Contacts of the helix formed by residues 276 - 297 (chain A) in PDB entry 5OIV
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 PRO 276 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A TRP* 3.9 7.2 - - + +
275A ARG* 1.3 93.1 - - + +
277A HIS* 1.3 66.4 + - - +
278A ALA* 4.4 5.6 - - + +
279A ASP* 3.0 39.9 + - - +
280A VAL* 3.2 10.6 + - - +
503A GOL 3.8 9.2 - - - +
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Residues in contact with HIS 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LYS* 6.3 2.0 - - - -
275A ARG 3.4 9.0 + - - -
276A PRO* 1.3 72.5 - - - +
278A ALA* 1.3 61.2 + - - +
280A VAL* 3.2 9.1 + - - +
281A LYS* 2.9 38.9 + - + +
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A PRO* 3.2 4.6 - - + +
277A HIS* 1.3 77.8 - - - +
279A ASP* 1.3 66.0 + - - +
281A LYS* 3.5 11.4 + - - +
282A ASP* 3.1 31.0 + - - +
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Residues in contact with ASP 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A TRP* 2.8 26.3 + - + +
153A MET* 3.7 23.4 - - - +
157A ARG* 4.1 3.3 + - - -
276A PRO* 3.0 20.0 + - - +
278A ALA* 1.3 78.4 - - - +
280A VAL* 1.3 66.1 + - - +
282A ASP* 3.2 5.3 + - - +
283A LEU* 2.9 28.6 + - - +
503A GOL 2.5 46.0 + - - -
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Residues in contact with VAL 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A TRP* 4.8 4.5 - - + -
267A ALA* 3.9 7.6 - - + +
270A GLY* 3.8 35.2 - - - +
271A GLU* 3.7 18.6 - - + +
275A ARG 4.6 3.4 - - - +
276A PRO 3.2 11.5 + - - +
277A HIS* 3.2 11.4 + - - +
279A ASP* 1.3 75.8 - - - +
281A LYS* 1.3 64.2 + - + +
283A LEU* 3.2 9.9 + - - +
284A TYR* 2.9 49.3 + - + -
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Residues in contact with LYS 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A HIS* 2.9 31.8 + - + +
278A ALA* 3.7 9.4 - - - +
280A VAL* 1.3 79.2 - - + +
282A ASP* 1.3 64.8 + - - +
284A TYR* 3.3 6.9 + - - +
285A LEU* 2.9 24.1 + - - +
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Residues in contact with ASP 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A MET* 4.6 1.8 - - + -
157A ARG* 4.8 12.1 + - - -
278A ALA* 3.1 23.3 + - - +
279A ASP* 3.2 7.5 + - - +
281A LYS* 1.3 77.2 - - - +
283A LEU* 1.3 57.8 + - - +
285A LEU* 3.3 14.0 + - - +
286A TRP* 2.9 63.4 + - + -
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A TRP* 3.8 18.8 - - + -
153A MET* 3.5 25.1 - - + -
156A HIS* 3.5 28.7 - - + +
263A CYS* 3.4 28.7 - - - +
266A LEU* 3.9 11.0 - - + -
267A ALA* 3.6 24.0 - - + +
279A ASP 2.9 16.7 + - - +
280A VAL* 3.6 5.6 - - - +
282A ASP* 1.3 76.4 - - - +
284A TYR* 1.3 56.8 + - - +
286A TRP* 3.3 20.2 + - + -
287A ALA* 2.8 25.3 + - - +
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Residues in contact with TYR 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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264A GLN* 3.9 26.9 - - + -
267A ALA* 3.6 16.6 - - + -
268A GLU* 3.5 15.6 + - + +
271A GLU* 2.5 33.4 + - - -
280A VAL* 2.9 42.1 + - + +
281A LYS* 3.8 5.8 - - - +
283A LEU* 1.3 76.3 - - - +
285A LEU* 1.3 62.0 + - - +
287A ALA* 3.3 4.0 + - + +
288A GLU* 3.1 23.7 + - - +
506A GOL 3.7 50.8 + - - +
334B HIS* 3.3 13.6 - + - -
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LYS 2.9 14.5 + - - +
282A ASP* 3.5 17.5 - - - +
283A LEU 3.3 0.2 - - - -
284A TYR* 1.3 77.0 - - - +
286A TRP* 1.3 63.3 + - + +
288A GLU* 3.3 20.7 + - - +
289A ARG* 2.9 55.4 + - + +
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Residues in contact with TRP 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A MET* 4.1 13.5 - - + -
156A HIS* 3.9 24.5 - - + -
157A ARG* 3.7 36.6 - - + -
160A ALA* 3.6 25.5 - - + +
161A GLU* 5.3 5.1 - - + +
259A PHE* 4.5 0.7 - + + -
263A CYS* 3.7 19.5 - - - -
282A ASP* 2.9 43.8 + - + +
283A LEU* 3.8 22.4 - - + +
285A LEU* 1.3 77.0 - - + +
287A ALA* 1.3 66.8 + - - +
289A ARG* 3.6 36.5 - - - +
290A PHE* 2.9 38.4 + + + +
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Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A SER* 2.8 44.8 + - - +
263A CYS* 3.7 3.3 - - - +
264A GLN* 3.8 24.9 - - + +
283A LEU 2.8 17.8 + - - +
284A TYR* 3.5 8.5 - - - +
286A TRP* 1.3 75.4 - - - +
288A GLU* 1.3 58.6 + - - +
291A ARG* 3.0 26.9 + - - +
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Residues in contact with GLU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A TYR 3.1 15.8 + - - +
285A LEU* 3.6 22.0 - - - +
287A ALA* 1.3 75.1 - - - +
289A ARG* 1.3 66.9 + - - +
291A ARG* 3.4 21.3 + - - +
292A ALA* 3.0 25.2 + - + +
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Residues in contact with ARG 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ALA* 4.5 13.5 + - - +
164A ASP* 3.7 18.3 + - - -
167A GLU* 3.8 47.1 + - - +
168A ARG 4.8 0.4 - - - -
169A GLY* 3.6 17.2 - - - +
285A LEU* 2.9 43.3 + - + +
286A TRP* 3.2 32.0 + - - +
288A GLU* 1.3 77.5 - - - +
290A PHE* 1.3 64.3 + - - +
292A ALA* 3.4 6.9 + - - +
293A GLY* 2.9 21.7 + - - -
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Residues in contact with PHE 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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160A ALA* 4.3 12.8 - - + -
164A ASP* 3.4 30.5 - - + -
169A GLY 3.1 31.3 - - - +
170A ARG* 3.5 11.0 - - - -
171A ILE* 3.5 23.1 - - + -
256A SER* 3.7 22.4 - - - +
259A PHE* 3.5 34.5 - + - -
260A SER* 4.0 11.4 - - - -
286A TRP* 2.9 30.3 + + + +
289A ARG* 1.3 85.0 - - + +
291A ARG* 1.3 64.6 + - - +
294A VAL* 2.9 30.5 + - - +
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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
----------------------------------------------------------
260A SER* 3.5 13.4 + - - +
264A GLN* 3.5 37.6 + - - +
287A ALA* 3.0 30.9 + - - +
288A GLU* 3.5 28.1 - - - +
290A PHE* 1.3 75.9 - - - +
292A ALA* 1.3 61.9 + - - +
294A VAL* 3.2 4.2 + - - +
295A VAL* 3.0 26.2 + - - +
329A CYS* 3.2 25.6 + - - +
330A GLY 3.3 23.8 - - - +
331A GLY* 4.1 14.6 - - - +
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Residues in contact with ALA 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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288A GLU* 3.0 19.1 + - + +
289A ARG* 3.6 6.5 - - - +
291A ARG* 1.3 76.9 - - - +
293A GLY* 1.3 58.0 + - - +
295A VAL* 3.3 6.7 + - - +
296A GLU* 3.0 29.5 + - - +
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Residues in contact with GLY 293 (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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168A ARG 3.7 16.6 - - - -
169A GLY 3.4 17.0 - - - -
170A ARG* 2.9 30.8 + - - -
289A ARG 2.9 12.1 + - - -
290A PHE 3.3 0.2 + - - -
291A ARG 3.2 0.2 - - - -
292A ALA* 1.3 77.3 - - - +
294A VAL* 1.3 60.2 + - - +
296A GLU* 3.5 6.2 + - - -
297A THR* 3.3 8.1 - - - +
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Residues in contact with VAL 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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170A ARG* 5.0 0.2 - - - -
253A VAL* 3.7 25.1 - - + +
256A SER* 3.8 9.9 - - - -
257A ALA* 3.5 31.6 - - - +
290A PHE 2.9 21.3 + - - +
291A ARG 3.2 4.0 + - - +
293A GLY* 1.3 74.1 - - - +
295A VAL* 1.3 65.5 + - + +
297A THR* 2.8 24.9 + - - -
298A THR* 3.5 3.8 - - - +
325A ALA* 4.2 3.6 - - + -
326A PRO* 3.9 28.3 - - + -
329A CYS* 3.9 17.5 - - - -
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Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ARG* 3.0 18.1 + - + +
292A ALA* 3.3 7.4 + - - +
294A VAL* 1.3 79.7 - - + +
296A GLU* 1.3 61.5 + - - +
298A THR* 2.7 30.4 + - - +
326A PRO* 5.2 1.3 - - + -
330A GLY 4.0 6.3 - - - +
331A GLY* 3.6 40.4 - - - +
332A LEU* 3.9 21.1 - - + +
333A PRO* 4.8 3.6 - - + -
336A ARG* 4.5 9.5 + - - +
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Residues in contact with GLU 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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168A ARG* 4.4 6.4 - - - +
170A ARG* 2.9 28.0 + - - +
292A ALA 3.0 17.4 + - - +
293A GLY* 3.7 6.2 - - - +
294A VAL 3.2 0.4 - - - -
295A VAL* 1.3 76.9 - - - +
297A THR* 1.3 60.4 + - - +
298A THR 3.5 1.4 + - - +
315A TRP* 4.6 4.5 - - + -
509A GOL 3.5 13.9 + - - -
513A GLY* 4.0 23.8 + - - +
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Residues in contact with THR 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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170A ARG* 3.4 23.1 - - - +
253A VAL* 3.6 5.8 - - + +
293A GLY 3.3 18.4 - - - +
294A VAL 2.8 13.8 + - - +
295A VAL 3.1 0.2 - - - -
296A GLU* 1.3 76.2 - - - +
298A THR* 1.3 58.0 + - - +
305A ALA* 3.5 8.8 - - - +
306A ARG* 3.2 44.6 + - - +
315A TRP* 3.5 20.6 - - + -
509A GOL 2.8 24.0 + - - -
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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