Contacts of the helix formed by residues 283 - 302 (chain B) in PDB entry 1WOI
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B ASP 3.0 11.3 + - - -
281B PRO 3.1 1.6 - - - -
282B THR* 1.3 77.6 + - - +
284B ARG* 1.3 62.1 + - - +
285B SER 3.3 2.7 - - - -
286B GLU* 3.3 37.8 - - - +
287B LEU* 3.4 18.2 - - - +
45C ARG* 4.1 6.7 - - - -
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Residues in contact with ARG 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ARG* 3.4 24.2 - - - +
236B ALA 2.9 29.9 + - - -
237B VAL 3.4 15.1 + - - +
239B PRO* 3.6 17.7 - - - +
280B ASP* 3.3 9.3 + - - +
282B THR* 2.9 37.6 + - - +
283B GLY* 1.3 76.2 - - - +
285B SER* 1.3 68.4 + - - +
287B LEU* 4.4 8.7 - - - -
288B LEU* 2.9 38.5 + - + +
235C PRO* 3.6 31.2 + - + -
236C ALA* 4.0 1.2 - - - +
239C PRO* 3.5 16.9 - - + +
244C PRO* 4.6 11.0 - - + -
284C ARG* 3.4 12.4 - - - +
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Residues in contact with SER 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ILE* 3.7 22.3 - - - +
239B PRO* 3.2 10.4 - - - +
240B GLY 3.0 23.0 + - - -
275B LEU* 3.9 15.7 - - - -
277B PRO* 6.0 0.2 - - - -
280B ASP* 2.6 26.6 + - - -
283B GLY 3.3 0.4 - - - -
284B ARG* 1.3 78.6 - - - +
286B GLU* 1.3 67.0 + - - +
288B LEU* 3.9 1.0 - - - +
289B MET* 3.0 30.7 + - - +
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Residues in contact with GLU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ALA* 4.0 24.2 - - + +
55B LEU* 4.1 2.1 - - - +
58B ALA* 3.3 10.0 - - + +
275B LEU* 4.0 25.2 - - + +
277B PRO* 3.8 27.5 - - - +
280B ASP* 4.2 5.4 - - - +
283B GLY* 3.3 31.1 - - - +
285B SER* 1.3 80.0 + - - +
287B LEU* 1.3 62.4 + - + +
289B MET* 4.6 1.1 - - - -
290B ALA* 2.9 33.6 + - - +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ALA* 3.8 23.2 - - + +
61B ARG* 3.7 31.5 - - + +
62B SER* 5.2 1.2 + - - -
283B GLY 3.4 18.3 + - - +
284B ARG* 3.8 4.5 - - - +
285B SER 3.3 0.6 - - - -
286B GLU* 1.3 81.6 - - + +
288B LEU* 1.3 67.3 + - + +
290B ALA* 3.6 2.3 + - - +
291B ARG* 3.2 21.7 + - - +
44C PHE* 4.1 18.4 - - + -
45C ARG* 3.9 15.3 - - - +
244C PRO* 3.8 35.4 - - + +
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B VAL* 3.7 36.3 - - + +
238B ILE* 3.8 15.0 - - + -
251B TYR* 3.3 17.8 - - + -
284B ARG* 2.9 29.1 + - + +
287B LEU* 1.3 84.4 - - + +
289B MET* 1.3 59.5 + - - +
291B ARG* 3.3 5.1 + - - +
292B LEU 2.9 21.3 + - - -
235C PRO* 4.7 14.4 - - + -
244C PRO* 4.5 11.2 - - + +
246C PRO* 3.7 44.0 - - + -
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Residues in contact with MET 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 4.0 16.4 - - + -
230B VAL* 3.5 28.9 - - + -
233B PHE* 3.9 24.2 - - + -
238B ILE* 4.3 17.9 - - + -
251B TYR* 6.0 2.0 - - - -
272B LEU* 3.1 26.9 - - + -
275B LEU* 4.7 3.4 - - + -
285B SER 3.0 21.2 + - - +
286B GLU* 4.6 0.7 - - - -
288B LEU* 1.3 74.8 - - - +
290B ALA* 1.3 68.1 + - - +
292B LEU* 3.1 38.8 + - + +
293B VAL* 3.2 27.4 + - - +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PHE* 4.7 4.7 - - + -
55B LEU* 3.8 17.0 - - + +
58B ALA* 3.7 21.5 - - + +
59B SER* 3.7 20.6 - - - +
62B SER* 4.9 1.3 - - - +
286B GLU 2.9 18.5 + - - +
287B LEU 3.9 2.5 - - - +
289B MET* 1.3 76.6 - - - +
291B ARG* 1.3 63.0 + - - +
293B VAL* 3.3 7.6 + - - +
294B MET* 3.2 27.3 + - - +
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B SER* 4.0 16.7 + - - +
251B TYR* 3.0 21.2 + - - +
287B LEU 3.2 12.4 + - - +
288B LEU* 3.5 9.2 - - - +
290B ALA* 1.3 78.4 - - - +
292B LEU* 1.3 58.9 + - - +
294B MET* 3.2 3.8 + - - +
295B GLU* 2.8 51.4 + - - +
182C ARG* 5.4 1.2 - - - +
183C GLY* 3.4 19.7 - - - +
184C LEU* 3.8 27.6 - - + +
245C GLU* 2.7 50.4 + - - +
246C PRO* 3.6 22.8 + - - +
247C ASP* 5.8 0.2 + - - -
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B VAL* 3.9 9.6 - - + -
233B PHE* 3.7 29.4 - - + -
251B TYR* 3.3 26.5 - - + -
255B MET* 3.6 26.6 - - + +
258B LEU* 3.9 22.9 - - + -
272B LEU* 4.5 2.9 - - + -
288B LEU 2.9 12.2 + - - +
289B MET* 3.1 37.4 + - + +
291B ARG* 1.3 77.4 - - - +
293B VAL* 1.3 57.3 + - + +
295B GLU* 3.8 1.2 - - - +
296B THR* 2.8 34.9 + - - +
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.6 29.6 - - + -
55B LEU* 5.5 1.3 - - + -
115B VAL* 3.7 22.7 - - + -
117B LEU* 5.1 3.1 - - + -
270B LEU* 4.4 15.4 - - + +
272B LEU* 4.0 32.3 - - + -
289B MET 3.2 13.8 + - - +
290B ALA* 3.6 8.3 - - - +
292B LEU* 1.3 77.7 - - + +
294B MET* 1.3 62.4 + - - +
296B THR* 3.3 6.9 + - - -
297B LEU* 3.0 34.2 + - + +
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Residues in contact with MET 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.7 30.7 - - + -
16B ALA* 4.3 7.4 - - - -
59B SER* 5.3 3.4 - - - -
62B SER* 3.5 25.6 - - - +
64B PRO* 3.7 29.2 - - + -
66B PHE* 3.9 22.9 - - + -
75B LEU* 4.0 5.2 - - + +
80B PHE* 3.8 22.7 - - + -
290B ALA 3.2 14.8 + - - +
291B ARG 3.7 5.6 - - - +
293B VAL* 1.3 76.8 - - - +
295B GLU* 1.3 57.9 + - - +
297B LEU* 3.2 11.5 + - + +
298B CYS* 3.0 31.5 + - - -
184C LEU* 4.3 2.2 - - + -
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Residues in contact with GLU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ARG* 4.9 7.1 + - - +
251B TYR* 2.7 21.9 + - - +
255B MET* 3.3 30.7 - - + +
291B ARG* 2.8 40.0 + - - +
292B LEU 3.8 3.1 - - - +
294B MET* 1.3 70.6 - - - +
296B THR* 1.3 65.3 + - - +
298B CYS* 3.1 8.8 + - - +
299B GLU* 3.1 32.0 + - - +
184C LEU* 3.8 26.2 - - + +
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Residues in contact with THR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B PHE* 4.2 21.1 - - + -
255B MET* 3.4 18.9 - - - +
258B LEU* 3.6 22.8 - - + +
262B ALA* 5.2 2.2 - - + -
270B LEU* 3.8 27.5 - - + +
292B LEU* 2.8 24.0 + - - +
293B VAL* 3.5 6.2 - - - -
294B MET 3.3 0.2 - - - -
295B GLU* 1.3 76.6 - - - +
297B LEU* 1.3 60.0 + - + +
299B GLU* 3.1 5.7 + - - +
300B VAL* 2.9 32.3 + - + +
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PHE* 4.8 1.3 - - + -
31B VAL* 3.9 11.4 - - + -
75B LEU* 3.6 14.9 - - + +
80B PHE* 3.8 28.5 - - + -
113B VAL* 4.2 20.0 - - + -
115B VAL* 4.3 10.5 - - + -
270B LEU* 6.2 4.0 - - + -
293B VAL* 3.0 30.7 + - + +
294B MET* 3.4 19.5 - - - +
296B THR* 1.3 76.5 - - + +
298B CYS* 1.3 64.0 + - - +
300B VAL* 4.2 7.0 - - + -
301B PHE* 3.0 47.7 + - + -
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Residues in contact with CYS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B PHE* 3.5 32.1 - - - -
74B ARG* 3.7 41.8 - - + +
75B LEU* 3.6 18.2 + - - +
294B MET 3.0 19.5 + - - -
295B GLU* 3.3 13.7 - - - +
297B LEU* 1.3 76.1 - - - +
299B GLU* 1.3 60.6 + - - +
301B PHE* 4.0 0.7 - - - +
302B ASP* 3.0 31.1 + - - +
184C LEU* 5.0 2.5 - - - -
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ARG* 3.2 22.5 + - - -
255B MET* 4.0 9.5 - - + +
259B ALA* 3.9 32.2 - - + +
262B ALA* 3.8 19.1 - - + +
295B GLU* 3.4 20.7 - - - +
296B THR* 3.1 7.8 + - - +
298B CYS* 1.3 75.6 - - - +
300B VAL* 1.3 65.6 + - - +
302B ASP* 3.3 5.0 + - - +
303B HIS* 3.0 43.0 + - - +
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 4.4 12.1 - - + -
226B PHE* 4.6 0.2 - - + -
262B ALA* 3.9 16.5 - - + +
267B VAL* 3.8 43.3 - - + +
296B THR* 2.9 28.6 + - + +
297B LEU* 3.2 13.4 + - + +
299B GLU* 1.3 79.7 - - - +
301B PHE* 1.3 79.7 + - + +
302B ASP 3.3 0.3 + - - -
303B HIS* 3.3 11.3 + - - +
304B VAL* 3.6 11.7 + - + +
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Residues in contact with PHE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ASP* 3.8 25.1 - - + -
31B VAL* 3.4 33.4 - - + -
75B LEU* 4.1 18.6 - - + +
78B VAL* 3.7 22.4 - - + -
112B ARG* 3.9 22.7 - - - -
113B VAL* 3.8 27.1 - - + -
297B LEU* 3.0 28.8 + - + +
298B CYS 4.6 0.4 - - - +
300B VAL* 1.3 81.4 - - + +
302B ASP* 1.3 57.9 + - - +
303B HIS 3.2 3.8 - - - -
304B VAL* 3.3 28.0 + - + +
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Residues in contact with ASP 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LYS* 4.8 8.9 + - - -
73B THR 5.1 1.6 - - - +
74B ARG* 3.2 37.8 + - - +
298B CYS 3.0 18.2 + - - +
299B GLU* 3.7 3.1 - - - +
300B VAL 3.2 1.0 - - - -
301B PHE* 1.3 77.7 - - - +
303B HIS* 1.3 82.2 + - + +
304B VAL 3.7 0.7 - - - -
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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