Contacts of the helix formed by residues 230 - 247 (chain A) in PDB entry 2V5Q
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 PHE 230 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A HIS* 3.3 70.8 - + + +
171A ARG* 3.9 20.2 - - + -
172A VAL 4.2 0.7 - - - -
173A ILE* 3.7 16.3 - - + +
201A VAL* 3.5 39.9 - - + -
229A SER* 1.3 96.0 + - - +
231A GLU* 1.3 64.8 + - + +
232A VAL 3.1 1.6 + - - -
233A ASP* 3.1 12.4 + - - +
234A VAL* 3.9 1.8 + - - +
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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
----------------------------------------------------------
207A ARG* 5.3 4.0 - - - -
221A GLU* 4.1 1.4 - - - +
229A SER* 3.4 29.5 + - - -
230A PHE* 1.3 80.1 - - + +
232A VAL* 1.3 60.6 + - - +
233A ASP 3.2 0.4 - - - -
234A VAL* 3.3 12.2 + - + +
235A TRP 3.1 11.6 + - - -
290A PRO* 3.4 39.4 - - + +
291A THR* 4.9 8.2 + - - +
293A ARG* 2.9 33.8 + - + +
294A PRO 6.1 1.1 - - - +
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ILE* 3.6 18.6 - - + -
175A ARG* 4.0 18.6 - - + -
217A TYR 5.7 0.2 - - - +
219A ALA* 3.9 16.2 - - + +
221A GLU* 3.5 17.7 - - - +
222A VAL* 4.0 8.5 - - + -
228A HIS* 3.6 31.2 - - + -
229A SER 3.1 12.3 + - - +
230A PHE 3.1 2.0 + - - -
231A GLU* 1.3 77.5 - - - +
233A ASP* 1.3 65.2 + - - +
235A TRP* 3.3 7.6 + - - +
236A SER* 3.1 26.5 + - - -
293A ARG* 4.3 2.0 - - - +
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Residues in contact with ASP 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A CYS* 3.8 10.8 - - - -
167A LEU* 5.2 0.2 - - - +
168A HIS* 2.8 36.8 + - + +
173A ILE* 3.5 8.1 - - - +
174A HIS* 2.9 29.6 + - - +
175A ARG* 2.8 29.3 + - - -
176A ASP 4.5 0.2 + - - -
177A LEU* 4.0 8.2 - - + +
230A PHE 3.1 3.2 + - - +
232A VAL* 1.3 74.1 - - - +
234A VAL* 1.3 61.0 + - - +
236A SER* 3.0 8.7 + - - -
237A ILE* 2.9 34.7 + - - +
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Residues in contact with VAL 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A HIS* 4.9 2.9 - - + -
230A PHE 4.6 6.7 - - - +
231A GLU* 3.3 15.4 + - + +
233A ASP* 1.3 75.6 - - - +
235A TRP* 1.3 58.5 + - - +
237A ILE* 3.3 5.6 + - - +
238A GLY 2.9 23.4 + - - -
285A MET* 3.6 31.9 - - + +
293A ARG* 4.1 15.7 - - + -
294A PRO* 3.6 28.7 - - + +
295A THR* 4.4 1.3 - - - -
296A ILE* 4.3 29.8 - - + +
299A LEU* 4.5 4.9 - - + -
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Residues in contact with TRP 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 4.3 8.7 - - + +
218A ILE 3.5 12.1 + - - -
219A ALA* 3.7 20.4 - - + -
220A PRO* 3.5 32.5 - - + -
231A GLU 3.1 5.9 + - - -
232A VAL 3.3 9.2 + - - +
234A VAL* 1.3 76.3 - - - +
236A SER* 1.3 60.9 + - - +
238A GLY* 3.1 4.2 + - - -
239A CYS* 3.0 37.0 + - - -
251A PHE* 3.3 41.0 - + - -
263A ILE* 4.0 16.6 - - + +
266A ASN* 4.1 8.5 - - - -
285A MET 3.9 11.7 - - - -
286A LEU* 3.5 30.9 - - + +
287A GLN 3.7 16.8 - - - -
293A ARG* 3.7 24.6 - - - +
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Residues in contact with SER 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ARG 6.2 1.1 - - - -
176A ASP* 6.0 0.9 - - - -
177A LEU* 3.2 41.8 + - - +
217A TYR* 4.0 19.5 - - - -
232A VAL 3.1 11.2 + - - -
233A ASP* 3.0 17.3 + - - -
235A TRP* 1.3 78.8 - - - +
237A ILE* 1.3 58.9 + - - +
239A CYS* 3.2 2.9 + - - +
240A ILE* 2.9 35.8 + - - +
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Residues in contact with ILE 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 4.4 14.8 - - + -
160A ILE* 4.2 17.5 - - + -
161A VAL* 4.3 14.6 - - + -
164A CYS* 4.0 18.2 - - + -
177A LEU* 3.8 13.7 - - + -
233A ASP 2.9 23.3 + - - +
234A VAL 3.8 4.5 - - - +
236A SER* 1.3 76.4 - - - +
238A GLY* 1.3 52.1 + - - +
240A ILE* 3.4 8.4 + - + +
241A MET* 2.7 32.8 + - - +
285A MET* 4.0 15.5 - - + -
296A ILE* 3.7 30.1 - - + -
299A LEU* 4.1 10.3 - - + -
305A PHE* 6.2 0.7 - - + -
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Residues in contact with GLY 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A VAL 2.9 12.1 + - - -
235A TRP 3.1 5.6 + - - -
237A ILE* 1.3 76.6 - - - +
239A CYS* 1.3 55.2 + - - +
241A MET* 3.4 1.9 + - - +
242A TYR* 2.9 29.5 + - - +
282A ILE* 4.5 4.0 - - - +
285A MET* 3.5 31.9 - - - -
286A LEU* 4.0 14.0 - - - +
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Residues in contact with CYS 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 3.6 34.8 - - + -
235A TRP* 3.0 42.2 + - - -
236A SER 3.2 6.7 + - - +
238A GLY* 1.3 72.7 - - - +
240A ILE* 1.3 59.2 + - - +
242A TYR* 3.4 3.1 + - - +
243A THR* 2.8 36.9 + - - -
250A PRO* 3.8 24.7 - - + +
251A PHE* 4.4 6.1 - - - -
286A LEU* 3.9 7.6 - - - -
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Residues in contact with ILE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 5.0 0.2 - - + -
157A LEU* 4.2 9.2 - - + -
160A ILE* 4.4 5.2 - - + -
177A LEU* 3.9 25.4 - - + -
178A LYS* 4.4 5.2 - - - -
179A LEU* 4.2 16.6 - - + +
182A LEU* 3.8 28.3 - - + -
217A TYR* 3.8 17.5 - - + +
236A SER 2.9 26.5 + - - +
237A ILE* 3.6 12.3 - - + +
239A CYS* 1.3 73.0 - - - +
241A MET* 1.3 67.8 + - - +
243A THR* 3.0 6.7 + - - +
244A LEU* 2.8 44.9 + - + +
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Residues in contact with MET 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 3.6 31.2 - - + +
237A ILE* 2.7 21.6 + - - +
238A GLY 3.6 4.9 - - - +
240A ILE* 1.3 72.9 - - - +
242A TYR* 1.3 63.9 + - - +
244A LEU* 3.4 1.5 + - - +
245A LEU* 3.1 30.8 + - + +
278A ALA* 3.7 44.2 - - + +
281A LEU* 3.8 17.3 - - + -
282A ILE* 3.8 11.0 - - + -
285A MET* 3.7 24.0 - - + -
304A PHE* 3.8 23.1 - - + -
305A PHE* 5.6 1.3 - - - -
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Residues in contact with TYR 242 (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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238A GLY 2.9 18.3 + - - +
239A CYS 3.5 4.7 - - - +
241A MET* 1.3 76.8 - - - +
243A THR* 1.3 54.0 + - - +
245A LEU* 4.9 0.2 - - - -
246A VAL* 2.8 69.3 + - + +
248A LYS* 3.1 31.1 - - + +
249A PRO 3.8 2.9 + - - -
250A PRO* 3.6 40.3 + - + +
268A TYR* 4.3 6.3 - + - -
269A SER 2.5 33.6 + - - -
270A ILE* 4.1 13.7 - - + -
271A PRO* 4.1 1.2 - - - +
282A ILE* 4.1 31.8 - - + +
286A LEU* 4.8 0.7 - - + -
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Residues in contact with THR 243 (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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142A HIS* 3.6 31.2 + - + +
146A LYS 4.7 0.5 - - - +
179A LEU* 3.9 19.7 - - + -
217A TYR* 3.8 12.3 + - - +
239A CYS 2.8 24.9 + - - -
240A ILE* 3.0 7.8 + - - -
242A TYR* 1.3 73.4 - - - +
244A LEU* 1.3 58.5 + - - +
247A GLY* 2.9 25.5 + - - -
248A LYS 3.7 16.8 - - - -
249A PRO* 3.5 21.4 - - + +
250A PRO* 3.8 0.5 - - - +
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Residues in contact with LEU 244 (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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138A LEU* 4.5 13.5 - - + -
141A LEU* 5.4 2.5 - - + -
142A HIS* 5.5 7.2 - - + +
146A LYS 5.1 2.5 - - - +
147A ALA* 3.5 2.3 - - - -
148A LEU* 2.8 51.5 + - + +
153A ALA* 4.3 20.0 - - + -
156A TYR* 4.5 13.9 - - + -
157A LEU* 4.0 33.9 - - + -
179A LEU* 3.8 26.7 - - + -
240A ILE* 2.8 27.8 + - + +
241A MET* 3.9 3.6 - - - +
243A THR* 1.3 71.9 - - + +
245A LEU* 1.3 60.8 + - - +
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Residues in contact with LEU 245 (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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147A ALA* 3.5 11.7 - - - +
148A LEU 4.5 6.1 - - - +
149A THR 4.8 0.7 - - - +
150A GLU* 3.9 28.9 - - + +
153A ALA* 3.7 26.7 - - + -
241A MET* 3.1 36.0 + - + +
242A TYR* 4.1 2.0 - - - +
244A LEU* 1.3 80.4 - - - +
246A VAL* 1.3 62.3 + - + +
273A HIS* 4.4 4.5 + - - -
274A ILE* 3.6 27.4 - - + +
278A ALA* 3.7 29.2 - - + -
282A ILE* 4.2 9.9 - - + -
304A PHE* 4.9 2.2 - - + -
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Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ALA* 3.8 8.3 - - - +
242A TYR* 2.8 60.2 + - + +
245A LEU* 1.3 76.0 - - + +
247A GLY* 1.3 55.6 + - - +
248A LYS* 4.0 17.2 - - + +
270A ILE* 5.3 1.3 - - + -
271A PRO* 3.6 40.8 - - + -
273A HIS* 5.1 7.3 + - + -
274A ILE* 4.0 13.0 - - + -
282A ILE* 5.5 1.6 - - + -
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Residues in contact with GLY 247 (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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142A HIS* 3.3 20.3 + - - -
146A LYS* 3.9 16.2 + - - +
147A ALA 3.5 23.8 - - - -
243A THR 2.9 15.6 + - - -
245A LEU 3.7 1.0 - - - -
246A VAL* 1.3 77.5 - - - +
248A LYS* 1.3 61.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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