Contacts of the helix formed by residues 445 - 467 (chain A) in PDB entry 4M8J
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 PRO 445 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A GLY* 4.0 25.6 - - - +
10A ILE* 5.6 0.9 - - + -
431A ALA* 4.9 1.8 - - + +
435A CYS* 4.0 28.0 - - + -
443A ASP 3.8 1.8 - - - +
444A PRO* 1.3 84.2 - - + +
446A LEU* 1.3 67.4 + - - +
447A LEU* 2.9 4.6 + - + +
448A VAL* 3.1 31.6 + - + +
449A ARG* 3.3 9.7 + - - +
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Residues in contact with LEU 446 (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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247A VAL* 3.5 33.0 - - + +
248A ALA* 3.6 35.4 - - + +
443A ASP* 4.8 6.1 - - - +
444A PRO 3.0 8.6 + - - +
445A PRO* 1.3 69.4 - - - +
447A LEU* 1.3 65.2 + - + +
449A ARG* 3.5 12.1 - - - +
450A ILE* 3.4 18.2 - - + +
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Residues in contact with LEU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A PRO* 2.9 1.9 + - + -
446A LEU* 1.3 79.7 - - + +
448A VAL* 1.3 68.1 + - + +
449A ARG 3.1 2.0 - - - -
450A ILE* 3.1 27.0 + - + +
451A GLY* 3.3 9.7 + - - -
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Residues in contact with VAL 448 (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 ILE* 3.9 25.1 - - + -
15A PHE* 3.6 24.0 - - + -
431A ALA* 4.6 9.0 - - + +
434A THR* 4.8 4.3 - - + -
435A CYS* 6.1 3.4 - - + +
445A PRO* 3.1 24.1 + - + +
447A LEU* 1.3 78.0 - - + +
449A ARG* 1.3 61.9 + - - +
451A GLY* 3.5 3.5 + - - +
452A TRP* 3.1 52.0 + - + +
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Residues in contact with ARG 449 (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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243A ASN* 5.1 2.6 - - - +
247A VAL* 3.2 42.3 - - + +
252A GLN* 6.3 1.0 - - - +
424A ASN* 3.2 33.5 + - - +
427A SER* 3.5 37.6 + - - +
428A TYR* 3.2 43.2 - - - +
431A ALA* 4.1 14.5 - - + +
443A ASP* 4.0 16.9 + - - -
444A PRO* 4.6 6.4 - - + +
445A PRO 3.3 8.9 + - - +
446A LEU 3.5 13.0 - - - +
448A VAL* 1.3 79.7 - - - +
450A ILE* 1.3 66.1 + - + +
452A TRP* 3.5 2.5 + - - +
453A SER* 3.4 13.0 + - - -
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Residues in contact with ILE 450 (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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240A ILE* 4.7 4.5 - - + -
243A ASN* 4.8 4.3 - - - +
244A ALA* 3.7 41.5 - - + +
247A VAL* 3.7 18.6 - - + -
446A LEU* 3.4 17.9 - - + +
447A LEU* 3.1 18.8 + - + +
449A ARG* 1.3 75.8 - - - +
451A GLY* 1.3 58.3 + - - +
453A SER* 2.4 38.1 + - - +
454A VAL* 3.1 17.7 + - + +
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Residues in contact with GLY 451 (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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19A LEU* 5.8 2.1 - - - +
447A LEU 3.3 8.3 + - - -
448A VAL* 3.5 4.9 + - - -
449A ARG 3.4 0.2 - - - -
450A ILE* 1.3 79.6 - - - +
452A TRP* 1.3 57.5 + - - +
454A VAL* 3.3 9.3 + - - +
455A LEU* 3.0 27.1 + - - +
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Residues in contact with TRP 452 (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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15A PHE* 4.2 15.7 - + - -
18A PRO* 4.2 22.0 - - + -
19A LEU* 3.6 29.8 - - + -
197A LEU* 6.2 1.6 - - + -
201A ILE* 3.6 25.4 - - + -
427A SER* 4.8 3.6 - - - -
430A LEU* 3.7 37.7 - - + -
431A ALA* 4.1 8.1 - - + -
434A THR* 3.3 38.1 + - + +
448A VAL* 3.1 41.5 + - + +
449A ARG* 3.9 5.8 - - - +
450A ILE 3.2 0.8 - - - -
451A GLY* 1.3 72.8 - - - +
453A SER* 1.3 61.1 + - - +
455A LEU* 3.1 19.4 + - + +
456A VAL* 2.9 36.5 + - + +
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Residues in contact with SER 453 (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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240A ILE* 3.7 23.8 - - - +
243A ASN* 3.6 21.9 + - - -
423A ILE* 4.2 22.7 - - - +
427A SER* 4.5 10.0 - - - +
449A ARG 3.4 7.6 + - - -
450A ILE* 2.4 30.8 + - - -
452A TRP* 1.3 78.0 - - - +
454A VAL* 1.3 58.5 + - - +
456A VAL* 4.0 8.2 + - - +
457A GLY* 3.6 13.0 + - - -
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Residues in contact with VAL 454 (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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240A ILE* 3.8 33.8 - - + +
450A ILE* 3.1 22.2 + - + +
451A GLY* 3.6 8.5 - - - +
452A TRP 3.1 0.6 - - - -
453A SER* 1.3 75.0 - - - +
455A LEU* 1.3 63.4 - - - +
456A VAL 3.1 1.8 - - - -
457A GLY* 3.1 11.4 + - - -
458A ILE* 3.2 31.1 + - + +
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Residues in contact with LEU 455 (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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19A LEU* 4.0 24.5 - - + +
22A VAL* 3.6 39.3 - - + +
23A GLY* 5.0 4.7 - - - +
201A ILE* 3.7 29.8 - - + -
451A GLY 3.0 18.4 + - - +
452A TRP* 3.1 16.4 + - + +
454A VAL* 1.3 77.3 - - - +
456A VAL* 1.3 61.9 + - + +
458A ILE* 3.8 20.1 + - + +
459A ILE* 3.7 15.8 + - + +
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Residues in contact with VAL 456 (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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201A ILE* 4.8 8.3 - - + -
204A MET* 4.1 31.6 - - + +
205A GLY* 3.7 24.7 - - - -
208A LEU* 4.2 16.4 - - + -
423A ILE* 4.9 9.2 - - + -
426A CYS* 5.7 5.6 - - + -
430A LEU* 4.7 6.5 - - + -
452A TRP 2.9 22.8 + - - +
453A SER* 4.0 8.1 - - - +
455A LEU* 1.3 78.1 - - + +
457A GLY* 1.3 60.1 + - - +
459A ILE* 2.9 27.1 + - - +
460A GLY 2.9 11.6 + - - -
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Residues in contact with GLY 457 (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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208A LEU* 4.1 10.3 - - - +
236A ILE* 3.8 24.4 - - - +
240A ILE* 5.3 1.6 - - - -
453A SER 3.6 7.9 + - - -
454A VAL* 3.1 8.6 + - - -
456A VAL* 1.3 79.1 - - - +
458A ILE* 1.3 56.8 + - - +
460A GLY* 3.7 0.2 - - - -
461A ILE* 2.8 37.8 + - - +
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Residues in contact with ILE 458 (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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26A CYS* 4.2 16.2 - - + -
454A VAL* 3.2 27.1 + - + +
455A LEU* 3.8 26.5 - - + +
456A VAL 3.2 0.2 - - - -
457A GLY* 1.3 76.3 - - - +
459A ILE* 1.3 59.4 + - + +
461A ILE* 3.4 6.5 + - - +
462A ILE* 3.0 49.0 + - + +
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Residues in contact with ILE 459 (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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22A VAL* 3.5 32.1 - - + +
26A CYS* 6.0 2.7 - - + -
201A ILE* 3.7 23.6 - - + +
202A LEU* 3.7 22.0 - - + +
205A GLY* 4.1 12.3 - - - -
455A LEU* 3.9 9.4 - - + +
456A VAL* 2.9 9.7 + - - +
458A ILE* 1.3 77.7 - - + +
460A GLY* 1.3 55.9 + - - +
462A ILE* 3.0 12.1 + - + +
463A LEU* 2.7 63.7 + - + +
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Residues in contact with GLY 460 (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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205A GLY 3.7 18.6 + - - -
208A LEU* 4.5 13.0 - - - -
209A GLY* 4.4 2.7 - - - -
236A ILE* 4.4 3.6 - - - -
456A VAL 2.9 11.9 + - - -
457A GLY 3.3 3.6 + - - -
459A ILE* 1.3 76.5 - - - +
461A ILE* 1.3 55.5 + - - +
463A LEU* 3.4 5.1 + - - +
464A LEU* 2.9 38.6 + - - +
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Residues in contact with ILE 461 (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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229A LEU* 4.8 18.7 - - + +
232A ASP* 3.7 6.3 - - + +
233A ALA* 3.5 38.6 - - + +
236A ILE* 3.6 22.7 - - + -
457A GLY 2.8 24.8 + - - +
458A ILE* 3.6 7.4 - - + +
460A GLY* 1.3 72.3 - - - +
462A ILE* 1.3 55.6 + - + +
464A LEU* 2.9 12.2 + - + +
465A ALA* 2.5 36.4 + - + +
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Residues in contact with ILE 462 (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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26A CYS* 3.6 49.4 - - + +
29A THR* 3.6 28.9 - - + -
30A VAL* 4.3 17.5 - - + +
33A LEU* 6.0 0.2 - - + -
458A ILE* 3.0 26.0 + - + +
459A ILE* 3.4 10.8 - - + +
461A ILE* 1.3 78.2 - - + +
463A LEU* 1.3 61.2 + - + +
465A ALA* 3.3 7.6 - - + +
466A LEU* 2.7 46.0 + - + +
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Residues in contact with LEU 463 (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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202A LEU 4.9 0.2 - - - +
205A GLY 3.8 10.3 - - - +
206A THR* 3.6 34.1 - - + -
209A GLY* 4.9 4.0 - - - -
459A ILE* 2.7 42.8 + - + +
460A GLY* 3.6 5.2 - - - +
462A ILE* 1.3 79.5 - - + +
464A LEU* 1.3 61.2 + - - +
466A LEU* 3.9 3.9 + - + -
467A GLY* 3.6 13.7 + - - -
468A GLY 4.5 0.9 - - - +
471A PRO* 4.0 36.4 - - + +
472A ILE* 4.3 22.0 - - + +
475A ALA* 4.6 7.9 - - + -
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Residues in contact with LEU 464 (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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209A GLY* 3.3 29.6 - - - +
212A THR* 3.1 33.0 - - + +
213A PRO* 3.8 11.4 - - + -
229A LEU* 4.3 11.0 - - + +
232A ASP* 3.8 30.1 - - + +
236A ILE* 4.4 0.4 - - + -
460A GLY 2.9 28.0 + - - +
461A ILE* 3.3 15.7 - - + +
463A LEU* 1.3 75.3 - - - +
465A ALA* 1.3 65.3 + - - +
467A GLY* 3.2 14.1 + - - -
472A ILE* 6.3 0.7 - - + -
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Residues in contact with ALA 465 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A VAL* 6.2 2.5 - - + -
33A LEU* 3.5 26.7 - - + +
229A LEU* 3.6 25.8 - - + +
461A ILE* 2.5 23.6 + - + +
462A ILE* 3.3 12.8 - - + +
464A LEU* 1.3 75.9 - - - +
466A LEU* 1.3 60.9 + - + +
467A GLY* 3.4 0.7 + - - -
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Residues in contact with LEU 466 (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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29A THR* 3.5 34.5 - - + +
33A LEU* 3.6 24.7 - - + -
36A SER* 4.1 3.8 - - - -
37A ASN* 3.4 32.3 + - - +
40A ILE* 4.0 28.7 - - + -
462A ILE* 2.7 33.2 + - + +
463A LEU* 4.3 3.6 - - + +
464A LEU 3.3 0.2 - - - -
465A ALA* 1.3 74.4 - - - +
467A GLY* 1.3 64.6 + - - +
471A PRO* 3.6 25.6 - - + -
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Residues in contact with GLY 467 (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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37A ASN* 4.1 2.9 - - - +
463A LEU 3.6 6.2 + - - -
464A LEU* 3.2 13.5 + - - -
465A ALA 3.2 4.3 - - - -
466A LEU* 1.3 85.5 - - - +
468A GLY* 1.3 67.1 + - - +
471A PRO* 3.4 12.6 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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