Contacts of the helix formed by residues 451 - 472 (chain A) in PDB entry 1RQG
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 ARG 451 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A GLU* 3.8 9.0 - - - +
446A LEU* 2.8 49.2 + - + +
447A ILE 4.2 0.2 + - - -
449A ASN* 3.5 25.7 - - + +
450A TYR* 1.3 75.8 - - - +
452A PHE* 1.3 59.2 + - - +
453A LYS 3.5 2.2 - - - -
454A ASP* 3.3 27.7 + - + -
455A ALA* 2.8 28.4 + - - +
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Residues in contact with PHE 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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28A PRO* 3.7 26.7 - - + -
31A ILE* 3.5 29.2 - - + -
32A PHE* 4.3 8.1 - - + -
294A PHE* 3.9 23.3 - + - -
333A PRO* 6.3 0.4 - - + -
335A ASN* 5.4 5.6 - - - -
372A THR* 3.7 9.1 - - + +
375A MET* 3.4 33.2 - - + -
377A GLU* 3.1 8.7 + - + -
447A ILE* 4.2 16.2 - - + -
450A TYR* 3.4 40.6 - + + -
451A ARG* 1.3 69.6 - - - +
453A LYS* 1.3 60.8 + - - +
454A ASP 3.1 1.3 - - - -
455A ALA* 3.5 5.3 - - - +
456A LEU* 2.7 36.2 + - - +
507A PHE* 3.9 1.4 - - + -
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Residues in contact with LYS 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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372A THR* 3.4 19.6 + - - +
373A THR* 3.1 27.8 + - - +
374A ILE* 3.6 12.7 + - - +
375A MET* 2.8 30.0 + - + +
377A GLU* 3.1 25.2 + - - +
379A ARG* 5.3 9.7 - - - +
381A SER* 4.2 5.7 + - - -
452A PHE* 1.3 75.4 - - - +
454A ASP* 1.3 64.5 + - - +
456A LEU* 3.9 2.8 + - - +
457A LYS* 3.3 40.7 + - + +
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Residues in contact with ASP 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLU* 4.8 2.2 + - - -
446A LEU* 3.3 23.1 - - + +
451A ARG* 3.3 35.8 + - + +
452A PHE 3.1 0.2 - - - -
453A LYS* 1.3 81.3 - - - +
455A ALA* 1.3 60.9 + - - +
457A LYS* 3.2 23.8 + - - +
458A ARG* 2.9 23.7 + - - +
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Residues in contact with ALA 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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443A VAL* 3.9 7.2 - - + +
446A LEU* 3.5 22.4 - - + -
447A ILE* 3.9 14.8 - - + -
451A ARG 2.8 19.5 + - - +
452A PHE* 3.0 8.0 + - - +
454A ASP* 1.3 75.1 - - - +
456A LEU* 1.3 66.4 + - - +
458A ARG* 3.0 15.6 + - - +
459A VAL* 3.2 14.6 + - - +
507A PHE* 3.8 16.8 - - + -
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Residues in contact with LEU 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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369A TYR* 3.6 47.8 - - + +
372A THR* 3.7 28.5 - - + -
373A THR* 4.3 8.3 - - - +
452A PHE 2.7 18.9 + - - +
453A LYS 4.1 3.4 - - - +
455A ALA* 1.3 75.0 - - - +
457A LYS* 1.3 58.0 + - - +
459A VAL* 3.2 10.3 + - + +
460A MET* 2.9 32.1 + - + +
504A LEU* 5.4 3.6 - - + -
507A PHE* 3.5 40.0 - - + -
508A LEU* 5.8 1.3 - - + -
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Residues in contact with LYS 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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373A THR 5.7 0.6 + - - -
391A ARG* 5.9 3.9 - - - +
453A LYS* 3.3 32.3 + - - +
454A ASP* 3.2 26.2 + - - +
455A ALA 3.1 0.8 - - - -
456A LEU* 1.3 77.1 - - - +
458A ARG* 1.3 65.1 + - - +
459A VAL 3.1 0.2 - - - -
460A MET* 3.3 7.4 + - + +
461A SER* 3.0 24.9 + - - -
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Residues in contact with ARG 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A GLU* 3.5 24.8 + - - -
438A LYS* 3.9 8.3 - - - +
439A ALA* 3.2 35.6 - - - +
442A GLU* 3.4 35.5 + - + +
443A VAL* 3.5 12.5 - - + +
446A LEU* 4.1 18.4 - - + -
454A ASP 2.9 10.0 + - - +
455A ALA 3.0 9.1 + - - +
457A LYS* 1.3 77.1 - - - +
459A VAL* 1.3 59.6 + - - +
461A SER* 2.6 38.5 + - - -
462A LEU* 3.4 17.5 + - - +
465A PHE* 5.8 0.2 - - - +
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Residues in contact with VAL 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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400A LEU* 5.9 0.2 - - + -
439A ALA* 5.9 0.2 - - - -
443A VAL* 3.8 25.4 - - + -
455A ALA 3.2 6.9 + - - +
456A LEU* 3.4 11.7 - - + +
457A LYS 3.1 0.4 - - - -
458A ARG* 1.3 74.2 - - - +
460A MET* 1.3 74.8 + - - +
461A SER 3.1 1.6 - - - -
462A LEU* 2.9 17.6 + - - +
463A ALA* 3.2 7.8 + - - +
500A LEU* 4.0 12.9 - - + +
503A LEU* 3.8 31.2 - - + +
504A LEU* 3.2 33.9 - - + -
507A PHE* 4.5 6.5 - - + -
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Residues in contact with MET 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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369A TYR* 3.4 41.1 - - + +
395A GLU* 3.7 28.9 - - + +
396A LEU* 4.3 4.7 - - + -
399A ASN* 3.6 10.8 - - + +
400A LEU* 3.7 35.4 - - + -
456A LEU* 2.9 24.9 + - + +
457A LYS* 3.3 8.7 + - + +
459A VAL* 1.3 83.7 - - - +
461A SER* 1.3 52.0 + - - +
463A ALA* 3.0 7.5 + - - +
464A SER* 2.7 35.0 + - - +
504A LEU* 5.1 1.1 - - - -
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Residues in contact with SER 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A LYS 3.0 13.9 + - - -
458A ARG* 2.6 42.6 + - - -
460A MET* 1.3 73.7 - - - +
462A LEU* 1.3 53.8 + - - +
464A SER* 3.0 13.1 + - - -
465A PHE* 2.6 34.8 + - - +
468A ARG* 4.8 2.5 + - - -
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Residues in contact with LEU 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A GLU* 4.3 24.9 - - + +
436A ILE* 4.6 8.5 - - + +
439A ALA* 4.1 9.2 - - + -
458A ARG* 3.4 14.3 + - - +
459A VAL* 2.9 12.0 + - - +
461A SER* 1.3 77.7 + - - +
463A ALA* 1.3 62.0 + - - +
465A PHE* 3.1 22.4 + - + +
466A GLY* 2.9 24.6 + - - -
496A ILE* 4.0 21.9 - - + +
499A ALA* 4.7 11.2 - - + -
500A LEU* 3.5 22.0 - - + -
503A LEU* 3.7 21.8 - - + -
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Residues in contact with ALA 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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399A ASN* 3.3 15.3 - - - +
400A LEU* 3.6 35.2 - - + -
403A PHE* 4.3 7.5 - - + -
459A VAL 3.2 4.3 + - - +
460A MET* 3.0 13.3 + - - +
462A LEU* 1.3 79.0 - - - +
464A SER* 1.3 63.7 + - - +
466A GLY* 3.0 2.3 + - - +
467A ASN* 3.0 26.3 + - - -
500A LEU* 3.7 14.1 - - + +
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Residues in contact with SER 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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399A ASN* 3.5 23.7 + - - +
460A MET* 2.7 22.1 + - - +
461A SER* 3.1 18.6 - - - -
463A ALA* 1.3 77.5 - - - +
465A PHE* 1.3 57.8 + - - +
467A ASN* 3.4 3.2 + - - +
468A ARG* 3.2 39.0 + - - -
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Residues in contact with PHE 465 (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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428A LEU* 4.5 18.4 - - + -
431A GLU* 4.3 15.9 - - - -
432A ALA* 3.5 44.6 - - + -
435A GLU* 3.7 33.0 - - + +
461A SER 2.6 15.9 + - - +
462A LEU* 3.1 24.9 + - + +
464A SER* 1.3 72.9 - - - +
466A GLY* 1.3 63.0 + - - +
468A ARG* 3.3 24.5 + - + +
469A TYR* 2.9 32.4 + + + +
496A ILE* 4.1 10.1 - - + -
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Residues in contact with GLY 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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403A PHE* 3.5 32.4 - - - -
462A LEU 2.9 13.8 + - - -
463A ALA 3.0 4.0 + - - -
465A PHE* 1.3 78.7 - - - +
467A ASN* 1.3 65.0 + - - +
469A TYR* 3.1 9.0 - - - +
470A PHE* 3.0 20.6 + - - +
496A ILE* 4.2 5.6 - - - -
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Residues in contact with ASN 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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398A ASN 4.5 2.0 + - - -
399A ASN* 3.0 51.5 + - - +
402A ASN* 4.2 4.1 - - - +
403A PHE* 3.5 17.4 + - - +
406A ARG* 2.8 41.6 + - - +
463A ALA 3.0 11.7 + - - -
464A SER 3.7 7.6 - - - +
466A GLY* 1.3 74.6 - - - +
468A ARG* 1.3 53.7 + - - +
470A PHE 3.1 1.6 + - - -
471A ASP* 2.7 39.6 + - - +
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Residues in contact with ARG 468 (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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461A SER* 4.8 1.4 + - - -
464A SER* 3.2 25.3 + - - -
465A PHE* 3.6 35.8 - - + +
467A ASN* 1.3 76.2 - - - +
469A TYR* 1.3 65.5 + - - +
471A ASP* 3.0 11.9 + - + +
472A HIS* 2.9 52.2 + - + +
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Residues in contact with TYR 469 (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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403A PHE* 6.0 0.2 - + - -
428A LEU* 3.8 48.0 - - + -
429A ASP* 2.8 21.9 + - - -
432A ALA* 4.1 13.5 - - + -
465A PHE* 2.9 22.5 + + + +
466A GLY* 3.1 14.1 - - - +
468A ARG* 1.3 79.2 - - - +
470A PHE* 1.3 73.1 + + - +
472A HIS* 3.2 15.8 + - - -
473A LYS* 3.0 29.6 - - + +
489A THR* 3.7 31.6 - - + -
492A ILE* 3.4 34.2 - - + +
493A SER* 4.4 4.5 - - - -
496A ILE* 4.9 4.7 - - + -
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Residues in contact with PHE 470 (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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403A PHE* 4.1 15.9 - + - -
406A ARG* 3.6 24.2 - - + +
407A ALA* 4.1 19.5 - - + -
410A PHE* 3.0 47.3 - + + -
466A GLY 3.0 3.4 + - - +
467A ASN 3.4 7.4 - - - +
469A TYR* 1.3 86.6 - + - +
471A ASP* 1.3 64.3 + - - +
472A HIS 3.1 1.0 + - - -
473A LYS* 3.2 5.8 + - - -
474A GLN* 3.2 20.8 + - - -
475A PRO* 3.5 34.0 - - + +
476A TRP* 3.9 4.4 - + - -
489A THR* 5.0 3.4 - - + -
490A VAL* 5.3 3.8 - - + -
493A SER* 3.2 37.5 - - - -
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Residues in contact with ASP 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ARG* 2.9 26.8 + - - -
467A ASN* 2.7 28.0 + - - +
468A ARG* 3.4 12.9 - - + +
470A PHE* 1.3 72.4 - - - +
472A HIS* 1.3 62.5 + - + +
474A GLN* 3.6 18.5 + - - +
476A TRP* 4.0 12.5 - - - -
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Residues in contact with HIS 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A LEU* 3.5 29.3 - - + +
468A ARG* 2.9 59.8 + - + +
469A TYR* 3.4 6.3 + - - -
471A ASP* 1.3 79.9 - - + +
473A LYS* 1.3 63.0 + - - +
474A GLN* 4.6 6.1 - - - +
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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