Contacts of the helix formed by residues 292 - 314 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 2.8 28.9 + - - +
301A THR* 4.0 7.4 - - + -
305A MET* 3.6 20.0 - - - -
54B ASN* 3.1 16.8 + - - -
142B CYS* 3.5 26.5 - - - -
144B THR* 3.7 14.6 - - - +
145B CYS* 3.6 4.1 - - - -
290B TYR* 3.5 14.3 + - + +
291B ARG* 1.3 93.1 + - - +
293B LEU* 1.3 66.0 + - - +
294B ALA 4.1 3.8 - - - +
295B THR* 3.0 12.6 + - - +
296B SER* 2.9 25.6 + - - -
448B FAD 3.1 16.1 - - - +
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PRO* 3.4 33.7 - - + -
46B ILE* 3.6 35.4 - - + -
52B VAL* 3.7 17.7 - - + -
55B PHE* 3.6 21.3 - - + -
67B LEU* 3.7 26.0 - - + -
71B MET* 4.7 3.4 - - + -
292B GLN* 1.3 71.1 - - - +
294B ALA* 1.3 56.6 + - - +
296B SER* 3.2 4.9 + - - -
297B VAL* 2.9 35.0 + - + +
448B FAD 2.8 33.7 + - + +
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Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 4.6 5.2 - - - +
297A VAL* 4.0 17.3 - - + +
298A GLY* 3.3 13.6 + - - -
301A THR* 3.2 31.2 - - + +
55B PHE* 3.9 9.7 - - - -
56B PRO* 4.4 15.5 - - + -
292B GLN* 3.3 2.0 - - - +
293B LEU* 1.3 78.7 - - - +
295B THR* 1.3 56.6 - - - +
297B VAL* 3.5 6.1 - - - +
298B GLY 3.1 21.7 + - - -
448B FAD 4.4 1.0 + - - -
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Residues in contact with THR 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A GLY* 3.6 24.9 - - - +
301A THR* 4.0 14.1 - - + -
302A ARG* 3.7 31.2 + - + +
283B GLY* 5.6 0.4 - - - -
287B ASP* 3.8 15.3 + - - -
290B TYR* 3.9 14.0 - - + +
292B GLN* 3.0 28.6 + - - +
294B ALA* 1.3 77.1 - - - +
296B SER* 1.3 58.0 + - - +
298B GLY* 3.4 1.2 + - - -
299B ALA* 3.0 29.5 + - - +
302B ARG* 5.0 1.4 + - - +
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Residues in contact with SER 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PRO* 4.5 2.7 - - - -
19B ALA* 3.5 20.3 - - - +
283B GLY* 4.0 11.4 - - - -
284B ASP* 3.5 10.2 + - - -
292B GLN 2.9 20.9 + - - -
293B LEU* 3.5 6.3 - - - -
295B THR* 1.3 76.7 + - - +
297B VAL* 1.3 57.9 + - - +
299B ALA* 3.5 2.3 + - - +
300B GLY 3.0 22.7 + - - -
448B FAD 3.2 40.1 + - - -
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PHE* 5.2 0.4 - - + -
56A PRO* 3.9 17.3 - - + -
294A ALA* 4.1 17.7 - - + +
297A VAL* 4.8 2.7 - - + -
18B PRO* 3.9 19.7 - - + +
22B THR* 3.3 28.5 - - - +
55B PHE* 4.0 19.3 - - + -
71B MET* 4.2 9.9 - - + -
293B LEU 2.9 23.2 + - - +
294B ALA* 3.5 12.1 - - - +
296B SER* 1.3 71.1 - - - +
298B GLY* 1.3 62.5 + - - +
300B GLY 3.3 0.2 + - - -
301B THR* 2.8 34.5 + - - -
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Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ALA 3.4 24.7 - - - -
295A THR* 3.7 1.5 - - - +
298A GLY* 5.1 1.3 - - - -
294B ALA 3.1 12.7 + - - -
295B THR 3.4 3.5 + - - -
297B VAL* 1.3 75.7 - - - +
299B ALA* 1.3 56.3 + - - +
301B THR* 3.3 3.1 + - - -
302B ARG* 2.9 51.0 + - - +
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ARG* 5.7 5.8 - - - +
271B GLU* 5.7 3.8 - - + +
272B ILE* 3.9 8.4 - - + +
282B ALA* 3.6 8.3 - - + +
283B GLY* 3.4 27.4 - - - +
286B SER* 5.8 0.4 - - - +
295B THR 3.0 17.1 + - - +
296B SER 3.6 1.6 - - - +
298B GLY* 1.3 76.6 - - - +
300B GLY* 1.3 61.0 + - - +
302B ARG* 3.4 13.0 + - - +
303B ALA* 3.0 24.9 + - - +
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Residues in contact with GLY 300 (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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19B ALA 3.6 23.3 - - - -
22B THR* 4.6 0.2 - - - -
23B ALA* 3.6 14.6 - - - -
282B ALA* 3.7 11.6 - - - +
296B SER 3.0 13.5 + - - -
297B VAL 3.3 3.5 + - - -
299B ALA* 1.3 74.1 - - - +
301B THR* 1.3 56.9 + - - +
303B ALA* 3.4 2.9 + - - +
304B ALA* 2.9 30.7 + - - +
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Residues in contact with THR 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLN* 4.0 5.6 - - + -
294A ALA* 3.2 15.0 - - + +
295A THR* 3.8 19.3 - - + -
22B THR* 3.3 12.5 - - - +
26B TYR* 3.5 40.8 - - + +
297B VAL 2.8 21.1 + - - -
298B GLY 3.4 4.9 - - - -
300B GLY* 1.3 73.0 - - - +
302B ARG* 1.3 66.3 + - - +
304B ALA* 3.3 2.5 + - - +
305B MET* 2.9 34.5 + - - +
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Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A GLU* 3.0 44.7 + - - +
287A ASP* 5.6 4.6 + - - +
290A TYR* 3.5 44.8 - - + +
295A THR* 3.3 39.2 + - + +
298A GLY* 5.5 2.4 - - - -
299A ALA* 4.6 3.0 - - - +
302A ARG* 5.5 1.6 - - - +
271B GLU* 4.5 17.4 - - - +
272B ILE* 3.7 10.8 - - + -
295B THR* 5.0 1.6 + - - +
298B GLY* 2.9 48.5 + - - +
299B ALA* 3.6 9.0 - - - +
301B THR* 1.3 71.5 - - - +
303B ALA* 1.3 63.6 + - - +
305B MET 3.3 0.2 + - - -
306B MET* 3.0 29.6 + - - +
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 3.9 28.9 - - + -
272B ILE* 3.8 15.3 - - + +
280B PHE* 4.0 17.4 - - + -
282B ALA* 4.1 7.0 - - + -
299B ALA 3.0 18.1 + - - +
300B GLY 3.6 4.7 - - - +
302B ARG* 1.3 74.6 - - - +
304B ALA* 1.3 55.3 + - - +
306B MET 3.7 0.3 + - - -
307B THR* 2.7 38.1 + - - -
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Residues in contact with ALA 304 (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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23B ALA* 3.4 19.7 - - + +
26B TYR* 3.4 30.9 - - + -
27B THR* 4.0 11.2 + - - +
116B ILE* 4.2 9.1 - - - +
300B GLY 2.9 18.3 + - - +
301B THR 3.7 1.8 - - - +
303B ALA* 1.3 76.6 - - - +
305B MET* 1.3 63.3 + - - +
307B THR* 3.4 3.6 + - - -
308B GLU* 3.1 23.2 + - - +
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Residues in contact with MET 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A THR* 3.7 21.3 - - + +
290A TYR* 3.6 40.2 - - + +
292A GLN* 3.6 25.1 - - - -
26B TYR* 3.9 20.6 - - + -
301B THR* 2.9 26.4 + - - +
302B ARG 3.9 2.5 - - - +
304B ALA* 1.3 77.8 - - - +
306B MET* 1.3 59.1 + - - +
308B GLU* 3.4 9.7 - - + +
309B ARG* 3.1 65.9 + - - +
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Residues in contact with MET 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ILE* 4.3 10.1 - - - -
290A TYR* 3.3 35.0 - - + +
272B ILE* 3.6 13.2 - - + -
273B TYR* 3.3 23.8 - - - +
280B PHE* 4.0 12.8 - - + -
302B ARG 3.0 16.9 + - - +
303B ALA 4.2 0.4 - - - +
305B MET* 1.3 73.6 - - - +
307B THR* 1.3 56.3 + - - +
309B ARG* 4.3 23.3 - - + -
310B GLN* 2.7 57.0 + - + +
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Residues in contact with THR 307 (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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11B VAL* 4.2 13.5 - - + -
27B THR* 4.5 1.3 - - - +
32B LEU* 4.2 10.8 - - + -
114B ALA* 3.6 27.5 - - + +
116B ILE* 3.8 10.3 - - - +
278B MET* 3.9 2.1 - - - +
280B PHE* 3.2 25.5 - - - -
303B ALA 2.7 23.1 + - - -
304B ALA* 3.4 8.5 - - - -
306B MET* 1.3 73.5 - - - +
308B GLU* 1.3 64.4 + - - +
311B LEU* 3.0 40.8 + - + +
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Residues in contact with GLU 308 (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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144A THR* 6.1 0.4 - - - +
170A PHE* 3.4 29.2 - - + -
173A LYS* 3.4 27.7 + - - -
27B THR* 6.1 0.2 - - - -
30B ALA* 4.3 12.1 - - + +
32B LEU* 3.8 25.4 - - + +
304B ALA 3.1 10.9 + - - +
305B MET* 3.4 14.8 - - + +
306B MET 3.3 0.4 - - - -
307B THR* 1.3 79.7 - - - +
309B ARG* 1.3 76.9 + - + +
311B LEU* 3.8 2.3 - - - +
312B ALA* 2.9 35.1 + - - +
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Residues in contact with ARG 309 (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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144A THR* 4.3 7.9 + - - -
167A GLU* 4.9 14.1 + - - -
289A ILE* 2.9 47.5 + - - +
290A TYR* 4.9 1.2 + - - -
305B MET* 3.1 45.1 + - - +
306B MET* 3.9 23.0 - - + +
308B GLU* 1.3 90.3 + - + +
310B GLN* 1.3 58.7 + - + +
312B ALA* 3.3 6.1 + - - +
313B ALA* 3.0 27.4 + - - +
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Residues in contact with GLN 310 (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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273B TYR* 4.2 13.5 + - - -
277B PRO* 6.0 0.2 - - - +
278B MET* 3.3 29.8 + - + +
280B PHE* 3.8 15.6 - - + -
306B MET* 2.7 48.2 + - + +
309B ARG* 1.3 71.0 - - - +
311B LEU* 1.3 60.3 + - - +
313B ALA* 3.3 9.4 + - - +
314B LEU 2.9 30.5 + - - +
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Residues in contact with LEU 311 (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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10B ASP* 4.0 22.2 - - + +
32B LEU* 4.2 22.9 - - + -
113B LYS* 3.7 33.9 - - + +
114B ALA* 4.5 0.4 - - + -
278B MET* 3.6 20.2 - - + -
307B THR* 3.0 37.9 + - + +
308B GLU* 3.8 3.4 - - - +
310B GLN* 1.3 76.8 - - - +
312B ALA* 1.3 64.7 + - - +
314B LEU* 3.0 28.8 + - - +
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Residues in contact with ALA 312 (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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173A LYS* 5.9 3.4 - - - -
196A ARG* 3.2 17.6 + - - -
308B GLU* 2.9 28.2 + - - +
309B ARG* 3.5 8.1 - - - +
310B GLN 3.2 0.2 - - - -
311B LEU* 1.3 78.1 - - - +
313B ALA* 1.3 61.8 + - - +
314B LEU* 3.6 8.5 - - - +
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ARG* 2.8 27.1 + - - +
309B ARG 3.0 13.4 + - - +
310B GLN* 3.6 12.1 - - - +
312B ALA* 1.3 74.4 - - - +
314B LEU* 1.3 62.5 + - - +
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ARG* 4.2 8.5 - - - +
278B MET* 5.5 6.6 - - - +
310B GLN 2.9 16.2 + - - +
311B LEU* 3.0 26.7 + - - +
312B ALA* 3.6 11.7 - - - +
313B ALA* 1.3 80.4 - - - +
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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) + - + + + + + -
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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