Contacts of the helix formed by residues 274 - 295 (chain B) in PDB entry 5U3W
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 PHE 274 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A VAL* 3.8 10.3 - - + -
257A VAL* 4.7 3.4 - - + -
258A ARG* 3.4 58.6 - - + -
261A THR* 5.7 0.2 - - - -
430A HIS* 4.9 5.2 - + - -
432A LEU* 3.3 34.3 - - + -
503A B7G 3.7 14.6 - - + -
272B SER 5.6 1.3 - - - -
273B LEU* 1.3 76.7 - - - +
275B LEU* 1.3 66.1 + - - +
276B ASN* 3.0 19.3 - - - +
277B ASP* 3.0 17.5 + - - +
278B GLN* 3.1 8.5 + - - +
365B MET* 3.7 24.9 - - + -
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A THR* 4.4 10.2 - - + +
265A LYS* 4.4 14.4 - - + +
270A PHE* 5.1 1.1 - - + -
275A LEU* 4.0 10.3 - - + -
278A GLN* 3.9 29.2 - - + +
279A VAL* 3.8 15.3 - - + -
282A LEU* 3.6 27.4 - - + -
503A B7G 3.5 18.2 - - + +
265B LYS* 3.9 12.3 - - - +
273B LEU 3.6 1.0 + - - -
274B PHE* 1.3 73.6 - - - +
276B ASN* 1.3 61.8 + - - +
278B GLN* 3.2 33.6 + - - +
279B VAL* 3.0 26.2 + - - +
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Residues in contact with ASN 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 4.0 5.2 - - - +
432A LEU* 3.6 13.5 - - - +
435A GLU* 4.1 15.4 - - - +
503A B7G 3.1 54.6 + - + +
274B PHE* 3.0 25.3 - - - +
275B LEU* 1.3 74.5 + - - +
277B ASP* 1.3 58.9 + - - +
279B VAL 3.4 0.7 + - - -
280B THR* 3.1 26.7 + - - -
365B MET* 3.5 32.7 - - - +
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Residues in contact with ASP 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 4.3 18.4 - - + +
274B PHE* 3.0 11.5 + - - +
276B ASN* 1.3 79.4 + - - +
278B GLN* 1.3 66.7 + - - +
280B THR* 3.7 6.2 + - - -
281B LEU* 2.9 30.7 + - - +
363B GLY 4.5 1.7 - - - +
364B LEU* 3.7 14.3 - - + +
365B MET* 2.8 41.5 + - - +
366B ASN* 3.0 30.8 + - - +
370B VAL* 5.3 1.3 - - + -
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Residues in contact with GLN 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LYS* 4.7 3.4 - - - +
275A LEU* 4.1 8.6 - - + +
265B LYS* 2.9 29.0 + - - +
270B PHE* 3.5 49.5 + - + +
271B SER* 3.3 20.4 + - - +
273B LEU* 3.1 23.2 + - + +
274B PHE 3.1 10.8 + - - +
275B LEU* 3.4 24.4 - - - +
277B ASP* 1.3 78.1 - - - +
279B VAL* 1.3 56.8 + - - +
281B LEU* 3.3 3.2 + - - +
282B LEU* 3.0 32.4 + - - +
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Residues in contact with VAL 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU* 3.5 34.3 - - + +
276A ASN* 4.1 3.8 - - + -
279A VAL* 3.4 29.6 - - + -
501A B7G 3.8 42.3 - - + +
503A B7G 3.8 13.9 - - - +
275B LEU 3.0 8.2 + - - +
276B ASN 3.7 7.0 - - - +
278B GLN* 1.3 71.5 - - - +
280B THR* 1.3 57.8 + - - +
282B LEU* 3.8 3.4 - - - +
283B LYS* 2.7 34.8 + - + +
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Residues in contact with THR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A B7G 3.8 15.2 - - - -
276B ASN 3.1 19.1 + - - -
277B ASP* 3.7 6.3 + - - -
279B VAL* 1.3 78.3 - - - +
281B LEU* 1.3 62.4 + - - +
283B LYS* 3.4 6.2 + - - -
284B TYR* 3.3 29.1 + - + +
361B ARG* 4.2 6.0 - - + +
362B PRO 3.3 26.4 + - - +
363B GLY* 4.5 7.6 + - - -
364B LEU* 3.7 27.6 - - + +
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Residues in contact with LEU 281 (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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270B PHE* 4.0 13.5 - - + -
273B LEU* 3.8 28.9 - - + -
277B ASP 2.9 19.2 + - - +
278B GLN 3.7 3.4 - - - +
280B THR* 1.3 75.2 - - - +
282B LEU* 1.3 59.2 + - - +
284B TYR* 3.9 0.7 - - - +
285B GLY* 3.0 28.1 + - - -
356B ILE* 3.5 26.9 - - + +
357B LEU* 4.0 15.5 - - + -
358B CYS 3.5 26.5 - - - +
361B ARG* 4.0 9.3 + - + -
364B LEU* 3.7 21.3 - - + -
370B VAL* 4.1 8.7 - - + -
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Residues in contact with LEU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU* 3.6 31.2 - - + -
501A B7G 3.9 17.0 - - + -
260B LEU* 4.2 19.1 - - + +
261B THR* 3.8 24.0 - - + +
264B ALA* 4.3 2.7 - - + -
270B PHE* 4.0 13.0 - - + -
278B GLN 3.0 12.2 + - - +
279B VAL 3.8 3.1 - - - +
281B LEU* 1.3 75.2 - - - +
283B LYS* 1.3 66.3 + - - +
285B GLY* 4.5 0.7 - - - +
286B VAL* 2.9 49.7 + - + +
356B ILE* 4.2 20.9 - - + -
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Residues in contact with LYS 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A B7G 3.4 59.4 + - + +
279B VAL* 2.7 22.8 + - + +
280B THR* 3.6 7.9 - - - +
282B LEU* 1.3 74.0 - - - +
284B TYR* 1.3 99.5 + - + +
286B VAL* 4.2 3.6 - - - +
287B HIS* 5.0 0.9 + - - -
435B GLU 3.9 1.6 - - - -
436B ILE* 3.2 53.5 - - - +
439B ASP* 3.5 23.4 + - - +
440B MET* 3.9 2.9 - - - +
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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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280B THR* 3.3 21.7 + - + +
283B LYS* 1.3 111.8 + - + +
285B GLY* 1.3 58.1 + - - +
286B VAL 3.8 0.4 - - - -
287B HIS* 5.3 1.2 + - - +
288B GLU* 3.8 9.7 + - - +
361B ARG* 3.4 42.7 + - + +
362B PRO* 3.7 54.4 + - + +
410B VAL* 5.4 3.8 - - - +
439B ASP* 3.4 24.0 + - - +
440B MET* 3.8 31.4 - - + +
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Residues in contact with GLY 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU 3.0 17.1 + - - -
284B TYR* 1.3 79.5 - - - +
286B VAL* 1.3 65.8 + - - +
287B HIS 3.3 2.2 - - - -
288B GLU* 3.3 7.0 + - - +
289B ALA* 3.0 18.7 + - - +
355B ILE* 3.6 6.5 - - - +
356B ILE* 3.7 12.3 - - - -
361B ARG* 3.7 16.4 - - - -
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A B7G 5.5 0.2 - - + -
257B VAL* 4.0 31.0 - - + -
260B LEU* 4.0 23.8 - - + -
282B LEU* 2.9 47.8 + - + +
283B LYS 4.2 2.7 - - - +
285B GLY* 1.3 76.5 - - - +
287B HIS* 1.3 69.0 + - + +
289B ALA* 3.2 1.9 + - - +
290B ILE* 2.7 33.5 + - + +
356B ILE* 4.2 1.5 - - + +
436B ILE* 4.0 27.1 - - + -
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Residues in contact with HIS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B THR* 4.1 13.8 - - + +
283B LYS 5.0 0.8 + - - -
284B TYR 5.3 1.6 + - - +
285B GLY 3.3 0.6 - - - +
286B VAL* 1.3 82.8 - - + +
288B GLU* 1.3 62.9 + - - +
290B ILE* 3.7 8.3 - - + +
291B PHE* 3.0 44.0 + + + -
410B VAL* 3.8 25.8 - - + +
413B HIS* 4.1 10.3 - + - -
433B LEU* 4.4 4.5 - - + -
436B ILE* 3.8 35.0 - - + +
437B TYR* 2.8 40.9 + + - -
440B MET* 5.3 1.8 - - - +
501B 7U1 3.1 17.0 + - - -
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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 3.8 8.0 + - - +
285B GLY 3.3 8.3 + - - +
287B HIS* 1.3 75.8 - - - +
289B ALA* 1.3 63.1 + - - +
291B PHE 3.5 0.2 + - - -
292B ALA* 3.1 23.4 + - - +
355B ILE* 3.6 17.8 - - + +
361B ARG* 2.9 42.0 + - - -
403B MET* 4.5 7.8 - - - +
406B LEU* 3.6 24.9 - - + +
407B ARG* 3.7 30.4 + - - +
410B VAL* 3.5 25.8 - - + +
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Residues in contact with ALA 289 (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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260B LEU* 3.8 28.5 - - + -
285B GLY 3.0 12.6 + - - +
286B VAL 3.5 7.6 - - - +
288B GLU* 1.3 75.6 - - - +
290B ILE* 1.3 66.0 + - - +
292B ALA* 3.2 2.6 + - - +
293B MET* 3.0 29.6 + - - +
352B ILE* 4.0 21.3 - - + -
355B ILE* 3.8 5.7 - - + +
356B ILE* 4.0 8.3 - - + -
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Residues in contact with ILE 290 (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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253B THR* 3.9 23.8 - - + +
256B THR* 3.6 24.5 - - + -
257B VAL* 3.9 28.5 - - + -
260B LEU* 3.9 4.0 - - + -
286B VAL* 2.7 28.4 + - + +
287B HIS* 3.7 11.2 - - + +
289B ALA* 1.3 72.4 - - - +
291B PHE* 1.3 65.0 + - + +
293B MET* 3.3 8.7 + - - +
294B LEU* 2.8 27.5 + - - +
501B 7U1 3.6 36.6 - - + -
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Residues in contact with PHE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B THR* 6.1 0.2 - - - -
287B HIS* 3.0 33.8 + + + +
290B ILE* 1.3 90.1 - - + +
292B ALA* 1.3 61.3 + - - +
294B LEU* 3.5 20.4 - - + +
295B ALA* 4.1 2.6 + - - +
331B LYS* 3.5 41.3 - - + +
334B PHE* 3.9 13.2 - - - -
335B ALA* 5.6 1.2 - - - +
406B LEU* 3.9 16.8 - - + -
409B LEU* 3.9 21.1 - - + -
410B VAL* 3.8 22.9 - - + -
413B HIS* 3.8 32.3 - + + -
501B 7U1 4.4 16.4 - + + -
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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
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288B GLU 3.1 17.7 + - - +
289B ALA 3.6 4.7 - - - +
290B ILE 3.2 0.2 - - - -
291B PHE* 1.3 77.7 - - - +
293B MET* 1.3 61.1 + - - +
294B LEU 3.4 0.7 + - - -
295B ALA* 3.4 19.6 + - - +
296B SER* 4.5 1.6 + - - -
334B PHE* 4.3 9.0 - - - -
338B PHE* 3.8 14.3 - - + -
348B LEU* 5.0 2.6 - - + +
351B PHE* 3.9 21.8 - - + -
352B ILE* 3.7 18.6 - - + -
355B ILE* 4.2 0.4 - - + -
406B LEU* 4.0 7.5 - - + +
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Residues in contact with MET 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B TYR* 4.8 9.6 - - + +
190B PHE* 3.9 33.0 - - + -
256B THR* 3.6 30.7 - - + -
260B LEU* 3.7 24.7 - - + -
289B ALA 3.0 22.8 + - - +
290B ILE* 3.9 3.8 - - - +
292B ALA* 1.3 72.0 - - - +
294B LEU* 1.3 65.5 + - - +
295B ALA 3.2 0.7 - - - -
296B SER* 3.0 26.9 + - - +
297B ILE* 4.2 3.1 + - - +
348B LEU* 5.9 5.4 - - + -
352B ILE* 3.8 24.0 - - + -
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ILE 2.8 16.6 + - - +
291B PHE* 3.5 15.3 - - + +
292B ALA 3.2 0.2 - - - -
293B MET* 1.3 77.4 - - - +
295B ALA* 1.3 62.1 + - - +
297B ILE* 3.0 26.5 + - + +
298B VAL* 3.2 32.1 - - + +
303B LEU* 3.9 20.6 - - + -
331B LYS* 3.8 28.9 - - + +
335B ALA* 5.4 0.9 - - + -
501B 7U1 3.5 50.7 - - + -
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ARG* 3.4 0.9 + - - -
291B PHE 4.1 2.8 + - - +
292B ALA 3.4 15.1 + - - +
293B MET 3.2 0.2 - - - -
294B LEU* 1.3 78.7 - - - +
296B SER* 1.3 62.0 + - - +
298B VAL* 3.2 10.2 + - - +
334B PHE* 5.4 0.4 - - + -
335B ALA* 3.9 30.5 - - + +
338B PHE* 3.7 18.6 - - + -
339B ASN* 2.9 39.3 + - - +
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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