Contacts of the helix formed by residues 276 - 297 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B TRP* 4.0 4.7 - - + +
274B LYS 4.7 0.7 - - - +
275B ARG* 1.3 98.9 - - + +
277B HIS* 1.3 67.0 + - - +
278B ALA* 4.5 5.4 - - + +
279B ASP* 3.1 39.3 + - - +
280B VAL* 3.2 11.4 + - - +
501B GOL 4.1 7.6 - - - +
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Residues in contact with HIS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ARG 3.4 3.7 + - - -
276B PRO* 1.3 72.3 - - - +
278B ALA* 1.3 61.5 + - + +
280B VAL* 3.3 10.0 + - - +
281B LYS* 2.9 51.3 + - + +
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B PRO* 3.2 4.8 - - + +
277B HIS* 1.3 86.1 - - + +
279B ASP* 1.3 63.9 + - - +
281B LYS* 3.5 7.7 + - - +
282B ASP* 3.1 30.9 + - - +
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Residues in contact with ASP 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B TRP* 2.8 25.0 + - + +
153B MET* 3.7 24.8 - - - +
157B ARG* 4.0 3.1 + - - -
276B PRO* 3.1 20.0 + - - +
278B ALA* 1.3 78.3 - - - +
280B VAL* 1.3 67.1 + - - +
282B ASP* 3.2 4.9 + - - +
283B LEU* 2.9 28.5 + - - +
501B GOL 2.5 45.9 + - - -
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B TRP* 4.8 4.5 - - + -
267B ALA* 4.0 6.3 - - + +
270B GLY* 3.8 36.1 - - - +
271B GLU* 3.6 25.6 - - + +
275B ARG 4.4 5.8 - - - +
276B PRO 3.2 12.2 + - - +
277B HIS* 3.7 11.4 - - - +
279B ASP* 1.3 75.5 - - - +
281B LYS* 1.3 64.0 + - - +
283B LEU* 3.1 10.1 + - - +
284B TYR* 3.0 40.8 + - + -
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Residues in contact with LYS 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B HIS* 2.9 39.4 + - + +
278B ALA* 3.9 7.9 - - - +
280B VAL* 1.3 79.3 - - - +
282B ASP* 1.3 58.0 + - - +
284B TYR* 3.5 8.0 + - - +
285B LEU* 3.0 29.3 + - + +
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Residues in contact with ASP 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B MET* 4.6 0.9 - - + -
157B ARG* 4.8 12.0 + - - -
278B ALA* 3.1 23.5 + - - +
279B ASP* 3.2 8.1 + - - +
281B LYS* 1.3 75.9 - - - +
283B LEU* 1.3 60.7 + - - +
285B LEU* 3.2 9.1 + - - +
286B TRP* 2.9 64.6 + - + -
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B TRP* 3.8 14.6 - - + -
153B MET* 3.7 26.7 - - + -
156B HIS* 3.6 28.5 - - + +
263B CYS* 3.4 27.3 - - - +
266B LEU* 3.8 17.0 - - + -
267B ALA* 3.7 24.0 - - + +
279B ASP 2.9 17.6 + - - +
280B VAL* 3.6 6.3 - - - +
282B ASP* 1.3 76.2 - - - +
284B TYR* 1.3 58.0 + - - +
286B TRP* 3.4 16.9 + - + -
287B ALA* 2.9 25.5 + - - +
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Residues in contact with TYR 284 (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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334A HIS* 3.3 14.1 - - - -
505A GOL 3.7 37.2 - - - +
264B GLN* 3.2 39.0 + - - -
267B ALA* 3.5 18.6 - - + -
268B GLU* 3.7 14.2 + - - +
271B GLU* 2.4 33.3 + - - -
280B VAL* 3.0 40.4 + - + +
281B LYS* 3.9 6.7 - - - +
283B LEU* 1.3 75.7 - - - +
285B LEU* 1.3 62.6 + - - +
287B ALA* 3.4 3.4 + - - +
288B GLU* 3.1 23.4 + - - +
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LYS* 3.0 20.3 + - + +
282B ASP* 3.4 11.9 - - - +
284B TYR* 1.3 76.4 - - - +
286B TRP* 1.3 63.2 + - + +
288B GLU* 3.3 9.4 + - + +
289B ARG* 2.9 60.6 + - + +
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Residues in contact with TRP 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B MET* 4.1 12.6 - - + -
156B HIS* 3.9 26.7 - - + -
157B ARG* 3.6 43.5 - - + -
160B ALA* 3.5 22.6 - - + +
161B GLU* 5.1 5.9 - - + +
259B PHE* 4.6 1.1 - - + -
263B CYS* 3.7 17.0 - - - -
282B ASP* 2.9 45.9 + - + +
283B LEU* 3.9 22.4 - - + +
285B LEU* 1.3 75.8 - - + +
287B ALA* 1.3 67.6 + - - +
289B ARG* 3.6 32.8 - - - +
290B PHE* 2.9 37.6 + + + +
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Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B SER* 2.8 44.6 + - - +
263B CYS* 3.7 3.5 - - - +
264B GLN* 3.5 33.7 - - + +
283B LEU 2.9 17.5 + - - +
284B TYR* 3.7 6.3 - - - +
286B TRP* 1.3 74.9 - - - +
288B GLU* 1.3 56.8 + - - +
291B ARG* 3.0 21.6 + - - +
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Residues in contact with GLU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B TYR 3.1 17.0 + - - +
285B LEU* 3.7 8.5 - - + +
287B ALA* 1.3 74.3 - - - +
289B ARG* 1.3 66.9 + - - +
291B ARG* 2.8 40.5 + - - +
292B ALA* 2.9 36.3 + - + +
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Residues in contact with ARG 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ALA* 4.6 13.1 + - - +
161B GLU* 6.3 1.0 - - - +
164B ASP* 4.0 10.5 + - - -
167B GLU* 3.7 50.3 + - - +
168B ARG 4.7 1.1 - - - +
169B GLY* 3.5 18.8 - - - +
285B LEU* 2.9 43.5 + - + +
286B TRP* 3.6 30.2 - - - +
288B GLU* 1.3 78.7 - - - +
290B PHE* 1.3 63.5 + - + +
292B ALA* 3.4 6.1 + - - +
293B GLY 2.9 21.7 + - - -
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Residues in contact with PHE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ALA* 4.3 13.5 - - + -
164B ASP* 3.4 30.5 - - + -
169B GLY* 3.1 29.9 - - - +
170B ARG* 3.4 8.3 - - - -
171B ILE* 3.4 28.7 - - + -
256B SER* 3.8 22.4 - - - +
259B PHE* 3.6 30.5 - + - -
260B SER* 3.9 12.3 - - - -
286B TRP* 2.9 30.9 + - + +
289B ARG* 1.3 85.9 - - + +
291B ARG* 1.3 61.1 + - - +
294B VAL* 2.9 35.3 + - - +
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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
----------------------------------------------------------
505A GOL 5.5 2.8 + - - -
260B SER* 3.5 12.8 + - - +
264B GLN* 2.9 35.6 + - - +
287B ALA* 3.0 26.2 + - - +
288B GLU* 2.8 49.3 + - - +
290B PHE* 1.3 76.5 - - - +
292B ALA* 1.3 61.6 + - - +
294B VAL* 3.3 3.3 + - - +
295B VAL* 3.0 27.9 + - + +
329B CYS* 3.2 25.8 + - - +
330B GLY* 3.3 24.6 - - - +
331B GLY* 3.9 15.5 - - - +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLU* 2.9 29.6 + - + +
289B ARG* 3.7 5.8 - - - +
291B ARG* 1.3 76.3 - - - +
293B GLY* 1.3 57.8 + - - +
295B VAL* 3.3 7.8 + - - +
296B GLU* 2.9 29.2 + - - +
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Residues in contact with GLY 293 (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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168B ARG 3.6 16.4 - - - -
169B GLY 3.4 20.9 - - - -
170B ARG* 2.9 25.8 + - - -
289B ARG 2.9 11.9 + - - -
290B PHE 3.3 0.2 + - - -
291B ARG 3.3 0.2 - - - -
292B ALA* 1.3 76.9 - - - +
294B VAL* 1.3 61.9 + - - +
296B GLU* 3.4 5.5 + - - -
297B THR* 3.4 8.7 - - - +
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Residues in contact with VAL 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B VAL* 3.7 26.2 - - + +
256B SER* 3.8 10.1 - - - -
257B ALA* 3.5 32.3 - - - +
290B PHE 2.9 21.0 + - - +
291B ARG 3.6 4.5 - - - +
293B GLY* 1.3 73.7 - - - +
295B VAL* 1.3 64.3 + - + +
297B THR* 2.8 25.3 + - - -
298B THR* 3.6 3.8 - - - +
325B ALA* 4.3 2.9 - - + -
326B PRO* 3.9 27.4 - - + -
329B CYS* 3.9 19.7 - - - -
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Residues in contact with VAL 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ARG 3.0 21.1 + - - +
292B ALA* 3.3 7.4 + - - +
294B VAL* 1.3 78.4 - - + +
296B GLU* 1.3 63.4 + - - +
298B THR* 2.8 31.1 + - - +
326B PRO* 5.3 0.9 - - + -
330B GLY 4.0 4.9 - - - +
331B GLY* 3.6 37.9 - - - +
332B LEU* 3.9 20.4 - - + +
333B PRO* 4.6 5.4 - - + -
336B ARG* 4.0 11.1 + - - +
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Residues in contact with GLU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 4.4 7.3 - - - +
170B ARG* 3.1 24.6 + - - +
292B ALA 2.9 16.9 + - - +
293B GLY* 3.7 6.6 - - - +
294B VAL 3.1 0.6 - - - -
295B VAL* 1.3 77.6 - - - +
297B THR* 1.3 60.7 + - - +
298B THR 3.4 0.9 + - - +
315B TRP* 4.4 10.1 - - + -
503B GOL 3.3 15.8 + - - -
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Residues in contact with THR 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ARG* 3.4 23.3 - - - +
253B VAL* 3.5 6.7 - - + +
293B GLY 3.4 17.9 - - - +
294B VAL 2.8 14.1 + - - +
296B GLU* 1.3 77.2 - - - +
298B THR* 1.3 57.3 + - - +
305B ALA* 3.4 10.4 - - - +
306B ARG* 3.2 40.9 + - - +
315B TRP* 3.6 20.2 - - + -
503B GOL 3.1 25.9 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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