Contacts of the helix formed by residues 283 - 303 (chain A) in PDB entry 1WOH
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 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280A ASP* 3.1 11.4 + - - -
281A PRO 3.2 1.9 - - - -
282A THR* 1.3 79.1 + - - +
284A ARG* 1.3 62.3 + - - +
285A SER 3.2 3.3 + - - -
286A GLU* 3.5 25.2 - - - +
287A LEU* 3.3 29.5 + - - +
45B ARG* 4.1 7.2 - - - -
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Residues in contact with ARG 284 (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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236A ALA 2.8 24.4 + - - -
237A VAL 3.2 20.6 + - - +
239A PRO* 3.6 17.5 - - - +
280A ASP* 3.4 6.7 + - - +
282A THR* 2.9 42.9 + - - +
283A GLY* 1.3 76.1 - - - +
285A SER* 1.3 64.0 + - - +
287A LEU* 4.3 8.7 - - - -
288A LEU* 2.9 44.5 + - + +
235B PRO* 3.5 29.6 + - + -
236B ALA* 4.0 1.4 - - - +
239B PRO* 3.5 11.2 - - + +
244B PRO* 4.5 12.1 - - + -
284B ARG* 3.5 23.8 - - - +
282C THR* 5.8 0.8 - - - +
284C ARG* 3.5 13.9 - - - +
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Residues in contact with SER 285 (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 ILE* 3.7 21.9 - - - +
239A PRO* 3.3 10.0 - - - +
240A GLY 3.0 23.3 + - - -
275A LEU* 3.9 16.2 - - - -
280A ASP* 2.6 27.4 + - - -
283A GLY 3.2 0.6 - - - -
284A ARG* 1.3 78.3 - - - +
286A GLU* 1.3 62.9 + - - +
289A MET* 3.0 35.3 + - - +
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Residues in contact with GLU 286 (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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54A ALA* 4.0 25.7 - - + +
55A LEU* 4.1 2.0 - - - +
58A ALA* 3.2 19.0 - - + +
275A LEU* 3.9 24.5 - - + +
277A PRO* 4.1 29.5 - - - +
280A ASP 4.4 2.9 - - - +
283A GLY* 3.5 30.0 - - - +
285A SER* 1.3 78.3 - - - +
287A LEU* 1.3 70.2 + - + +
289A MET* 4.6 0.2 - - - -
290A ALA* 3.0 19.6 + - - +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ALA* 3.8 24.4 - - + +
61A ARG* 4.0 29.2 - - + -
62A SER* 5.3 1.0 + - - -
283A GLY* 3.3 19.6 + - - +
284A ARG* 3.8 4.7 - - - +
285A SER 3.3 0.6 - - - -
286A GLU* 1.3 80.6 - - + +
288A LEU* 1.3 68.3 + - + +
290A ALA* 3.5 2.6 + - - +
291A ARG* 3.2 21.3 + - - +
44B PHE* 4.0 15.3 - - + -
45B ARG* 3.7 32.1 - - - +
244B PRO* 4.0 20.6 - - + +
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Residues in contact with LEU 288 (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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237A VAL* 3.7 33.9 - - + +
238A ILE* 3.8 13.7 - - + -
251A TYR* 3.4 17.2 - - + -
284A ARG* 2.9 30.5 + - + +
287A LEU* 1.3 83.8 - - + +
289A MET* 1.3 57.1 + - - +
291A ARG* 3.3 6.2 + - - +
292A LEU 2.9 21.8 + - - -
235B PRO* 4.8 12.6 - - + -
244B PRO* 4.4 15.0 - - + +
246B PRO* 3.8 44.6 - - + -
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Residues in contact with MET 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.1 16.3 - - + +
230A VAL* 3.6 27.6 - - + -
233A PHE* 3.9 24.7 - - + -
238A ILE* 4.2 17.0 - - + -
251A TYR* 6.1 1.8 - - - -
272A LEU* 3.1 34.5 - - + -
275A LEU* 4.6 3.6 - - + -
285A SER 3.0 22.2 + - - +
286A GLU* 4.6 0.7 - - - -
288A LEU* 1.3 74.7 - - - +
290A ALA* 1.3 64.2 + - - +
292A LEU* 3.2 30.6 - - + +
293A VAL* 3.2 27.0 + - - +
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Residues in contact with ALA 290 (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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15A PHE* 4.6 3.8 - - + -
55A LEU* 3.8 16.9 - - + +
58A ALA* 3.7 19.5 - - + +
59A SER* 3.8 20.9 - - - +
62A SER* 4.9 1.3 - - - +
286A GLU 3.0 19.7 + - - +
287A LEU 3.8 2.7 - - - +
289A MET* 1.3 75.8 - - - +
291A ARG* 1.3 63.1 + - - +
293A VAL* 3.3 8.0 + - - +
294A MET* 3.1 26.5 + - - +
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Residues in contact with ARG 291 (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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62A SER* 4.0 17.2 + - - +
251A TYR* 3.0 18.2 + - - -
287A LEU 3.2 12.1 + - - +
288A LEU* 3.5 10.1 - - - +
290A ALA* 1.3 76.9 - - - +
292A LEU* 1.3 56.0 + - - +
294A MET* 3.1 3.3 + - - +
295A GLU* 2.7 58.3 + - - +
182B ARG* 5.5 0.6 - - - +
183B GLY* 3.5 22.8 - - - +
184B LEU* 3.7 31.5 - - + +
245B GLU* 3.0 31.5 + - - +
246B PRO* 3.5 30.4 + - - +
247B ASP* 5.7 0.6 + - - -
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Residues in contact with LEU 292 (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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228A VAL* 3.9 15.7 - - + -
233A PHE* 3.8 26.7 - - + -
251A TYR* 3.3 27.5 + - + +
255A MET* 3.6 27.3 - - + +
258A LEU* 4.0 13.9 - - + -
270A LEU* 6.5 0.2 - - + -
272A LEU* 4.7 1.6 - - + -
288A LEU 2.9 12.6 + - - +
289A MET* 3.2 37.0 - - + +
290A ALA 3.3 0.2 - - - -
291A ARG* 1.3 76.1 - - - +
293A VAL* 1.3 57.5 + - + +
295A GLU* 3.8 1.0 - - - +
296A THR* 2.7 39.9 + - - +
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.6 28.7 - - + -
55A LEU* 5.6 0.9 - - + -
115A VAL* 3.8 23.1 - - + -
117A LEU* 5.0 3.1 - - + -
270A LEU* 4.5 14.3 - - + +
272A LEU* 4.0 30.5 - - + -
289A MET 3.2 15.5 + - - +
290A ALA* 3.6 8.3 - - - +
291A ARG 3.2 0.2 - - - -
292A LEU* 1.3 78.9 - - + +
294A MET* 1.3 59.0 + - - +
296A THR* 3.3 6.9 + - - -
297A LEU* 3.0 36.5 + - + +
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Residues in contact with MET 294 (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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15A PHE* 3.7 30.3 - - + -
16A ALA* 4.2 6.5 - - + -
59A SER* 5.3 3.4 - - - -
62A SER* 3.5 26.5 - - - +
64A PRO* 3.6 32.8 - - + -
66A PHE* 3.9 21.5 - - + -
75A LEU* 4.1 5.4 - - + +
80A PHE* 3.7 28.0 - - + -
290A ALA 3.1 17.6 + - - +
291A ARG 3.7 5.8 - - - +
293A VAL* 1.3 77.2 - - - +
295A GLU* 1.3 62.0 - - - +
297A LEU* 3.3 7.6 + - + +
298A CYS* 3.1 26.2 + - - -
184B LEU* 4.4 2.7 - - + -
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Residues in contact with GLU 295 (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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74A ARG* 4.7 9.3 + - - +
251A TYR* 2.8 24.1 + - - +
255A MET* 3.4 30.5 - - + +
291A ARG* 2.7 45.1 + - - +
292A LEU 4.0 0.2 - - - +
294A MET* 1.3 70.6 - - - +
296A THR* 1.3 65.7 + - - +
298A CYS* 3.1 15.0 + - - +
299A GLU* 3.1 23.4 + - + +
184B LEU* 3.8 23.5 - - + +
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Residues in contact with THR 296 (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 PHE* 4.3 13.9 - - + -
255A MET* 3.4 20.0 - - - +
258A LEU* 3.5 26.3 - - + +
262A ALA* 5.5 0.2 - - + -
270A LEU* 3.8 27.5 - - + +
292A LEU* 2.7 24.9 + - - +
293A VAL* 3.6 5.1 - - - -
295A GLU* 1.3 77.2 - - - +
297A LEU* 1.3 58.9 + - + +
299A GLU* 3.1 5.9 + - + +
300A VAL* 2.8 38.1 + - + +
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Residues in contact with LEU 297 (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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15A PHE* 4.9 1.1 - - + -
31A VAL* 3.9 18.2 - - + -
75A LEU* 3.7 13.6 - - + +
80A PHE* 3.7 31.0 - - + -
113A VAL* 4.1 20.4 - - + -
115A VAL* 4.1 24.2 - - + -
270A LEU* 6.1 4.7 - - + -
293A VAL* 3.0 26.2 + - + +
294A MET* 3.6 14.6 - - - +
295A GLU 3.2 0.2 - - - -
296A THR* 1.3 75.2 - - + +
298A CYS* 1.3 66.8 + - - +
300A VAL* 4.1 7.4 - - + -
301A PHE* 2.9 34.4 + - + -
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Residues in contact with CYS 298 (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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66A PHE* 3.5 30.7 - - - -
74A ARG* 3.7 42.5 - - - +
75A LEU* 3.7 19.0 + - - +
294A MET 3.1 19.1 + - - -
295A GLU* 3.1 13.9 + - - +
297A LEU* 1.3 75.6 - - - +
299A GLU* 1.3 64.0 + - - +
301A PHE* 3.6 1.7 + - - +
302A ASP* 3.1 27.4 + - - +
184B LEU* 5.1 1.8 - - - -
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Residues in contact with GLU 299 (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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74A ARG* 3.1 23.4 + - - +
255A MET* 4.0 11.4 - - + +
259A ALA* 3.8 32.8 - - + +
262A ALA* 4.2 16.6 - - + +
295A GLU* 3.5 18.9 - - + +
296A THR* 3.1 8.9 + - + +
298A CYS* 1.3 78.3 - - - +
300A VAL* 1.3 67.6 + - - +
302A ASP* 3.1 11.7 + - - +
303A HIS* 3.2 37.0 + - - +
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Residues in contact with VAL 300 (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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113A VAL* 4.2 17.3 - - + -
226A PHE* 4.4 0.4 - - + -
262A ALA* 4.0 15.6 - - + +
267A VAL* 3.9 41.3 - - + +
296A THR* 2.8 33.1 + - + +
297A LEU* 3.2 15.9 + - + +
299A GLU* 1.3 74.4 - - - +
301A PHE* 1.3 72.2 + - + +
302A ASP 3.1 1.2 + - - -
303A HIS* 3.2 2.3 + - - +
304A VAL* 2.8 37.3 + - + +
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Residues in contact with PHE 301 (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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30A ASP* 3.9 17.7 - - + -
31A VAL* 3.5 33.0 - - + -
75A LEU* 3.9 23.8 - - + +
78A VAL* 4.0 16.4 - - + -
112A ARG* 3.6 34.5 - - - -
113A VAL* 3.9 28.7 - - + -
297A LEU* 2.9 29.5 + - + +
298A CYS 3.9 1.3 - - - +
300A VAL* 1.3 77.2 - - + +
302A ASP* 1.3 62.1 + - - +
303A HIS 3.4 0.4 - - - -
304A VAL* 3.6 17.7 + - + +
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Residues in contact with ASP 302 (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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72A LYS* 5.3 5.3 + - - -
73A THR 5.3 1.0 - - - +
74A ARG* 3.1 39.2 + - - +
75A LEU 5.4 1.0 + - - -
298A CYS 3.1 16.4 + - - +
299A GLU* 3.1 8.9 + - - +
300A VAL 3.1 1.0 - - - -
301A PHE* 1.3 79.6 - - - +
303A HIS* 1.3 78.8 + - + +
304A VAL 3.7 0.8 - - - +
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Residues in contact with HIS 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ALA 3.7 8.9 - - - +
263A ALA* 3.6 50.0 + - + +
265A ASN 5.1 1.7 - - - +
299A GLU* 3.2 30.4 + - - +
300A VAL 3.2 4.4 + - - -
302A ASP* 1.3 97.2 + - + +
304A VAL* 1.3 63.5 + - - +
305A LEU* 3.1 18.2 - - - +
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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
------------------------------------------------------------
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