Contacts of the helix formed by residues 225 - 237 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A THR* 4.9 0.7 - - - -
223A GLY 3.4 1.4 - - - -
224A GLN* 1.3 76.1 - - - +
226A ALA* 1.3 52.2 + - - +
227A LEU 3.3 0.9 - - - -
228A SER* 3.0 29.6 + - - +
229A VAL* 2.7 42.2 + - + +
41D ALA* 4.4 12.6 - - - +
43D ASP* 4.4 3.9 + - - +
231D VAL* 4.3 19.0 - - + +
260D THR* 2.9 32.0 + - - +
261D ALA* 3.6 33.0 - - + +
262D LYS* 6.2 0.2 - - - +
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Residues in contact with ALA 226 (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* 4.7 7.9 - - + +
222A THR* 4.0 12.7 - - + +
223A GLY 3.3 16.5 + - - +
224A GLN 3.1 1.6 - - - +
225A GLU* 1.3 75.8 - - - +
227A LEU* 1.3 53.5 + - - +
229A VAL* 3.8 5.2 - - - +
230A ALA* 2.8 38.3 + - - +
255A ALA* 3.5 37.2 - - + +
258A SER* 4.1 5.8 - - - -
259A ALA* 4.9 1.2 - - + +
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Residues in contact with LEU 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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44A ASN* 3.4 40.8 - - + +
46A GLU* 4.5 18.8 - - + +
47A VAL* 3.5 21.5 - - + -
224A GLN 3.9 1.2 + - - -
225A GLU 3.3 0.4 - - - -
226A ALA* 1.3 76.0 - - - +
228A SER* 1.3 61.4 + - - +
230A ALA 3.4 0.2 + - - -
231A ARG* 2.9 74.2 + - - +
258A SER* 3.8 17.6 - - - +
261A HIS* 5.4 2.2 - - + -
262A VAL* 3.8 17.7 - - + +
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Residues in contact with SER 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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44A ASN* 5.4 0.2 - - - +
193A GLN* 3.1 17.0 + - - +
224A GLN 4.7 0.4 + - - -
225A GLU* 3.0 33.1 + - - -
227A LEU* 1.3 87.3 - - - +
229A VAL* 1.3 59.9 + - - +
231A ARG* 4.1 9.9 - - - +
232A ALA* 3.3 24.1 + - - +
260D THR* 4.0 1.6 + - - +
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Residues in contact with VAL 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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106A LEU* 3.8 39.0 - - + -
193A GLN* 3.6 31.4 - - - +
216A LEU* 4.9 8.7 - - + -
218A LEU* 5.0 9.9 - - + -
222A THR* 6.0 0.4 - - + -
225A GLU* 2.7 32.1 + - + +
226A ALA* 3.8 4.3 - - - +
228A SER* 1.3 72.0 - - - +
230A ALA* 1.3 66.7 + - - +
232A ALA* 3.4 2.1 + - - +
233A PHE* 3.1 40.2 + - + -
231D VAL* 5.3 0.4 - - + -
260D THR* 5.0 0.2 - - - +
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Residues in contact with ALA 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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216A LEU* 3.9 20.7 - - + +
218A LEU* 6.2 0.7 - - + -
226A ALA 2.8 21.4 + - - +
227A LEU 3.9 2.2 - - - +
229A VAL* 1.3 74.6 - - - +
231A ARG* 1.3 63.2 + - - +
233A PHE* 3.5 1.9 + - - +
234A ASP* 3.1 24.9 + - - +
239A VAL* 5.1 0.5 - - - +
259A ALA* 3.8 31.4 - - + -
262A VAL* 4.0 2.0 - - + -
263A THR* 3.8 15.1 - - + +
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Residues in contact with ARG 231 (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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46A GLU* 4.9 7.3 + - - -
227A LEU* 2.9 54.5 + - - +
228A SER* 4.1 11.3 - - - +
230A ALA* 1.3 75.7 - - - +
232A ALA* 1.3 57.4 + - - +
234A ASP* 3.3 4.3 + - - +
235A GLU* 2.8 60.1 + - + +
262A VAL* 3.8 30.3 - - + +
263A THR* 4.8 1.1 - - - -
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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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193A GLN* 3.4 37.2 - - + +
199A MET* 4.1 1.8 - - - -
228A SER 3.3 9.0 + - - +
230A ALA 3.4 0.2 - - - -
231A ARG* 1.3 77.0 - - - +
233A PHE* 1.3 60.5 + - - +
235A GLU* 4.5 4.0 - - - +
236A LYS* 2.8 57.9 + - - +
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Residues in contact with PHE 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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104A VAL* 4.0 18.2 - - + -
105A GLY* 3.5 41.3 - - - -
106A LEU* 4.2 4.3 - - + -
191A ARG* 3.7 22.2 - - + -
193A GLN* 3.9 22.2 - - + -
199A MET* 3.8 20.9 - - + -
202A LEU* 4.1 16.6 - - + -
216A LEU* 4.3 10.5 - - + -
229A VAL* 3.1 42.1 + - + +
230A ALA 4.0 2.5 - - - +
232A ALA* 1.3 76.7 - - - +
234A ASP* 1.3 57.5 + - - +
237A VAL* 2.9 29.2 + - + +
238A GLY 3.0 6.2 + - - -
239A VAL* 3.9 16.7 - - + +
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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 ALA 3.1 18.9 + - - +
231A ARG* 3.7 3.6 - - - +
233A PHE* 1.3 75.9 - - - +
235A GLU* 1.3 67.1 + - + +
238A GLY* 3.1 23.5 + - - +
239A VAL* 3.0 35.3 + - + +
262A VAL 4.9 1.9 - - - +
263A THR* 4.1 24.5 - - + +
265A LYS* 3.7 16.5 + - - -
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Residues in contact with GLU 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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231A ARG* 2.8 50.0 + - + +
232A ALA* 4.1 3.9 - - - +
234A ASP* 1.3 82.7 - - + +
236A LYS* 1.3 63.9 + - + +
237A VAL 5.0 0.5 - - - -
238A GLY 4.8 0.5 + - - -
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Residues in contact with LYS 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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193A GLN 2.8 29.8 + - - +
194A ILE* 4.1 7.3 - - - +
196A GLU* 3.1 39.0 + - - +
199A MET* 3.8 21.8 - - + +
203A ALA* 3.6 16.6 - - - +
232A ALA* 2.8 35.1 + - + +
235A GLU* 1.3 76.9 - - + +
237A VAL* 1.3 62.1 + - + +
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Residues in contact with VAL 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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102A PHE* 5.5 0.9 - - + -
104A VAL* 5.4 0.7 - - + -
199A MET* 3.9 30.1 - - + +
202A LEU* 3.8 38.1 - - + +
203A ALA* 4.1 6.2 - - - +
206A LYS* 3.1 44.8 + - + +
214A VAL* 4.5 12.1 - - + -
233A PHE* 2.9 15.5 + - + +
235A GLU 3.4 1.1 - - - -
236A LYS* 1.3 84.5 - - - +
238A GLY* 1.3 63.5 + - - +
239A VAL* 5.8 0.4 - - + -
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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