Contacts of the helix formed by residues 283 - 302 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280D ASP* 3.1 15.5 + - - -
281D PRO 3.1 1.4 - - - -
282D THR* 1.3 79.3 + - - +
284D ARG* 1.3 63.7 + - - +
285D SER 3.2 3.0 + - - -
286D GLU* 3.3 34.0 - - - +
287D LEU* 3.3 15.9 + - - +
45E ARG* 4.1 6.7 - - - -
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Residues in contact with ARG 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D ALA 2.8 29.7 + - - -
237D VAL* 3.4 16.2 + - - +
239D PRO* 3.5 18.0 - - - +
280D ASP* 3.5 6.5 + - - +
282D THR* 2.9 43.1 + - - +
283D GLY* 1.3 77.7 - - - +
285D SER* 1.3 60.5 + - - +
287D LEU* 3.2 9.8 + - - -
288D LEU* 2.8 45.6 + - + +
235E PRO* 3.5 30.7 + - + -
236E ALA* 4.0 1.2 - - - +
239E PRO* 3.5 12.1 - - + +
244E PRO* 4.6 10.3 - - + -
284E ARG* 3.5 23.3 - - - +
282F THR* 5.8 0.8 - - - +
284F ARG* 3.5 13.9 - - - +
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Residues in contact with SER 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D ILE* 3.6 24.9 - - - +
239D PRO* 3.3 9.2 - - - +
240D GLY* 3.0 24.2 + - - -
275D LEU* 3.8 17.0 - - - -
280D ASP* 2.6 28.2 + - - -
283D GLY 3.2 0.2 - - - -
284D ARG* 1.3 78.0 - - - +
286D GLU* 1.3 63.0 + - - +
288D LEU* 3.9 1.4 - - - +
289D MET* 3.0 32.2 + - - +
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Residues in contact with GLU 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D ALA* 4.0 23.6 - - + +
55D LEU* 3.9 2.5 - - + +
58D ALA* 3.3 11.0 - - + +
275D LEU* 3.9 24.0 - - + +
277D PRO* 4.0 30.6 - - - +
280D ASP* 4.4 3.8 - - - +
283D GLY* 3.3 29.1 - - - +
285D SER* 1.3 79.8 - - - +
287D LEU* 1.3 69.8 + - + +
289D MET 4.5 0.2 - - - +
290D ALA* 2.9 27.9 + - - +
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Residues in contact with LEU 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D ALA* 3.8 23.2 - - + +
61D ARG* 3.9 28.2 - - + +
62D SER* 5.3 0.9 + - - -
283D GLY 3.3 15.2 + - - +
284D ARG* 3.2 7.3 + - - +
286D GLU* 1.3 80.9 - - + +
288D LEU* 1.3 67.2 + - + +
290D ALA* 3.5 2.4 + - - +
291D ARG* 3.2 22.0 + - - +
44E PHE* 4.0 15.0 - - + -
45E ARG* 3.6 33.2 - - - +
244E PRO* 3.7 22.0 - - + +
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Residues in contact with LEU 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D VAL* 3.8 31.6 - - + +
238D ILE* 3.8 14.4 - - + -
251D TYR* 3.3 17.9 - - + -
284D ARG* 2.8 34.0 + - + +
287D LEU* 1.3 82.2 - - + +
289D MET* 1.3 59.4 + - - +
291D ARG* 3.4 5.0 + - - +
292D LEU* 3.0 21.1 + - - +
235E PRO* 4.8 11.9 - - + -
244E PRO* 4.6 13.0 - - + +
246E PRO* 3.7 47.3 - - + -
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Residues in contact with MET 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LEU* 4.1 14.0 - - + +
230D VAL* 3.3 36.3 - - + -
233D PHE* 3.8 24.7 - - + -
238D ILE* 3.1 53.6 - - + -
251D TYR* 6.1 2.0 - - - -
272D LEU* 3.5 19.7 - - + -
275D LEU* 4.7 2.9 - - + -
285D SER 3.0 18.8 + - - +
286D GLU* 4.6 0.4 - - - -
288D LEU* 1.3 76.5 - - - +
290D ALA* 1.3 64.5 + - - +
292D LEU* 3.4 13.6 + - - +
293D VAL* 3.3 26.5 + - - +
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Residues in contact with ALA 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D PHE* 4.6 4.2 - - + -
55D LEU* 3.8 15.8 - - + +
58D ALA* 3.7 20.9 - - + +
59D SER* 3.7 20.6 - - - +
62D SER* 5.0 1.3 - - - +
286D GLU 2.9 18.2 + - - +
287D LEU 3.8 3.4 - - - +
289D MET* 1.3 76.8 - - - +
291D ARG* 1.3 64.0 - - - +
293D VAL* 3.3 7.5 + - - +
294D MET* 3.2 26.8 + - - +
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Residues in contact with ARG 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D SER* 4.0 18.3 + - - +
251D TYR* 3.0 22.7 + - - +
287D LEU 3.2 11.3 + - - +
288D LEU* 3.7 8.7 - - - +
289D MET 3.3 0.2 - - - -
290D ALA* 1.3 79.0 - - - +
292D LEU* 1.3 54.6 + - - +
294D MET* 3.2 3.7 + - - +
295D GLU* 2.7 56.6 + - - +
182E ARG* 5.4 1.0 - - - +
183E GLY* 3.5 16.9 - - - +
184E LEU* 3.7 31.1 - - + +
245E GLU* 2.7 50.2 + - - +
246E PRO* 3.5 21.4 + - - +
247E ASP* 5.8 0.4 + - - -
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Residues in contact with LEU 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D VAL* 3.9 19.5 - - + -
233D PHE* 3.5 39.0 - - + -
251D TYR* 3.4 22.2 + - + -
255D MET* 3.5 30.1 - - + +
258D LEU* 4.2 16.2 - - + -
272D LEU* 4.5 5.2 - - + -
288D LEU 3.0 13.8 + - - +
289D MET* 3.5 18.8 - - - +
290D ALA 3.2 0.2 - - - -
291D ARG* 1.3 77.1 - - - +
293D VAL* 1.3 54.6 + - + +
295D GLU* 3.7 1.3 - - - +
296D THR* 2.8 38.3 + - - +
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Residues in contact with VAL 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PHE* 3.5 29.2 - - + -
55D LEU* 5.6 1.3 - - + -
115D VAL* 3.7 24.5 - - + -
117D LEU* 5.0 3.8 - - + -
270D LEU* 4.6 12.5 - - + +
272D LEU* 4.0 30.5 - - + -
289D MET 3.3 15.1 + - - +
290D ALA* 3.7 8.3 - - - +
291D ARG 3.3 0.4 - - - -
292D LEU* 1.3 75.4 - - + +
294D MET* 1.3 57.7 + - - +
296D THR* 3.3 6.5 + - - -
297D LEU* 3.0 40.0 + - + +
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Residues in contact with MET 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D PHE* 3.6 31.2 - - + -
16D ALA* 4.2 7.0 - - + -
59D SER* 5.2 3.6 - - - -
62D SER* 3.6 25.4 - - - +
64D PRO* 3.6 36.1 - - + -
66D PHE* 3.7 22.4 - - + -
75D LEU* 4.0 4.3 - - + +
80D PHE* 3.9 16.2 - - + -
290D ALA 3.2 14.2 + - - +
291D ARG* 3.7 5.8 - - - +
293D VAL* 1.3 77.0 - - - +
295D GLU* 1.3 56.3 + - - +
297D LEU* 3.2 12.5 + - + +
298D CYS* 3.0 30.7 + - - -
184E LEU* 4.5 2.2 - - + -
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Residues in contact with GLU 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D ARG* 4.7 7.9 + - - +
251D TYR* 2.6 30.2 + - - +
255D MET* 3.4 29.9 - - + +
291D ARG* 2.7 40.5 + - - +
292D LEU 3.9 2.0 - - - +
294D MET* 1.3 70.8 - - - +
296D THR* 1.3 67.5 + - - +
298D CYS* 3.1 8.0 + - - +
299D GLU* 3.1 29.2 + - + +
184E LEU* 3.8 28.0 - - + +
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Residues in contact with THR 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D PHE* 4.3 14.4 - - + -
255D MET* 3.3 19.9 - - + +
258D LEU* 3.5 26.7 - - + +
262D ALA* 5.2 0.7 - - + -
270D LEU* 3.9 27.5 - - + +
292D LEU* 2.8 26.0 + - - +
293D VAL* 3.6 5.3 - - - -
295D GLU* 1.3 76.1 - - - +
297D LEU* 1.3 60.1 + - + +
299D GLU* 3.1 4.7 + - - +
300D VAL* 2.8 42.2 + - + +
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Residues in contact with LEU 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D PHE* 4.8 1.6 - - + -
31D VAL* 4.0 16.2 - - + -
75D LEU* 3.6 14.0 - - + +
80D PHE* 3.5 31.2 - - + -
113D VAL* 4.1 20.0 - - + -
115D VAL* 4.1 17.9 - - + -
270D LEU* 6.1 4.3 - - + -
293D VAL* 3.0 34.0 + - + +
294D MET* 3.4 19.7 - - - +
295D GLU 3.2 0.2 - - - -
296D THR* 1.3 74.8 - - + +
298D CYS* 1.3 64.9 + - - +
300D VAL* 4.1 8.1 - - + -
301D PHE* 3.0 34.0 + - + -
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Residues in contact with CYS 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D PHE* 3.5 32.5 - - - -
74D ARG* 3.7 42.6 - - - +
75D LEU* 3.5 21.7 - - - +
294D MET 3.0 12.7 + - - -
295D GLU* 3.1 14.3 + - - +
297D LEU* 1.3 77.6 - - - +
299D GLU* 1.3 63.0 + - - +
301D PHE* 3.6 1.6 + - - +
302D ASP* 3.3 28.7 + - - +
184E LEU* 5.1 1.8 - - - -
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Residues in contact with GLU 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D ARG* 3.0 23.3 + - - -
255D MET* 4.0 9.4 - - + +
259D ALA* 3.8 34.4 - - + +
262D ALA* 4.2 17.1 - - + +
263D ALA* 5.7 0.2 - - - +
295D GLU* 3.1 19.8 + - + +
296D THR* 3.3 7.6 - - - +
298D CYS* 1.3 79.9 - - - +
300D VAL* 1.3 63.2 + - - +
302D ASP* 3.3 5.9 + - - +
303D HIS* 3.0 40.2 + - - +
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Residues in contact with VAL 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D VAL* 4.1 17.0 - - + -
226D PHE* 4.8 0.2 - - + -
262D ALA* 3.9 23.1 - - + +
267D VAL* 4.0 35.2 - - + +
296D THR* 2.8 33.1 + - + +
297D LEU* 3.1 15.0 + - + +
299D GLU* 1.3 72.2 - - - +
301D PHE* 1.3 70.9 + - + +
302D ASP 3.1 4.3 + - - -
303D HIS* 3.2 16.8 + - - +
304D VAL* 3.3 15.0 - - + +
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Residues in contact with PHE 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ASP* 3.6 26.2 - - + -
31D VAL* 3.5 32.5 - - + -
75D LEU* 4.1 19.1 - - + +
78D VAL* 3.9 20.2 - - + -
112D ARG* 3.6 29.8 - - - -
113D VAL* 3.9 23.8 - - + -
297D LEU* 3.0 25.4 + - + +
298D CYS 4.5 0.4 - - - +
300D VAL* 1.3 77.2 - - + +
302D ASP* 1.3 62.1 + - - +
303D HIS 3.2 5.1 + - - -
304D VAL* 3.4 24.4 + - + +
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Residues in contact with ASP 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D LYS* 5.3 5.0 + - - -
73D THR 5.2 0.7 - - - +
74D ARG* 3.2 40.4 + - - +
75D LEU 4.9 2.8 + - - -
298D CYS 3.3 18.5 + - - +
299D GLU* 3.3 4.3 + - - +
300D VAL 3.1 1.8 - - - -
301D PHE* 1.3 79.8 - - - +
303D HIS* 1.3 83.5 + - + +
304D VAL 3.8 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
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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