0.8 - - - -
226B ALA* 1.3 77.1 - - - +
228B SER* 1.3 55.2 + - - +
230B ALA* 3.2 2.4 + - - +
231B ARG* 2.8 75.4 + - - +
258B SER* 3.8 19.6 - - - +
261B HIS* 4.5 4.5 - - + +
262B VAL* 3.7 29.8 - - + +
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Residues in contact with SER 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLN* 3.4 19.3 + - - +
224B GLN 5.0 0.8 + - - -
225B GLU* 3.2 24.4 + - - -
227B LEU* 1.3 86.6 - - - +
229B VAL* 1.3 62.5 + - - +
231B ARG* 3.9 12.8 - - - +
232B ALA* 3.2 25.1 + - - +
260E THR* 5.1 1.0 - - - +
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 3.9 37.9 - - + -
193B GLN* 3.7 28.3 - - - +
216B LEU* 4.9 8.5 - - + -
218B LEU* 5.2 9.0 - - + -
222B THR* 5.9 0.4 - - + -
225B GLU* 2.9 29.8 + - + +
226B ALA* 3.6 6.1 - - - +
228B SER* 1.3 73.7 - - - +
230B ALA* 1.3 64.6 + - - +
231B ARG 3.4 0.2 + - - -
232B ALA* 3.5 1.4 + - - +
233B PHE* 3.2 42.1 + - + -
231E VAL* 5.3 0.9 - - + -
260E THR* 4.9 1.1 - - - +
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Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU* 3.8 21.5 - - + +
218B LEU* 6.1 0.4 - - + -
226B ALA 2.8 20.1 + - - +
227B LEU 3.7 3.4 - - - +
229B VAL* 1.3 74.8 - - - +
231B ARG* 1.3 60.7 + - - +
233B PHE* 3.9 1.6 + - - +
234B ASP* 3.2 24.3 + - - +
239B VAL* 5.0 0.3 - - - +
259B ALA* 3.8 25.8 - - + +
262B VAL* 3.8 15.7 - - + -
263B THR* 3.6 8.6 - - + +
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Residues in contact with ARG 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLU* 5.2 5.3 + - - -
227B LEU* 2.8 53.0 + - - +
228B SER* 3.9 14.5 - - - +
229B VAL 3.2 0.2 - - - -
230B ALA* 1.3 75.0 - - - +
232B ALA* 1.3 59.8 + - - +
234B ASP* 3.3 4.6 + - - +
235B GLU* 2.8 61.5 + - + +
262B VAL* 3.8 26.6 - - + +
263B THR* 5.2 0.4 - - - -
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Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLN* 3.4 39.0 - - + +
199B MET* 4.1 1.6 - - - -
228B SER 3.2 10.3 + - - +
229B VAL 3.5 0.4 + - - +
231B ARG* 1.3 75.5 - - - +
233B PHE* 1.3 60.0 + - - +
235B GLU* 4.8 3.4 - - - -
236B LYS* 2.9 53.5 + - + +
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Residues in contact with PHE 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B VAL* 4.1 15.5 - - + -
105B GLY* 3.6 39.9 - - - -
106B LEU* 4.3 1.3 - - + -
191B ARG* 3.7 24.2 - - + -
193B GLN* 3.9 20.9 - - + -
199B MET* 3.8 24.0 - - + -
202B LEU* 3.9 18.4 - - + -
216B LEU* 4.2 11.2 - - + -
229B VAL* 3.2 40.0 + - + +
230B ALA* 4.3 2.0 - - - +
232B ALA* 1.3 78.1 - - - +
234B ASP* 1.3 57.0 + - - +
237B VAL* 3.0 33.3 + - + +
238B GLY 3.2 2.1 + - - -
239B VAL* 4.2 16.4 - - + +
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Residues in contact with ASP 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ALA 3.2 19.1 + - - +
231B ARG* 3.6 4.7 - - - +
232B ALA 3.2 0.6 - - - -
233B PHE* 1.3 77.2 - - - +
235B GLU* 1.3 63.4 + - + +
238B GLY* 2.9 24.0 + - - +
239B VAL* 3.0 33.5 + - + +
262B VAL 4.4 2.8 - - - +
263B THR* 3.5 36.3 - - + +
265B LYS* 4.6 4.3 - - - -
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Residues in contact with GLU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B ARG* 2.8 49.2 + - + +
232B ALA* 4.2 3.9 - - - +
234B ASP* 1.3 81.0 - - + +
236B LYS* 1.3 67.7 + - + +
237B VAL 3.5 0.7 + - - -
238B GLY 4.8 0.2 + - - -
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Residues in contact with LYS 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B GLN 3.2 24.0 + - - -
196B GLU* 2.8 30.2 + - - -
199B MET* 3.9 29.3 - - + +
203B ALA* 3.7 17.2 - - + +
232B ALA* 2.9 40.2 + - + +
235B GLU* 1.3 83.1 - - + +
237B VAL* 1.3 64.6 + - + +
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Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B PHE* 5.4 1.1 - - + -
104B VAL* 5.2 0.9 - - + -
199B MET* 4.2 11.4 - - + +
202B LEU* 3.8 39.5 - - + -
203B ALA* 4.0 14.1 - - - +
206B LYS* 2.5 57.6 + - + +
214B VAL* 4.0 21.8 - - + -
233B PHE* 3.0 16.3 + - + +
234B ASP 4.0 0.2 - - - -
235B GLU 3.3 1.1 - - - -
236B LYS* 1.3 89.2 - - + +
238B GLY* 1.3 50.9 + - - +
239B VAL* 6.1 0.2 - - + -
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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