Contacts of the helix formed by residues 476 - 498 (chain A) in PDB entry 4FWF
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 ASP 476 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474A ILE 3.5 2.9 + - - -
475A THR* 1.3 76.4 - - - +
477A PRO* 1.3 78.2 - - - +
478A THR* 2.5 43.0 + - - +
479A ILE* 2.9 30.5 + - + +
480A ASP* 3.3 6.2 + - - +
531A LEU* 5.9 0.6 - - + +
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Residues in contact with PRO 477 (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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474A ILE* 6.1 0.9 - - + -
475A THR 3.3 7.3 - - - +
476A ASP* 1.3 90.2 - - - +
478A THR* 1.3 61.7 + - + +
479A ILE 3.2 0.2 + - - -
480A ASP* 3.4 6.1 + - + +
481A LYS* 3.2 30.4 + - - +
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Residues in contact with THR 478 (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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476A ASP* 2.5 29.6 + - - +
477A PRO* 1.3 75.7 - - + +
479A ILE* 1.3 57.4 + - - +
481A LYS* 4.3 8.0 - - + +
482A ARG* 3.0 37.7 + - - +
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Residues in contact with ILE 479 (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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475A THR* 3.9 17.5 - - + -
476A ASP* 2.9 21.2 + - + +
478A THR* 1.3 79.4 + - - +
480A ASP* 1.3 66.3 + - - +
481A LYS 3.3 0.2 - - - -
482A ARG* 3.5 27.1 + - - +
483A MET* 3.2 30.0 + - + +
531A LEU* 5.0 12.6 - - + -
532A GLU* 4.7 14.4 - - + -
535A VAL* 5.1 3.8 - - + -
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Residues in contact with ASP 480 (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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465A CYS 4.5 9.0 - - - +
467A LEU* 3.8 30.2 - - + +
475A THR* 4.7 6.5 - - + +
476A ASP 3.3 7.0 + - - +
477A PRO* 4.0 7.6 - - + +
479A ILE* 1.3 74.7 - - - +
481A LYS* 1.3 67.3 + - - +
483A MET* 3.2 1.7 + - - +
484A ASP* 2.9 25.2 + - - +
535A VAL* 4.5 9.0 - - - -
539A HIS* 3.4 23.6 + - - -
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Residues in contact with LYS 481 (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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477A PRO 3.2 15.7 + - - +
478A THR* 4.5 7.2 - - + -
480A ASP* 1.3 80.7 - - - +
482A ARG* 1.3 57.3 + - + +
484A ASP* 3.4 7.2 + - - +
485A PHE* 3.1 24.3 + - - +
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Residues in contact with ARG 482 (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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478A THR* 3.0 39.6 + - - +
479A ILE* 3.7 22.5 - - - +
481A LYS* 1.3 78.4 - - + +
483A MET* 1.3 72.9 + - + +
485A PHE* 3.4 12.1 - - + +
486A HIS* 3.0 25.6 + - - +
532A GLU* 2.8 31.5 + - - -
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Residues in contact with MET 483 (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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479A ILE* 3.2 19.6 + - + +
480A ASP 3.9 0.4 - - - +
482A ARG* 1.3 101.4 - - + +
484A ASP* 1.3 61.6 + - - +
485A PHE 3.2 0.4 - - - -
486A HIS* 3.8 13.2 - - + +
487A PHE* 3.0 28.6 + - - +
528A PHE* 3.8 29.2 - - + -
532A GLU* 3.5 43.7 - - + +
535A VAL* 3.7 25.1 - - + -
536A LEU* 4.4 14.0 - - - +
539A HIS* 4.0 5.9 - - + -
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Residues in contact with ASP 484 (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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480A ASP* 2.9 20.9 + - - +
481A LYS* 3.4 7.6 - - - +
483A MET* 1.3 73.2 - - - +
485A PHE* 1.3 64.0 + - - +
487A PHE* 3.6 6.0 + - - +
488A ASN* 3.1 40.2 + - - +
539A HIS* 2.7 37.3 + - + +
8E ARG* 4.2 9.8 - - - +
9E LYS 4.5 7.9 - - - +
10E SER* 5.6 0.3 - - - -
11E THR* 4.9 3.1 + - - -
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Residues in contact with PHE 485 (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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481A LYS 3.1 13.5 + - - +
482A ARG* 3.4 15.5 - - + +
483A MET 3.2 0.2 - - - -
484A ASP* 1.3 73.6 - - - +
486A HIS* 1.3 73.2 + + + +
488A ASN* 3.0 17.2 + - - +
489A ALA* 3.1 23.1 + - + +
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Residues in contact with HIS 486 (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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482A ARG 3.0 17.3 + - - +
483A MET* 3.6 15.2 + - + +
485A PHE* 1.3 83.6 - + + +
487A PHE* 1.3 63.7 + - - +
489A ALA* 3.2 8.8 + - + +
490A LEU* 3.1 46.9 + - + +
517A TYR* 4.3 11.9 - + - -
520A PHE* 3.8 33.0 - + + +
528A PHE* 3.5 39.1 - + - -
536A LEU* 4.7 9.1 - - + +
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Residues in contact with PHE 487 (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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483A MET 3.0 19.9 + - - +
484A ASP* 3.7 7.0 - - - +
485A PHE 3.2 0.2 - - - -
486A HIS* 1.3 78.0 + - - +
488A ASN* 1.3 69.7 + - - +
490A LEU* 3.4 13.0 + - + +
491A LEU* 3.4 41.3 + - + +
513A ILE* 5.4 0.4 - - + -
536A LEU* 3.9 15.9 - - + +
539A HIS* 3.7 45.3 - + + -
540A LEU* 3.6 31.0 - - + -
542A ASN* 6.1 0.2 - - + -
543A LEU* 3.8 20.2 - - + -
5E GLN* 5.3 1.8 - - - -
10E SER* 3.5 25.8 - - - -
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Residues in contact with ASN 488 (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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484A ASP* 3.1 27.3 + - - +
485A PHE* 3.0 7.3 + - - +
487A PHE* 1.3 92.6 - - - +
489A ALA* 1.3 59.8 + - - +
491A LEU* 3.4 0.7 + - - +
492A ASP* 2.9 27.7 + - - +
10E SER* 3.7 5.5 - - - +
11E THR* 2.9 46.8 + - - +
12E GLY* 3.0 27.7 - - - +
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Residues in contact with ALA 489 (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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485A PHE* 3.1 25.4 + - + +
486A HIS* 3.5 16.6 - - + +
488A ASN* 1.3 75.8 - - - +
490A LEU* 1.3 66.9 + - + +
492A ASP* 3.1 11.7 + - - +
493A VAL* 2.8 28.2 + - + +
520A PHE* 5.3 9.2 - - + -
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Residues in contact with LEU 490 (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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486A HIS* 3.1 46.6 + - + +
487A PHE* 3.5 17.5 - - + +
488A ASN 3.3 0.2 - - - -
489A ALA* 1.3 75.5 - - - +
491A LEU* 1.3 59.5 + - + +
493A VAL* 2.9 20.3 + - - +
494A VAL* 2.9 17.8 + - - +
513A ILE* 3.8 37.5 - - + +
516A ILE* 4.3 16.6 - - + +
517A TYR* 4.6 12.8 - - + -
520A PHE* 4.0 18.4 - - + -
536A LEU* 4.6 15.0 - - + -
540A LEU* 5.6 0.2 - - + -
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Residues in contact with LEU 491 (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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487A PHE* 3.4 43.4 + - + +
488A ASN* 3.7 1.8 - - - +
489A ALA 3.2 0.2 - - - -
490A LEU* 1.3 78.7 - - + +
492A ASP* 1.3 57.4 + - - +
494A VAL* 3.1 9.3 + - + +
495A SER* 2.9 29.3 + - - -
509A LEU* 4.2 20.0 - - + -
513A ILE* 4.3 11.2 - - + -
543A LEU* 4.0 23.1 - - + -
559A TRP* 4.3 15.7 - - + +
2E ARG* 4.5 4.7 - - - +
10E SER* 4.2 7.9 - - - +
12E GLY* 3.6 32.5 - - - -
13E GLY 4.3 3.6 - - - +
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Residues in contact with ASP 492 (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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488A ASN* 2.9 17.3 + - - +
489A ALA* 3.3 13.9 - - - +
491A LEU* 1.3 75.9 - - - +
493A VAL* 1.3 60.7 + - + +
495A SER* 3.1 18.1 + - - -
496A GLU* 3.3 14.2 + - - +
11E THR 4.7 2.8 - - - +
12E GLY 2.7 24.3 + - - +
13E GLY* 3.8 7.6 - - - -
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Residues in contact with VAL 493 (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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489A ALA* 2.8 22.8 + - + +
490A LEU 3.3 7.0 - - - +
492A ASP* 1.3 71.1 - - + +
494A VAL* 1.3 60.9 + - - +
496A GLU* 3.1 8.9 + - + +
497A TRP* 2.8 29.8 + - + +
516A ILE* 3.7 37.7 - - + -
520A PHE* 4.3 17.0 - - + -
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Residues in contact with VAL 494 (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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490A LEU 2.9 19.3 + - - +
491A LEU* 3.1 14.6 + - + +
493A VAL* 1.3 76.5 - - - +
495A SER* 1.3 58.8 + - - +
497A TRP* 3.1 10.7 + - + +
498A ARG* 3.0 32.7 + - - +
509A LEU* 4.1 27.6 - - + -
512A LYS* 3.8 17.9 - - + -
513A ILE* 4.5 10.1 - - + -
516A ILE* 3.7 17.5 - - + -
556A ALA* 4.1 21.3 - - + +
559A TRP* 4.9 2.0 - - - +
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Residues in contact with SER 495 (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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491A LEU 2.9 5.8 + - - -
492A ASP* 3.1 17.3 + - - -
493A VAL 3.3 0.2 - - - -
494A VAL* 1.3 76.4 - - - +
496A GLU* 1.3 60.5 + - - +
498A ARG* 3.5 34.8 + - - +
499A LYS* 3.8 21.8 + - - +
13E GLY* 3.4 35.5 + - - -
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Residues in contact with GLU 496 (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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492A ASP 3.3 14.2 + - - +
493A VAL* 3.1 13.8 + - + +
495A SER* 1.3 75.4 + - - +
497A TRP* 1.3 66.1 - - - +
498A ARG 3.2 0.5 + - - -
499A LYS* 3.1 45.2 + - - +
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Residues in contact with TRP 497 (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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493A VAL* 2.8 16.1 + - + +
494A VAL* 3.4 11.4 - - + +
496A GLU* 1.3 78.2 - - - +
498A ARG* 1.3 88.7 + - + +
499A LYS 3.3 2.9 + - - +
501A LYS* 3.3 46.9 - - + +
505A GLN 3.8 24.2 - - - -
506A ASP* 4.3 4.0 - - - -
507A VAL* 4.2 20.4 - - + -
512A LYS* 3.1 42.9 - - + +
516A ILE* 5.5 0.9 - - + -
556A ALA* 4.0 20.6 - - + -
557A ARG* 4.4 8.1 - - + -
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Residues in contact with ARG 498 (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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494A VAL* 3.0 10.1 + - - +
495A SER* 3.5 32.3 + - - +
496A GLU 3.2 0.8 - - - -
497A TRP* 1.3 98.0 - - + +
499A LYS* 1.3 64.7 + - + +
500A ASP 3.4 0.7 + - - -
501A LYS* 3.4 20.6 + - - +
556A ALA 3.4 13.3 + - - +
557A ARG* 3.5 31.7 + - + +
559A TRP* 3.1 22.4 - - - +
560A ASP* 2.7 42.4 + - - -
13E GLY 3.2 18.2 + - - -
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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