Contacts of the helix formed by residues 225 - 239 (chain A) in PDB entry 3BIL
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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224A TYR* 1.3 90.0 + - - +
226A GLN* 1.3 64.7 + - - +
227A SER* 3.6 16.6 - - - +
228A VAL* 3.1 38.0 + - + +
229A GLY 3.5 3.6 + - - -
250A MET* 5.3 0.4 - - - -
251A MET* 3.6 7.4 - - - +
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Residues in contact with GLN 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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224A TYR 3.8 1.6 + - - -
225A GLU* 1.3 72.8 - - - +
227A SER* 1.3 62.9 + - - +
229A GLY* 3.2 3.3 + - - -
230A PHE* 3.0 20.8 + - - +
250A MET* 4.6 17.2 - - + +
253A ILE* 3.6 35.2 - - + +
254A GLY* 4.0 6.4 - - - +
257A GLU* 3.0 29.2 + - - +
279B PRO* 3.8 25.6 + - - +
283B LEU* 4.5 5.9 - - - +
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Residues in contact with SER 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 GLU* 3.0 13.1 - - - +
226A GLN* 1.3 79.7 - - - +
228A VAL* 1.3 58.4 + - - +
230A PHE* 3.3 12.4 + - - +
231A GLU* 2.9 40.8 + - - +
257A GLU* 5.5 0.9 - - - -
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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
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220A PHE* 4.1 10.4 - - + -
221A LEU 5.3 0.2 - - - +
222A GLY* 3.7 11.9 - - - -
223A GLY* 3.5 28.7 - - - +
224A TYR 4.7 2.0 - - - +
225A GLU* 3.1 37.8 + - + +
227A SER* 1.3 78.5 - - - +
229A GLY* 1.3 55.9 + - - +
231A GLU* 3.8 4.8 - - - +
232A GLY* 2.8 24.9 + - - -
251A MET* 4.6 1.1 - - + -
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Residues in contact with GLY 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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189A LEU* 3.7 14.2 - - - +
226A GLN 3.2 5.8 + - - -
228A VAL* 1.3 74.6 - - - +
230A PHE* 1.3 56.6 + - - +
231A GLU 3.2 0.2 - - - -
232A GLY 4.4 0.2 - - - -
233A ALA* 2.7 38.1 + - - +
251A MET* 3.3 27.1 - - - +
254A GLY* 3.7 11.2 - - - -
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Residues in contact with PHE 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 GLN 3.0 10.5 + - - +
227A SER* 3.6 14.1 - - - +
229A GLY* 1.3 77.1 - - - +
231A GLU* 1.3 75.0 + - - +
234A THR* 2.5 58.2 + - + -
254A GLY* 3.5 11.8 - - - +
257A GLU* 3.6 27.8 - - + +
258A ALA* 3.6 27.0 - - - +
261A LYS* 3.6 39.9 - - + -
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Residues in contact with GLU 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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220A PHE* 4.9 3.6 - - + -
227A SER* 2.9 23.9 + - - +
228A VAL* 3.8 4.9 - - - +
230A PHE* 1.3 94.8 - - - +
232A GLY* 1.3 68.8 + - - +
234A THR* 3.2 10.3 + - - +
235A LYS* 3.0 52.0 + - + +
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Residues in contact with GLY 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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189A LEU* 3.8 12.3 - - - -
220A PHE* 3.6 28.8 - - - -
228A VAL 2.8 19.0 + - - -
229A GLY 3.7 1.3 - - - -
231A GLU* 1.3 76.2 - - - +
233A ALA* 1.3 61.7 + - - +
235A LYS* 3.1 4.9 + - - +
236A LEU* 3.0 25.7 + - - +
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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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189A LEU* 3.8 3.4 - - + +
229A GLY 2.7 21.5 + - - +
232A GLY* 1.3 73.4 - - - +
234A THR* 1.3 61.4 + - - +
236A LEU* 3.4 12.9 + - - +
237A LEU* 3.2 27.5 + - - +
244A LEU* 4.1 10.2 - - + +
255A VAL* 4.1 24.7 - - + -
258A ALA* 3.6 22.0 - - + -
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Residues in contact with THR 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 PHE* 2.5 46.5 + - + -
231A GLU* 3.7 11.7 - - - +
233A ALA* 1.3 78.3 - - - +
235A LYS* 1.3 60.7 + - + +
237A LEU* 3.6 11.9 + - + +
238A ASP* 3.1 40.6 + - - +
258A ALA* 3.8 6.0 + - - +
262A ALA* 6.1 4.5 - - + -
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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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220A PHE* 4.7 15.3 - - + -
231A GLU* 3.0 44.2 + - + +
232A GLY* 3.1 5.1 + - - +
234A THR* 1.3 77.7 - - - +
236A LEU* 1.3 59.0 + - - +
238A ASP* 3.2 18.0 + - + +
239A GLN* 2.9 44.4 + - - +
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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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187A GLY* 3.9 16.4 - - - +
188A TYR 4.0 10.1 - - - +
189A LEU* 3.9 14.4 - - + -
218A LEU* 3.6 37.8 - - + +
219A VAL 4.4 3.8 - - - +
220A PHE* 3.7 26.2 - - + +
232A GLY 3.0 16.3 + - - +
233A ALA* 3.4 8.9 + - - +
235A LYS* 1.3 72.0 - - - +
237A LEU* 1.3 57.3 + - - +
239A GLN* 3.2 16.7 + - - +
240A GLY 3.1 6.6 + - - -
241A ALA* 2.8 33.8 + - + +
244A LEU* 3.8 13.5 - - + -
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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 3.2 22.4 + - - +
234A THR* 3.8 11.7 - - + +
236A LEU* 1.3 72.7 - - - +
238A ASP* 1.3 66.8 - - - +
240A GLY* 3.3 11.6 + - - -
241A ALA* 3.9 20.1 + - - +
244A LEU* 3.7 29.4 - - + -
258A ALA* 4.3 17.7 - - + +
259A CYS* 5.0 0.7 - - - +
262A ALA* 4.4 6.5 - - + -
264A LEU* 4.0 26.7 - - + -
270A VAL* 4.0 16.2 - - + -
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Residues in contact with ASP 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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234A THR* 3.1 26.7 + - - +
235A LYS* 3.2 21.3 + - + +
237A LEU* 1.3 79.3 - - - +
239A GLN* 1.3 58.1 + - + +
240A GLY* 3.0 6.2 + - - -
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Residues in contact with GLN 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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185A PRO* 5.6 0.7 - - - +
218A LEU* 3.8 29.6 - - + +
220A PHE* 5.8 3.4 - - - -
235A LYS* 2.9 39.6 + - - +
236A LEU* 3.2 20.5 + - - +
238A ASP* 1.3 74.6 - - + +
240A GLY* 1.3 56.7 + - - +
241A ALA 3.6 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