Contacts of the helix formed by residues 292 - 314 (chain A) in PDB entry 2Q7V
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 GLN 292 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASN* 2.9 18.2 + - - -
142A CYS* 3.5 6.9 - - - -
144A THR* 3.8 15.3 - - - +
145A CYS* 3.4 20.5 - - - -
284A ASP* 4.2 0.2 + - - -
290A TYR* 3.6 6.2 + - + +
291A ARG* 1.3 96.0 + - - +
293A LEU* 1.3 65.8 + - - +
294A ALA 4.0 4.5 - - - +
295A THR* 3.1 11.2 + - - +
296A SER* 3.0 25.5 + - - -
348A FAD 3.2 18.1 + - - +
26B TYR* 2.6 28.9 + - - +
301B THR* 4.0 6.7 - - + -
305B MET* 3.6 24.9 - - - -
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PRO* 3.5 34.5 - - + -
46A ILE* 3.7 26.9 - - + -
52A VAL* 3.8 18.8 - - + -
55A PHE* 3.5 20.9 - - + -
67A LEU* 3.6 29.8 - - + -
71A MET* 4.9 3.1 - - + -
292A GLN* 1.3 71.9 - - - +
294A ALA* 1.3 57.2 + - - +
296A SER* 3.2 4.8 + - - -
297A VAL* 2.9 35.8 + - + +
348A FAD 2.6 34.7 + - + +
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PHE* 4.0 10.2 - - + -
56A PRO* 4.3 16.4 - - + -
292A GLN* 3.2 1.8 - - - +
293A LEU* 1.3 78.1 - - - +
295A THR* 1.3 63.5 + - - +
297A VAL* 3.4 5.1 - - - +
298A GLY 3.1 17.8 + - - -
348A FAD 4.3 0.6 + - - -
26B TYR* 4.7 5.2 - - - +
294B ALA 3.9 0.3 - - - +
297B VAL* 4.0 18.2 - - + +
298B GLY* 3.4 11.7 + - - -
301B THR* 3.2 29.2 - - + +
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Residues in contact with THR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLY* 5.6 0.2 - - - -
287A ASP* 3.8 12.3 + - - -
290A TYR* 3.9 13.3 - - + +
292A GLN* 3.1 23.1 + - + +
294A ALA* 1.3 76.7 - - - +
296A SER* 1.3 59.5 + - - +
298A GLY* 3.5 0.3 + - - -
299A ALA* 3.1 25.6 + - - +
298B GLY* 3.7 23.8 - - - +
301B THR* 3.8 19.1 - - + -
302B ARG* 3.3 40.8 + - + +
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Residues in contact with SER 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PRO* 4.7 2.0 - - - -
19A ALA* 3.6 18.4 - - - +
283A GLY* 3.9 15.5 - - - -
284A ASP* 3.2 21.3 + - - -
287A ASP* 5.6 0.2 + - - -
292A GLN 3.0 22.0 + - - -
293A LEU* 3.2 6.0 + - - -
295A THR* 1.3 78.6 + - - +
297A VAL* 1.3 58.9 + - - +
299A ALA* 3.4 2.1 + - - +
300A GLY 3.0 22.2 + - - -
348A FAD 3.3 27.0 + - - -
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Residues in contact with VAL 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PRO* 4.0 19.5 - - + +
22A THR* 3.3 29.7 - - - +
55A PHE* 4.2 17.5 - - + -
71A MET* 4.6 3.4 - - - -
293A LEU* 2.9 24.3 + - + +
294A ALA* 3.4 15.9 - - - +
296A SER* 1.3 69.7 - - - +
298A GLY* 1.3 68.5 + - - +
300A GLY 3.3 0.2 + - - -
301A THR* 2.9 28.7 + - - -
55B PHE* 5.3 0.4 - - + -
56B PRO* 3.8 24.0 - - + -
294B ALA* 4.2 12.8 - - + +
297B VAL* 4.8 2.9 - - + -
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Residues in contact with GLY 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A GLU* 4.5 2.9 - - - -
294A ALA 3.1 14.2 + - - -
295A THR 3.5 2.0 + - - -
296A SER 3.3 0.2 - - - -
297A VAL* 1.3 79.4 - - - +
299A ALA* 1.3 60.4 + - - +
301A THR* 3.3 3.5 + - - -
302A ARG* 3.0 28.8 + - - +
294B ALA* 3.3 26.5 - - - -
295B THR* 3.6 6.6 - - - +
298B GLY* 5.1 2.9 - - - -
302B ARG* 5.5 1.8 - - - -
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A GLU* 3.8 22.8 + - + +
272A ILE* 3.4 14.4 - - + +
282A ALA* 3.7 6.5 - - + -
283A GLY* 3.5 26.9 - - - +
295A THR 3.1 17.4 + - - +
296A SER 3.7 0.9 - - - +
297A VAL 3.3 0.2 - - - -
298A GLY* 1.3 76.1 - - - +
300A GLY* 1.3 63.4 + - - +
302A ARG* 3.2 4.0 + - - -
303A ALA* 3.0 20.1 + - - +
302B ARG* 4.6 2.7 - - - +
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Residues in contact with GLY 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA 3.6 22.0 - - - -
22A THR* 4.7 0.2 - - - -
23A ALA* 3.5 22.6 - - - +
282A ALA* 3.8 12.5 - - - +
296A SER 3.0 12.7 + - - -
297A VAL 3.7 3.4 - - - -
298A GLY 3.3 0.4 - - - -
299A ALA* 1.3 76.6 - - - +
301A THR* 1.3 61.0 + - - +
303A ALA* 3.4 1.0 + - - +
304A ALA 3.1 18.0 + - - -
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Residues in contact with THR 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 3.3 14.1 - - - +
26A TYR* 3.5 39.6 - - + +
297A VAL 2.9 17.8 + - - -
298A GLY 3.5 5.4 - - - -
300A GLY* 1.3 73.2 - - - +
302A ARG* 1.3 59.7 + - - +
304A ALA* 3.3 3.7 + - - +
305A MET* 2.9 42.6 + - - +
292B GLN* 4.0 9.6 - - + -
294B ALA* 3.2 17.3 - - + +
295B THR* 4.0 10.1 - - + -
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Residues in contact with ARG 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ASP* 3.6 25.0 + - - +
271A GLU* 3.3 28.9 + - - -
272A ILE* 3.7 10.1 - - + -
298A GLY 3.0 15.8 + - - +
299A ALA 3.5 7.6 - - - +
301A THR* 1.3 74.6 - - - +
303A ALA* 1.3 57.7 + - - +
305A MET 3.3 0.7 + - - -
306A MET* 2.9 34.8 + - - +
271B GLU* 2.8 32.6 + - - +
287B ASP* 5.5 8.5 - - - +
290B TYR* 3.5 47.3 + - + +
295B THR* 3.7 23.2 + - + +
299B ALA* 5.7 5.5 - - - +
302B ARG* 5.5 1.6 - - - +
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 4.0 20.0 - - + -
272A ILE* 3.7 21.3 - - + +
280A PHE* 4.0 21.6 - - + -
282A ALA* 4.1 4.9 - - + -
299A ALA 3.0 16.0 + - - +
300A GLY 3.7 4.9 - - - +
301A THR 3.2 0.2 - - - -
302A ARG* 1.3 75.9 - - - +
304A ALA* 1.3 59.0 + - - +
306A MET* 4.1 0.2 - - - -
307A THR* 2.8 34.0 + - - -
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Residues in contact with ALA 304 (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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23A ALA* 3.3 29.4 - - + +
26A TYR* 3.5 20.9 - - + -
27A THR* 3.9 13.8 + - - +
32A LEU* 5.0 0.2 - - - +
116A ILE* 4.0 8.9 - - - +
300A GLY 3.1 16.4 + - - +
301A THR 3.8 1.1 - - - +
303A ALA* 1.3 74.8 - - - +
305A MET* 1.3 59.3 + - - +
307A THR* 3.3 3.2 + - - -
308A GLU* 3.0 28.1 + - - +
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Residues in contact with MET 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 3.9 20.9 - - + -
301A THR* 2.9 26.6 + - - +
302A ARG 3.9 3.1 - - - +
304A ALA* 1.3 75.4 - - - +
306A MET* 1.3 63.0 + - + +
308A GLU* 3.3 7.2 + - - +
309A ARG* 3.0 63.7 + - - +
144B THR* 3.9 20.6 - - + +
290B TYR* 3.7 37.7 - - + +
292B GLN* 3.6 24.5 - - - -
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Residues in contact with MET 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ILE* 3.7 12.1 - - + -
273A TYR* 3.4 25.8 - - - +
280A PHE* 4.0 13.2 - - + -
302A ARG 2.9 16.2 + - - +
305A MET* 1.3 78.0 - - + +
307A THR* 1.3 60.3 + - - +
309A ARG* 3.4 46.4 - - - +
310A GLN* 2.9 41.8 + - - +
289B ILE* 4.1 7.0 - - + -
290B TYR* 3.4 33.4 - - + +
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Residues in contact with THR 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 4.2 17.7 - - + -
27A THR* 4.3 2.0 - - - +
32A LEU* 4.2 9.6 - - + -
114A ALA* 3.8 22.0 - - + +
116A ILE* 3.7 9.7 - - - +
278A MET* 4.0 2.4 - - - +
280A PHE* 3.1 26.4 - - - -
303A ALA 2.8 23.7 + - - -
304A ALA* 3.4 7.6 - - - -
306A MET* 1.3 72.4 - - - +
308A GLU* 1.3 66.9 + - - +
311A LEU* 3.0 43.1 + - + +
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Residues in contact with GLU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 3.8 17.3 - - + -
32A LEU* 4.0 14.7 - - + +
304A ALA 3.0 13.4 + - - +
305A MET* 3.5 11.0 - - - +
306A MET 3.3 0.2 - - - -
307A THR* 1.3 78.3 - - - +
309A ARG* 1.3 73.7 + - - +
311A LEU* 3.8 2.4 - - - +
312A ALA* 2.9 38.3 + - - +
170B PHE* 3.4 51.3 - - + +
173B LYS* 3.9 15.4 + - - +
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Residues in contact with ARG 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A MET* 3.0 41.3 + - - +
306A MET* 3.4 22.3 - - + +
307A THR 3.4 0.2 - - - -
308A GLU* 1.3 90.2 + - - +
310A GLN* 1.3 63.0 + - + +
312A ALA* 3.4 6.4 + - - +
313A ALA* 3.2 21.8 + - - +
144B THR* 4.5 8.1 + - - -
167B GLU* 4.8 16.7 + - - -
289B ILE* 2.9 47.2 + - - +
290B TYR 4.9 1.2 + - - -
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Residues in contact with GLN 310 (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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273A TYR* 3.4 34.4 + - - -
277A PRO* 5.7 0.9 - - - +
278A MET* 3.4 35.5 + - - +
280A PHE* 3.4 13.5 - - - -
306A MET* 2.9 25.6 + - + +
309A ARG* 1.3 75.4 - - + +
311A LEU* 1.3 63.9 + - - +
313A ALA* 3.5 8.7 + - - +
314A LEU 3.3 22.0 + - - +
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Residues in contact with LEU 311 (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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10A ASP* 4.2 20.9 - - + +
32A LEU* 4.3 24.5 - - + -
113A LYS* 3.7 35.0 - - + +
114A ALA* 4.5 0.7 - - + -
278A MET* 3.6 20.6 - - + -
307A THR* 3.0 40.3 + - + +
308A GLU* 3.8 2.7 - - - +
310A GLN* 1.3 75.3 - - - +
312A ALA* 1.3 65.5 + - - +
314A LEU* 2.9 28.8 + - - +
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLU* 2.9 32.3 + - - +
309A ARG* 3.5 9.2 - - - +
310A GLN 3.4 0.2 - - - -
311A LEU* 1.3 75.7 - - - +
313A ALA* 1.3 55.8 + - - +
314A LEU* 3.1 19.5 - - - +
169B MET* 6.4 2.0 - - + -
170B PHE* 6.6 0.2 - - - -
173B LYS* 5.9 2.7 - - - +
196B ARG* 3.6 22.0 + - - +
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ARG 3.2 11.1 + - - +
310A GLN* 3.7 11.0 - - - +
311A LEU 3.2 0.4 - - - -
312A ALA* 1.3 76.9 - - - +
314A LEU* 1.3 67.7 - - - +
196B ARG* 3.9 31.2 - - - +
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A MET* 5.9 2.4 - - - +
310A GLN 3.3 11.8 + - - +
311A LEU* 2.9 24.0 + - - +
312A ALA* 3.1 26.0 - - - +
313A ALA* 1.3 82.2 - - - +
196B ARG* 5.7 5.4 - - + +
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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