Contacts of the helix formed by residues 426 - 448 (chain A) in PDB entry 2PY5
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A VAL 4.6 0.2 - - - -
211A PHE* 3.5 33.7 - + + -
212A PRO* 3.7 29.8 - - + -
214A LEU* 4.5 11.0 - - + -
264A PRO 3.5 19.3 - - - -
265A TYR* 3.0 20.4 + - - -
266A GLY 2.6 29.4 + - - -
353A PHE* 3.7 14.9 - - - -
393A PHE* 2.9 21.2 + - + +
424A PRO* 5.5 0.7 - - - -
425A VAL* 1.3 81.8 - - + +
427A THR* 1.3 66.4 + - - +
428A PRO* 3.6 26.7 - - + -
429A MET* 3.0 30.5 + - + +
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Residues in contact with THR 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 5.9 0.4 - - - +
219A ASP* 2.6 30.0 + - - +
222A VAL* 3.8 16.8 - - + -
223A ARG* 3.3 37.9 + - + +
226A TYR* 5.0 1.6 - - + -
393A PHE 3.3 11.3 + - - -
394A ALA* 3.8 19.4 - - + +
395A SER 4.3 2.3 + - - -
424A PRO* 4.7 2.3 - - - +
425A VAL 4.1 0.2 - - - -
426A TYR* 1.3 72.2 - - - +
428A PRO* 1.4 69.6 - - - +
430A GLY* 3.0 11.8 + - - -
431A VAL* 3.0 15.5 + - + +
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Residues in contact with PRO 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 4.3 10.5 - - + -
222A VAL* 3.5 21.1 - - + -
264A PRO* 3.4 10.0 - - + +
285A ILE* 5.3 0.4 - - + -
353A PHE* 3.4 37.2 - - + -
426A TYR* 3.2 35.2 - - + -
427A THR* 1.4 92.1 - - - +
429A MET* 1.3 60.8 + - - +
431A VAL* 3.3 3.3 + - + -
432A PHE* 3.1 30.9 + - + -
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Residues in contact with MET 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A PHE* 3.7 18.2 - - + -
263A LEU* 3.7 28.0 - - + -
264A PRO* 3.4 27.1 - - - +
359A LEU* 3.7 14.8 - - + -
360A PHE* 3.7 30.5 - - + -
393A PHE* 3.8 24.7 - - + -
426A TYR* 3.0 20.6 + - + +
428A PRO* 1.3 77.8 - - - +
430A GLY* 1.3 58.7 + - - +
432A PHE* 3.4 0.7 + - - -
433A ILE* 2.9 47.4 + - + +
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Residues in contact with GLY 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A TYR* 3.5 19.9 - - - -
390A TYR* 4.5 9.2 - - - -
393A PHE* 3.9 12.6 - - - +
394A ALA* 4.5 4.9 - - - -
426A TYR 3.9 2.0 + - - -
427A THR 3.0 8.0 + - - -
429A MET* 1.3 76.7 - - - +
431A VAL* 1.3 64.9 + - - +
433A ILE* 3.3 4.8 + - - -
434A THR* 3.1 26.0 + - - +
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Residues in contact with VAL 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A VAL* 3.5 32.3 - - + +
225A ALA* 3.6 24.5 - - + +
226A TYR* 3.7 28.8 - - + +
285A ILE* 4.1 5.4 - - + -
329A SER* 4.1 14.4 - - - -
427A THR* 3.0 17.7 + - + +
428A PRO* 3.5 9.2 - - + +
430A GLY* 1.3 76.2 - - - +
432A PHE* 1.3 69.9 + - + +
434A THR* 3.3 3.9 + - - -
435A ALA* 3.1 25.5 + - - +
438A ARG* 4.4 2.1 + - - -
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Residues in contact with PHE 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 3.9 9.0 - - + -
264A PRO* 3.7 31.6 - - + -
283A LEU* 3.8 26.9 - - + -
284A HIS 3.5 15.0 - - - -
285A ILE* 4.2 20.0 - - + -
329A SER* 3.8 17.9 - - - -
330A ASN* 3.2 29.4 - - - -
331A VAL* 4.4 14.6 - - + -
353A PHE* 4.5 8.1 - + - -
428A PRO 3.1 23.3 + - - +
429A MET 4.2 0.2 - - - +
431A VAL* 1.3 81.4 - - + +
433A ILE* 1.3 67.1 + - - +
435A ALA* 4.1 2.0 - - - -
436A TRP* 2.9 34.5 + - + -
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Residues in contact with ILE 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A TYR* 3.8 24.7 - - + +
257A GLN* 4.0 6.7 - - + +
258A MET* 3.6 37.9 - - + +
263A LEU* 4.1 17.7 - - + -
360A PHE* 4.4 1.1 - - + -
390A TYR* 3.8 33.4 - - + -
393A PHE* 5.0 0.4 - - + -
429A MET* 2.9 45.4 + - + +
430A GLY* 4.0 4.0 - - - +
432A PHE* 1.3 76.4 - - - +
434A THR* 1.3 62.2 + - - +
436A TRP* 3.9 3.6 - - - +
437A ALA* 3.1 21.7 + - - +
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Residues in contact with THR 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A TYR* 4.0 9.6 - - + +
227A ARG 2.8 29.8 + - - +
228A GLY* 4.6 5.6 - - - +
254A TYR* 4.0 17.4 + - + +
390A TYR* 3.6 33.0 - - + +
430A GLY 3.1 12.1 + - - +
431A VAL 3.3 9.9 + - - -
433A ILE* 1.3 73.5 - - - +
435A ALA* 1.3 60.5 + - - +
437A ALA* 3.2 2.3 + - - +
438A ARG* 2.9 41.8 + - - +
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Residues in contact with ALA 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A SER* 3.4 26.5 - - - +
331A VAL* 3.7 15.7 - - + +
332A ASP* 3.4 11.6 - - - +
335A LEU* 5.3 0.2 - - - +
431A VAL 3.1 20.3 + - - +
432A PHE* 3.8 7.4 - - - +
433A ILE 3.3 0.2 - - - -
434A THR* 1.3 76.3 + - - +
436A TRP* 1.3 56.9 + - - +
438A ARG* 3.3 15.3 + - - +
439A TYR* 2.9 28.1 + - - +
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Residues in contact with TRP 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLN* 3.5 16.8 - - + +
261A ARG* 3.5 57.7 + - + +
262A LEU* 2.9 34.9 + - + -
263A LEU* 3.7 11.4 - - + -
283A LEU* 5.2 5.4 - - + -
330A ASN* 5.6 0.7 - - - -
331A VAL* 3.8 21.1 - - + +
432A PHE* 2.9 30.8 + - + +
433A ILE 3.9 3.1 - - - +
435A ALA* 1.3 76.8 - - - +
437A ALA* 1.3 58.1 + - - +
439A TYR* 3.3 18.7 + + + +
440A THR* 2.9 32.6 + - - -
8004A EDO 6.2 0.2 - - - -
9007A EDO 3.7 37.0 - - - -
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Residues in contact with ALA 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 3.7 22.9 - - + +
254A TYR* 3.4 32.5 - - + +
257A GLN* 3.7 12.3 - - + +
433A ILE 3.1 9.8 + - - +
434A THR 3.2 8.9 + - - +
436A TRP* 1.3 72.2 - - - +
438A ARG* 1.3 66.0 + - + +
440A THR* 3.2 12.3 + - - -
441A THR* 3.2 17.0 + - - -
457A THR 4.4 1.5 - - - +
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Residues in contact with ARG 438 (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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225A ALA 4.6 2.6 + - - -
227A ARG* 3.1 44.3 + - - +
228A GLY 2.8 38.1 + - - +
229A GLY* 4.5 2.2 - - - -
230A PHE* 4.1 27.4 - - + +
315A TYR* 5.3 4.3 - - - -
332A ASP* 2.9 40.9 + - - +
335A LEU* 5.3 0.9 - - + -
431A VAL 4.4 1.8 + - - -
434A THR* 2.9 26.4 + - - +
435A ALA* 3.4 18.1 - - - +
437A ALA* 1.3 75.6 - - + +
439A TYR* 1.3 58.5 + - - +
441A THR* 3.2 3.0 + - - -
442A ILE* 2.8 50.0 + - + +
457A THR 5.5 1.1 - - - -
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Residues in contact with TYR 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ARG* 3.8 23.1 - - - -
331A VAL* 3.7 24.5 - - + -
335A LEU* 4.0 25.7 - - + +
435A ALA 2.9 14.5 + - - +
436A TRP* 3.4 22.7 - + - +
438A ARG* 1.3 75.9 - - - +
440A THR* 1.3 58.3 + - - +
442A ILE* 4.7 0.4 - - - -
443A THR* 2.7 67.2 + - + +
9007A EDO 3.5 27.9 + - - -
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Residues in contact with THR 440 (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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250A VAL* 4.2 12.1 - - + -
253A LEU* 4.3 3.4 - - + -
257A GLN* 3.1 13.9 + - - -
261A ARG* 3.0 18.6 + - - +
436A TRP 2.9 15.3 + - - -
437A ALA 3.2 9.2 + - - -
439A TYR* 1.3 82.8 - - - +
441A THR* 1.3 61.3 + - - +
443A THR* 3.3 11.9 + - - -
444A ALA* 3.4 8.1 + - - +
481A GLY 5.0 0.9 - - - +
483A TRP* 3.6 26.2 + - + +
9008A EDO 3.7 21.5 - - - +
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Residues in contact with THR 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PHE* 4.3 10.8 - - + +
253A LEU* 4.3 3.8 - - - +
437A ALA 3.2 6.4 + - - -
438A ARG* 3.2 8.3 + - - -
440A THR* 1.3 75.8 - - - +
442A ILE* 1.3 65.8 + - - +
444A ALA* 3.3 2.8 + - - +
445A ALA* 2.9 23.0 + - - +
455A CYS* 4.1 20.4 - - + -
457A THR 2.8 30.2 + - - +
458A ASP* 3.8 3.5 - - - -
459A SER 4.3 5.8 - - - +
460A ILE* 4.0 19.0 - - + +
483A TRP* 3.8 16.8 - - + -
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Residues in contact with ILE 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PHE* 3.7 43.5 - - + -
299A ILE* 4.4 6.9 - - + +
301A THR* 3.9 23.1 - - + +
332A ASP* 6.1 0.2 - - - +
335A LEU* 4.1 23.1 - - + -
339A HIS* 3.8 26.9 - - + +
438A ARG* 2.8 38.7 + - + +
439A TYR 4.3 1.3 - - - +
441A THR* 1.3 72.0 - - - +
443A THR* 1.3 57.8 + - - +
445A ALA* 3.4 6.0 + - - +
446A GLN* 2.8 28.3 + - + +
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Residues in contact with THR 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU* 4.2 11.9 - - + -
439A TYR* 2.7 64.0 + - + +
440A THR* 3.3 8.0 + - - -
442A ILE* 1.3 76.2 - - - +
444A ALA* 1.3 59.7 + - - +
446A GLN* 3.5 3.1 + - - -
447A ALA* 3.0 16.5 + - - +
9013A EDO 2.7 41.0 + - - -
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Residues in contact with ALA 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A THR 3.4 3.7 + - - +
441A THR 3.3 1.2 + - - +
442A ILE 3.3 0.4 - - - -
443A THR* 1.3 77.7 + - - +
445A ALA* 1.3 67.5 + - - +
447A ALA* 3.2 9.5 + - - +
448A CYS* 3.2 24.8 + - - -
460A ILE* 4.1 12.1 - - + -
471A ILE* 4.7 11.2 - - + -
474A ILE* 5.0 4.9 - - + -
483A TRP* 3.5 41.5 - - + +
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Residues in contact with ALA 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PHE* 5.6 0.2 - - + -
299A ILE* 3.4 21.8 - - + +
441A THR 2.9 17.2 + - - +
442A ILE* 3.7 3.1 - - - +
444A ALA* 1.3 77.0 - - - +
446A GLN* 1.3 61.8 + - - +
448A CYS* 3.0 15.6 + - - +
449A TYR* 3.1 12.0 + - - -
452A ILE* 3.8 17.8 - - + +
455A CYS* 3.5 25.1 - - - -
460A ILE* 4.1 6.3 - - + +
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Residues in contact with GLN 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLY 2.9 26.1 + - - -
298A TYR* 3.6 18.1 - - + -
299A ILE* 2.9 34.4 + - + +
339A HIS* 3.2 18.7 - - + -
442A ILE 2.8 20.7 + - - +
443A THR* 3.8 4.7 - - - +
445A ALA* 1.3 74.1 - - - +
447A ALA* 1.3 62.3 + - - +
449A TYR* 3.1 28.0 + - - +
9013A EDO 3.9 26.2 - - - +
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Residues in contact with ALA 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A THR 3.0 18.3 + - - +
444A ALA* 3.4 9.4 - - - +
446A GLN* 1.3 75.6 - - - +
448A CYS* 1.3 61.9 + - - +
449A TYR 3.4 2.1 + - - -
450A ASP* 5.2 1.0 - - - +
470A VAL* 3.8 38.5 - - + +
471A ILE* 4.7 4.3 - - + -
9013A EDO 3.6 10.0 + - - +
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Residues in contact with CYS 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ALA 3.2 15.2 + - - +
445A ALA* 3.0 8.5 + - - +
447A ALA* 1.3 78.4 - - - +
449A TYR* 1.3 63.3 + - - +
450A ASP* 3.2 10.5 - - - +
451A ARG* 2.9 15.3 + - + -
452A ILE* 3.0 9.9 + - - +
460A ILE* 4.7 2.0 - - - -
462A LEU* 3.8 24.7 - - + -
468A PRO* 3.8 31.4 - - + -
470A VAL* 5.6 0.9 - - - -
471A ILE* 3.8 24.5 - - - -
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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