Contacts of the helix formed by residues 195 - 210 (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 ASP 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B LEU* 3.3 25.1 + - + +
194B ILE* 1.3 75.5 - - - +
196B GLU* 1.3 51.8 + - - +
197B PRO* 3.3 12.5 - - - +
198B LEU* 2.9 55.9 + - + +
199B MET* 2.8 36.4 + - - +
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Residues in contact with GLU 196 (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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194B ILE* 2.8 28.7 + - - +
195B ASP* 1.3 68.4 - - - +
197B PRO* 1.4 64.6 - - + +
199B MET* 4.0 2.6 - - - +
200B GLY* 2.7 33.3 + - - -
236B LYS* 2.8 30.1 + - - -
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Residues in contact with PRO 197 (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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195B ASP* 3.3 12.8 - - - +
196B GLU* 1.4 93.4 - - + +
198B LEU* 1.3 56.2 + - + +
200B GLY* 3.4 2.4 + - - -
201B GLU* 2.8 32.4 + - - +
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Residues in contact with LEU 198 (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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107B GLN* 6.3 0.2 - - - +
191B ARG* 3.0 51.3 + - + +
192B LEU 5.7 0.2 - - - +
195B ASP* 2.9 41.6 + - + +
197B PRO* 1.3 74.6 - - + +
199B MET* 1.3 64.5 + - - +
200B GLY 3.2 0.9 - - - -
201B GLU* 3.2 20.6 + - + +
202B LEU 3.1 11.3 + - - -
284E GLU* 5.6 5.2 - - - +
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Residues in contact with MET 199 (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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191B ARG* 3.8 20.9 - - - +
192B LEU 3.7 17.0 - - - +
193B GLN* 3.6 25.6 - - - +
195B ASP 2.8 23.2 + - - +
196B GLU* 4.0 3.8 - - - +
198B LEU* 1.3 70.0 - - - +
200B GLY* 1.3 65.3 + - - +
202B LEU* 3.4 4.0 + - - +
203B ALA* 3.0 24.0 + - - +
232B ALA 3.9 9.6 - - - +
233B PHE* 3.8 46.2 - - + +
236B LYS* 3.9 28.6 - - + +
237B VAL* 4.2 9.9 - - + +
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Residues in contact with GLY 200 (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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196B GLU 2.7 19.7 + - - -
197B PRO* 3.5 2.9 - - - -
199B MET* 1.3 76.2 - - - +
201B GLU* 1.3 61.8 + - - +
203B ALA* 3.0 9.8 + - - +
204B ARG* 3.0 22.7 + - - +
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Residues in contact with GLU 201 (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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134B ALA 5.6 1.4 - - - +
191B ARG* 3.6 18.8 + - - -
197B PRO 2.8 17.5 + - - +
198B LEU* 3.2 22.7 + - + +
200B GLY* 1.3 72.7 - - - +
202B LEU* 1.3 57.8 + - - +
204B ARG* 3.4 5.8 + - - +
205B LEU* 3.0 40.5 + - - +
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Residues in contact with LEU 202 (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* 3.8 24.5 - - + -
104B VAL* 3.7 26.2 - - + -
188B THR* 3.9 25.6 - - + +
191B ARG* 4.0 19.7 - - - +
198B LEU 3.1 14.5 + - - +
199B MET* 3.8 5.6 - - - +
200B GLY 3.3 0.2 - - - -
201B GLU* 1.3 76.1 - - - +
203B ALA* 1.3 57.7 + - - +
205B LEU* 3.4 9.4 + - + +
206B LYS* 2.9 28.9 + - - +
233B PHE* 3.9 18.8 - - + -
237B VAL* 3.8 25.4 - - + -
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Residues in contact with ALA 203 (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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199B MET 3.0 14.3 + - - +
200B GLY* 3.3 12.6 - - - +
202B LEU* 1.3 77.0 - - - +
204B ARG* 1.3 56.6 + - - +
206B LYS* 3.3 8.3 + - - +
207B GLU* 2.9 26.4 + - - +
236B LYS 3.7 19.5 - - - +
237B VAL* 4.0 7.8 - - - +
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Residues in contact with ARG 204 (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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164B SER* 4.9 2.2 - - - -
165B PRO* 3.4 27.9 - - + +
166B GLU* 2.8 39.6 + - - -
200B GLY 3.0 11.9 + - - +
201B GLU* 4.0 8.2 - - + +
203B ALA* 1.3 73.6 - - - +
205B LEU* 1.3 61.6 + - - +
207B GLU* 3.0 23.7 + - - +
208B VAL* 2.8 34.4 + - + +
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Residues in contact with LEU 205 (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* 3.4 27.1 - - + -
134B ALA* 4.9 9.6 - - + -
165B PRO* 3.8 26.8 - - + +
168B ILE* 4.1 18.8 - - + -
186B VAL* 4.8 5.6 - - + -
188B THR* 4.4 19.1 - - + -
191B ARG* 6.2 0.4 - - - +
201B GLU* 3.0 31.0 + - + +
202B LEU* 3.5 11.2 - - + +
204B ARG* 1.3 76.5 - - - +
206B LYS* 1.3 55.7 + - - +
209B LEU* 3.0 48.1 + - + +
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Residues in contact with LYS 206 (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* 3.5 16.5 - - + -
202B LEU 2.9 14.0 + - - +
203B ALA* 3.5 10.3 - - - +
205B LEU* 1.3 75.7 - - - +
207B GLU* 1.3 58.4 + - - +
210B GLY* 2.8 34.9 + - - -
211B PRO* 3.3 24.9 - - + +
214B VAL* 4.4 5.2 - - + +
237B VAL* 2.5 40.0 + - + +
238B GLY* 3.1 22.4 + - - -
240B THR* 5.8 2.0 - - - +
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Residues in contact with GLU 207 (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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169B ARG* 5.3 0.5 + - - -
203B ALA 2.9 13.6 + - - +
204B ARG* 3.0 27.1 + - - +
206B LYS* 1.3 79.2 - - - +
208B VAL* 1.3 64.8 + - + +
210B GLY* 4.2 3.8 + - - -
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Residues in contact with VAL 208 (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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165B PRO* 3.3 43.5 - - + +
166B GLU* 3.7 23.3 - - + +
169B ARG* 3.1 49.4 + - + +
204B ARG* 2.8 25.8 + - + +
205B LEU 4.1 0.9 - - - +
207B GLU* 1.3 86.5 - - + +
209B LEU* 1.3 61.8 + - + +
210B GLY 3.4 0.2 - - - -
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Residues in contact with LEU 209 (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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100B LEU* 4.2 25.9 - - + +
102B PHE* 3.7 30.7 - - + -
165B PRO 4.0 5.8 - - - +
168B ILE* 4.4 13.7 - - + -
169B ARG* 3.5 44.1 - - + +
172B VAL* 5.6 4.7 - - + -
186B VAL* 4.4 16.4 - - + -
205B LEU* 3.0 35.7 + - + +
208B VAL* 1.3 77.1 - - + +
210B GLY* 1.3 67.3 + - - +
211B PRO 3.5 0.2 - - - -
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Residues in contact with GLY 210 (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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100B LEU* 4.8 1.7 - - - +
206B LYS* 2.8 14.7 + - - -
207B GLU 4.2 3.7 + - - -
208B VAL 3.4 2.0 - - - -
209B LEU* 1.3 79.9 - - - +
211B PRO* 1.4 70.4 - - - +
212B ASP* 3.7 9.9 + - - +
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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