Contacts of the helix formed by residues 226 - 241 (chain A) in PDB entry 2W3C
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 GLY 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLU* 5.1 4.4 + - - +
225A GLY* 1.3 73.7 - - - +
227A ILE* 1.3 58.6 + - - -
228A VAL* 2.8 18.5 + - - +
229A VAL* 3.0 19.0 + - - +
230A GLU 3.4 3.5 + - - -
275A GLN* 3.8 14.6 + - - -
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Residues in contact with ILE 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLY* 1.3 70.1 - - - -
228A VAL* 1.3 63.4 + - + +
230A GLU* 3.8 25.1 - - - +
231A ASP* 2.9 47.6 + - - +
275A GLN* 4.1 11.0 + - - +
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Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A GLU* 5.5 1.8 - - - +
183A ARG* 4.0 10.3 - - - +
184A ASN* 3.5 42.2 - - + +
187A VAL* 5.3 3.0 - - + +
216A ILE* 4.4 8.3 - - + -
220A GLU* 4.3 29.4 - - + +
226A GLY* 2.8 7.0 + - - +
227A ILE* 1.3 83.8 - - + +
229A VAL* 1.3 61.3 + - - +
231A ASP* 3.5 7.2 + - - +
232A CYS* 3.2 26.0 + - - -
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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
----------------------------------------------------------
217A ILE* 3.8 26.7 - - + +
220A GLU* 4.8 6.8 - - + +
222A ASN 3.4 18.8 - - - +
225A GLY* 3.3 31.6 - - - -
226A GLY 3.0 16.2 - - - +
228A VAL* 1.3 71.8 - - - +
230A GLU* 1.3 65.0 + - - +
231A ASP 3.2 0.4 - - - -
232A CYS* 3.3 7.2 + - - +
233A LEU* 3.0 42.7 + - + +
279A ASN* 3.4 12.3 - - - +
283A MET* 4.2 3.6 - - + -
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Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLY 3.4 1.4 + - - -
227A ILE* 3.5 27.2 - - - +
229A VAL* 1.3 79.9 - - - +
231A ASP* 1.3 57.7 + - - +
233A LEU* 3.3 3.9 + - - +
234A ILE* 3.1 42.9 + - + +
275A GLN* 3.1 24.6 + - - +
278A THR* 3.7 17.5 - - + +
279A ASN* 3.4 19.3 + - - +
282A LEU* 3.9 20.4 - - + +
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Residues in contact with ASP 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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184A ASN 5.1 1.6 - - - +
187A VAL* 3.5 19.0 - - + +
188A LEU* 3.8 30.7 - - + +
191A GLN* 2.7 32.5 + - - +
227A ILE* 2.9 40.8 + - - +
228A VAL* 3.8 7.4 - - - +
229A VAL 3.2 0.6 - - - -
230A GLU* 1.3 76.8 - - - +
232A CYS* 1.3 60.1 + - - +
234A ILE* 4.4 8.1 - - - +
235A LEU 3.1 13.9 + - - -
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Residues in contact with CYS 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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187A VAL* 4.2 15.3 - - - -
213A LEU* 4.1 27.1 - - + +
216A ILE* 4.1 31.6 - - - -
217A ILE* 3.8 24.5 - - + -
228A VAL* 3.2 18.1 + - - -
229A VAL* 3.3 2.4 + - - +
231A ASP* 1.3 72.4 - - - +
233A LEU* 1.3 59.0 + - - +
235A LEU* 3.9 2.3 - - - +
236A LEU* 2.9 34.0 + - - +
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ILE* 3.9 18.8 - - + -
229A VAL* 3.0 39.9 + - + +
230A GLU* 3.6 5.2 - - - +
232A CYS* 1.3 73.4 - - - +
234A ILE* 1.3 60.5 + - - +
236A LEU* 3.4 4.1 + - + +
237A GLN* 3.0 32.2 + - - +
262A TRP* 4.0 5.6 - - + -
279A ASN* 3.4 31.9 - - - +
282A LEU* 3.9 20.4 - - + -
283A MET* 3.8 20.2 - - + +
286A LEU* 3.4 27.5 - - + +
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Residues in contact with ILE 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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191A GLN* 3.7 29.4 - - + +
230A GLU* 3.1 38.7 + - + +
231A ASP* 4.4 9.2 - - - +
232A CYS 3.5 0.2 - - - -
233A LEU* 1.3 75.7 - - - +
235A LEU* 1.3 56.6 + - - +
237A GLN* 3.2 25.1 + - - +
238A ASN* 2.9 32.8 + - - +
282A LEU* 4.1 14.1 - - + -
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Residues in contact with LEU 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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175A LEU* 5.1 0.9 - - + -
187A VAL* 4.1 13.5 - - + +
190A LEU* 3.7 54.1 - - + +
191A GLN* 3.8 10.9 - - + +
194A THR* 3.7 17.5 - - + +
204A VAL* 5.3 4.3 - - + -
209A ALA* 6.0 0.2 - - + -
213A LEU* 3.6 35.4 - - + -
231A ASP 3.1 18.2 + - - +
232A CYS 3.9 3.8 - - - +
234A ILE* 1.3 76.1 - - - +
236A LEU* 1.3 63.3 + - - +
238A ASN* 3.0 16.5 + - - +
239A LEU* 3.1 22.0 + - + +
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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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210A PHE* 3.6 35.9 - - + +
213A LEU* 3.8 24.5 - - + -
214A LEU* 4.1 17.0 - - + -
217A ILE* 3.9 22.9 - - + -
232A CYS 2.9 27.6 + - - +
233A LEU* 3.4 5.6 + - + +
235A LEU* 1.3 72.1 - - - +
237A GLN* 1.3 56.8 + - - +
239A LEU* 3.3 7.4 + - - +
240A LEU* 3.2 34.6 + - + +
250A PHE* 4.9 9.0 - - + -
262A TRP* 4.2 3.6 - - + -
286A LEU* 4.0 23.3 - - + -
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Residues in contact with GLN 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 LEU 3.0 11.9 + - - +
234A ILE* 3.5 25.3 + - - +
236A LEU* 1.3 73.4 - - - +
238A ASN* 1.3 65.7 + - - +
239A LEU 3.2 0.9 - - - -
240A LEU* 4.4 1.1 - - - +
241A LYS* 2.8 49.1 + - + +
282A LEU* 4.1 19.1 - - - +
285A GLN* 3.9 22.4 + - - +
286A LEU* 3.3 24.5 - - + +
289A VAL* 5.5 5.4 - - + +
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Residues in contact with ASN 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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191A GLN* 3.0 28.3 + - - +
194A THR* 2.9 30.7 + - - +
195A ARG* 3.7 19.1 - - - +
196A SER 5.7 0.2 - - - -
201A GLN* 3.1 28.8 + - - +
234A ILE* 2.9 24.2 + - - +
235A LEU* 3.0 10.7 + - + +
237A GLN* 1.3 80.3 + - - +
239A LEU* 1.3 59.9 + - - +
240A LEU 3.4 0.3 + - - -
241A LYS* 3.9 7.2 - - - +
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Residues in contact with LEU 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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194A THR* 4.1 16.8 - - + -
201A GLN* 3.7 22.2 - - + +
204A VAL* 3.7 23.1 - - + -
205A ALA 5.3 1.1 - - - +
209A ALA* 3.9 13.0 - - + -
210A PHE* 3.5 31.9 - - + -
213A LEU* 3.9 27.8 - - + -
235A LEU* 3.1 20.5 + - + +
236A LEU* 3.6 8.3 - - - +
237A GLN 3.2 0.4 - - - -
238A ASN* 1.3 76.2 - - - +
240A LEU* 1.3 59.1 + - - +
243A ASN* 3.5 9.3 + - - +
246A ASN* 2.9 32.8 + - - +
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Residues in contact with LEU 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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210A PHE* 3.9 12.3 - - + -
236A LEU* 3.2 25.4 + - + +
237A GLN* 4.5 2.2 - - - +
239A LEU* 1.3 80.7 - - - +
241A LYS* 1.3 65.5 + - - +
243A ASN* 3.3 9.5 + - - +
246A ASN 3.5 25.8 - - - +
247A GLN* 2.8 42.8 + - + -
250A PHE* 3.9 33.4 - - + -
259A MET* 5.8 1.3 - - + -
286A LEU* 4.5 15.9 - - + +
289A VAL* 3.9 14.4 - - + -
290A LEU* 4.1 11.4 - - + -
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Residues in contact with LYS 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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201A GLN* 4.4 4.2 + - - +
237A GLN* 2.8 30.5 + - + +
238A ASN* 3.9 10.3 - - - +
240A LEU* 1.3 78.7 - - - +
242A ASN* 1.3 87.2 + - - +
243A ASN* 3.4 3.3 + - - +
289A VAL* 4.2 26.4 - - + +
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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