Contacts of the helix formed by residues 426 - 448 (chain B) in PDB entry 1XI1
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 TYR 426 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B VAL 4.2 0.4 - - - -
211B PHE* 3.6 28.9 - + + -
212B PRO* 3.8 29.8 - - + -
214B LEU* 4.5 7.4 - - + -
264B PRO 3.4 21.3 - - - -
265B TYR* 2.9 15.5 + - - -
266B GLY 2.3 38.1 + - - -
353B PHE* 3.8 11.8 - - - -
393B PHE* 3.5 19.9 - - + +
424B PRO* 3.7 1.3 - - - -
425B VAL* 1.3 81.9 - - - +
427B THR* 1.3 66.3 + - - +
428B PRO* 3.2 29.4 - - + -
429B MET* 3.2 38.9 + - + +
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Residues in contact with THR 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 5.5 0.6 - - - +
219B ASP* 2.7 29.8 + - - -
222B VAL* 3.3 22.4 - - + -
223B ARG* 3.7 39.5 + - + +
226B TYR* 5.6 0.4 - - + -
393B PHE 3.8 11.2 + - - +
394B ALA* 6.3 0.2 - - - -
395B SER 5.1 2.6 + - - -
397B PRO* 5.8 0.2 - - - +
424B PRO* 4.1 8.8 - - - +
425B VAL 4.7 0.6 + - - +
426B TYR* 1.3 74.0 - - - +
428B PRO* 1.3 71.8 - - - +
429B MET 3.0 1.2 + - - -
430B GLY* 3.0 12.3 + - - -
431B VAL* 3.1 15.0 + - + +
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Residues in contact with PRO 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 3.8 24.9 - - + -
222B VAL* 3.7 16.4 - - + -
264B PRO* 3.3 16.3 - - + +
285B ILE* 5.6 0.2 - - + -
353B PHE* 3.5 35.7 - - + -
426B TYR* 3.3 31.2 - - + -
427B THR* 1.3 95.5 - - - +
429B MET* 1.3 58.9 + - - +
431B VAL* 3.6 2.3 + - + +
432B PHE* 3.3 21.7 + - + -
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Residues in contact with MET 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B PHE* 3.7 19.7 - - + -
263B LEU* 3.7 35.2 - - + -
264B PRO* 3.1 29.6 - - - +
359B LEU* 3.8 12.8 - - + -
360B PHE* 3.8 18.4 - - + -
393B PHE* 3.7 22.4 - - + -
426B TYR* 3.2 21.9 + - + +
427B THR 3.0 0.4 - - - -
428B PRO* 1.3 78.4 - - - +
430B GLY* 1.3 63.8 + - - +
432B PHE* 3.4 0.9 + - - -
433B ILE* 3.0 45.4 + - + +
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Residues in contact with GLY 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B TYR* 4.0 6.5 - - - -
390B TYR* 4.5 6.1 - - - -
393B PHE* 3.8 5.1 - - - +
394B ALA* 3.8 28.9 - - - -
426B TYR 3.8 3.4 + - - -
427B THR 3.0 7.2 + - - -
429B MET* 1.3 75.2 - - - +
431B VAL* 1.3 65.4 + - - +
433B ILE* 4.0 1.1 - - - +
434B THR* 3.1 30.5 + - - +
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Residues in contact with VAL 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B VAL* 3.6 31.2 - - + +
225B ALA* 3.6 20.0 - - + +
226B TYR* 3.6 28.2 - - + +
285B ILE* 4.2 11.9 - - + -
329B SER* 4.2 11.9 - - - -
427B THR* 3.1 14.3 + - + +
428B PRO* 3.7 9.2 - - + +
430B GLY* 1.3 76.1 - - - +
432B PHE* 1.3 70.1 + - + +
434B THR* 3.0 4.3 + - - -
435B ALA* 3.0 26.1 + - + +
438B ARG* 4.7 1.2 + - - -
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Residues in contact with PHE 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 4.0 6.5 - - + -
264B PRO* 3.7 27.4 - - + -
283B LEU* 3.7 26.2 - - + -
284B HIS 3.4 23.3 - - - -
285B ILE* 3.9 22.0 - - + -
329B SER* 3.7 16.8 - - - -
330B ASN* 2.9 30.7 - - - -
331B VAL* 4.5 12.1 - - + -
353B PHE* 4.7 9.2 - + - -
428B PRO 3.3 16.1 + - - +
429B MET 4.3 0.4 - - - +
431B VAL* 1.3 83.4 - - + +
433B ILE* 1.3 61.3 + - - +
435B ALA* 3.8 4.0 - - - +
436B TRP* 2.9 41.5 + - + -
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Residues in contact with ILE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B TYR* 3.8 15.9 - - + -
257B GLN* 4.0 8.3 - - + +
258B MET* 3.8 40.4 - - + +
263B LEU* 4.0 23.1 - - + -
390B TYR* 3.5 29.8 - - + -
393B PHE* 4.7 5.2 - - + -
429B MET* 3.0 45.7 + - + +
430B GLY 4.0 2.9 - - - +
432B PHE* 1.3 77.6 - - - +
434B THR* 1.3 57.3 + - - +
436B TRP* 3.5 3.6 + - - +
437B ALA* 3.1 25.6 + - - +
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Residues in contact with THR 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B TYR* 3.7 11.1 - - + +
227B ARG 3.2 22.0 + - - +
228B GLY* 4.6 3.6 - - - -
254B TYR* 4.2 11.0 - - - +
390B TYR* 2.8 37.9 - - + +
430B GLY 3.1 13.1 + - - +
431B VAL* 3.0 11.6 + - - -
433B ILE* 1.3 73.4 - - - +
435B ALA* 1.3 62.8 + - - +
437B ALA* 3.1 7.6 + - - +
438B ARG* 2.8 40.8 + - - +
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Residues in contact with ALA 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B SER* 3.5 11.0 - - - +
331B VAL* 3.7 15.9 - - + +
332B ASP* 3.4 25.5 - - - +
335B LEU* 5.8 0.2 - - - +
431B VAL 3.0 20.4 + - - +
432B PHE* 3.8 7.9 - - - +
433B ILE 3.3 0.2 - - - -
434B THR* 1.3 78.2 + - - +
436B TRP* 1.3 57.2 + - - +
438B ARG* 3.2 14.6 + - - +
439B TYR* 2.8 28.8 + - - +
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Residues in contact with TRP 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B GLN* 3.7 15.7 - - + +
261B ARG* 3.5 55.9 + - + +
262B LEU* 3.0 36.6 + - + -
263B LEU* 3.9 9.9 - - + -
283B LEU* 5.2 5.2 - - + -
330B ASN* 5.5 2.2 - - - -
331B VAL* 3.7 28.8 - - + +
432B PHE* 2.9 31.6 + - + +
433B ILE* 4.0 3.4 - - - +
435B ALA* 1.3 76.9 - - - +
437B ALA* 1.3 58.3 + - - +
439B TYR* 3.2 30.3 + + - +
440B THR* 2.9 32.4 + - - -
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Residues in contact with ALA 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 3.8 21.2 - - + +
254B TYR* 3.3 37.5 - - + +
257B GLN* 4.0 12.1 - - + +
433B ILE 3.1 12.1 + - - +
434B THR 3.1 4.9 + - - +
436B TRP* 1.3 78.6 - - - +
438B ARG* 1.3 61.5 + - + +
440B THR* 3.3 4.2 + - - -
441B THR* 3.3 24.1 + - - -
457B THR 4.4 1.4 - - - +
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Residues in contact with ARG 438 (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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225B ALA 4.7 3.4 + - - -
227B ARG* 3.1 42.7 + - - +
228B GLY 3.0 31.6 + - - +
229B GLY* 4.4 2.5 - - - -
230B PHE* 3.9 33.7 - - + +
303B GLN* 4.5 9.4 - - - -
332B ASP* 2.7 41.3 + - - +
335B LEU* 5.0 1.1 - - + -
431B VAL 4.7 0.8 + - - -
434B THR* 2.8 27.5 + - - +
435B ALA* 3.5 15.6 - - - +
437B ALA* 1.3 77.0 - - + +
439B TYR* 1.3 58.5 + - - +
440B THR 3.2 0.3 + - - -
441B THR* 3.3 1.9 + - - -
442B ILE* 2.8 43.9 + - + +
457B THR 5.6 0.4 - - - -
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Residues in contact with TYR 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ARG* 4.0 14.4 - - - -
331B VAL* 3.6 22.0 - - + -
334B GLU* 4.0 22.5 + - - -
335B LEU* 3.6 43.7 - - + +
435B ALA 2.8 17.4 + - - +
436B TRP* 3.4 31.4 - + - +
438B ARG* 1.3 78.1 - - - +
440B THR* 1.3 59.6 + - - +
443B THR* 2.9 43.1 + - + +
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Residues in contact with THR 440 (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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250B VAL* 4.4 13.5 - - + -
253B LEU* 4.7 1.1 - - + -
257B GLN* 3.1 19.0 + - - +
261B ARG* 2.9 28.7 + - - +
436B TRP 2.9 12.6 + - - -
437B ALA 3.5 9.2 - - - -
438B ARG 3.1 0.4 - - - -
439B TYR* 1.3 78.6 - - - +
441B THR* 1.3 61.0 - - - +
443B THR* 3.4 14.3 + - - -
444B ALA* 3.6 7.6 + - - +
481B GLY 5.1 8.3 - - - +
483B TRP* 3.6 24.5 + - + +
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Residues in contact with THR 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B PHE* 4.3 13.9 - - + +
253B LEU* 4.5 4.0 - - - +
437B ALA 3.3 11.5 + - - -
438B ARG* 3.9 4.3 - - - -
440B THR* 1.3 76.2 - - - +
442B ILE* 1.3 64.5 + - - +
444B ALA* 3.6 2.4 + - - +
445B ALA* 3.2 21.8 + - - +
455B CYS* 4.3 23.6 - - + -
457B THR* 2.4 35.9 + - - +
458B ASP* 3.9 2.8 - - - -
459B SER 4.4 2.9 - - - +
460B ILE* 4.2 4.8 - - + +
483B TRP* 3.8 22.7 - - + -
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Residues in contact with ILE 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B PHE* 3.7 44.4 - - + -
299B ILE* 4.3 4.5 - - + +
301B THR* 3.8 22.9 - - + +
335B LEU* 3.9 26.0 - - + -
339B HIS* 3.9 27.4 - - + +
438B ARG* 2.8 34.9 + - + +
439B TYR 4.3 0.2 - - - +
441B THR* 1.3 71.0 - - - +
443B THR* 1.3 62.6 + - - +
445B ALA* 3.3 4.7 + - - +
446B GLN* 3.0 28.1 + - - +
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Residues in contact with THR 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B LEU* 3.9 15.5 - - + -
338B GLU* 5.7 2.5 - - - +
339B HIS* 5.9 0.7 - - - +
439B TYR* 2.9 52.7 + - + +
440B THR* 3.4 7.1 + - - -
442B ILE* 1.3 76.9 - - - +
444B ALA* 1.3 62.7 + - - +
446B GLN* 4.0 6.5 - - - +
447B ALA* 3.2 23.0 + - - +
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Residues in contact with ALA 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B THR 3.6 5.7 + - - +
441B THR 3.9 1.3 - - - +
442B ILE 3.1 0.4 - - - -
443B THR* 1.3 79.9 + - - +
445B ALA* 1.3 65.0 + - - +
447B ALA* 3.2 14.6 + - - +
448B CYS* 3.3 20.7 + - - -
460B ILE* 4.6 8.3 - - + -
471B ILE* 4.6 9.7 - - + +
474B ILE* 5.1 4.3 - - + -
483B TRP* 3.4 44.6 - - + +
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Residues in contact with ALA 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ILE* 3.8 14.9 - - + +
441B THR 3.2 10.5 + - - +
442B ILE* 3.9 1.6 - - - +
444B ALA* 1.3 76.1 - - - +
446B GLN* 1.3 66.2 + - - +
448B CYS* 3.1 8.9 + - - +
449B TYR* 3.1 19.4 + - - -
452B ILE* 3.7 22.0 - - + +
455B CYS* 3.5 32.8 - - - -
460B ILE* 4.2 7.1 - - + +
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Residues in contact with GLN 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLY 2.9 27.1 + - - -
298B TYR* 3.6 22.0 - - + +
299B ILE* 2.7 42.5 + - + +
338B GLU* 5.2 2.9 - - - +
339B HIS* 3.1 22.6 - - + +
442B ILE 3.0 17.4 + - - +
443B THR* 4.0 6.3 - - - +
445B ALA* 1.3 76.3 - - - +
447B ALA* 1.3 64.0 + - - +
449B TYR* 3.1 28.4 + - - +
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Residues in contact with ALA 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B THR 3.2 19.5 + - - +
444B ALA* 3.2 8.9 + - - +
446B GLN* 1.3 77.8 - - - +
448B CYS* 1.3 59.3 + - - +
449B TYR 3.4 0.7 + - - -
470B VAL* 3.5 33.9 - - + +
471B ILE* 5.2 2.9 - - + -
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Residues in contact with CYS 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B ALA 3.4 14.4 - - - +
445B ALA* 3.1 9.7 + - - +
446B GLN 3.0 0.4 - - - -
447B ALA* 1.3 79.8 - - - +
449B TYR* 1.3 64.0 + - - +
450B ASP* 3.1 3.8 - - - -
451B ARG* 2.9 18.1 + - + +
452B ILE* 3.0 9.2 + - - +
460B ILE* 4.7 2.2 - - - -
462B LEU* 3.6 27.4 - - + -
468B PRO* 4.0 26.0 - - + -
470B VAL* 4.1 2.2 - - - -
471B ILE* 3.8 26.0 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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