Contacts of the helix formed by residues 477 - 498 (chain A) in PDB entry 1W1J
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 477 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474A ASN* 2.8 28.7 + - + +
476A LYS* 1.3 75.0 - - - +
478A LEU* 1.3 59.3 + - - +
479A ILE* 3.3 15.5 + - - +
480A GLN* 3.2 38.7 + - + +
481A LYS* 3.2 29.5 + - - +
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Residues in contact with LEU 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 LYS* 3.2 13.4 + - - +
477A ASP* 1.3 70.7 + - - +
479A ILE* 1.3 67.0 + - + +
480A GLN 3.1 1.1 - - - -
481A LYS* 3.7 14.2 - - + +
482A ARG* 3.1 51.0 + - - +
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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
----------------------------------------------------------
477A ASP* 3.3 10.6 + - - +
478A LEU* 1.3 78.5 - - + +
480A GLN* 1.3 61.5 + - - +
482A ARG* 3.8 22.4 + - - +
483A LYS* 3.2 50.7 + - + +
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Residues in contact with GLN 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LEU* 4.0 14.3 - - - +
450A ALA 5.6 1.1 - - - +
451A GLY 5.0 4.4 + - - -
452A LEU* 3.7 30.6 - - + +
473A PHE* 3.1 11.8 - - + +
474A ASN* 2.7 35.8 + - - +
477A ASP* 3.2 32.5 + - + +
478A LEU 3.1 0.4 - - - -
479A ILE* 1.3 75.8 - - - +
481A LYS* 1.3 67.5 + - - +
483A LYS* 2.7 24.1 + - + +
484A VAL* 2.9 17.0 + - + +
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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
----------------------------------------------------------
62A HIS* 3.1 35.1 + - - -
63A VAL* 3.5 18.9 - - - +
64A MET 2.6 31.7 + - - -
65A ASP* 4.1 6.9 - - - +
66A GLN* 4.2 1.2 - - - +
473A PHE* 4.2 17.4 - - + -
475A LYS* 3.3 28.0 + - - +
476A LYS 5.2 0.7 - - - -
477A ASP 3.2 22.6 + - - +
478A LEU* 3.3 15.9 + - + +
480A GLN* 1.3 77.7 - - - +
482A ARG* 1.3 56.7 + - - +
484A VAL* 3.4 7.4 + - - +
485A GLN* 2.9 31.8 + - - +
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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
----------------------------------------------------------
478A LEU* 3.1 48.2 + - - +
479A ILE* 3.9 23.7 - - - +
481A LYS* 1.3 76.7 - - - +
483A LYS* 1.3 57.1 + - + +
485A GLN* 3.3 19.3 + - - +
486A TRP* 2.8 26.9 + - - +
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Residues in contact with LYS 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A GLU 5.4 2.7 - - - +
450A ALA* 4.0 34.9 + - + +
451A GLY* 5.9 0.9 - - - -
452A LEU* 6.1 0.7 - - + -
479A ILE* 3.2 42.3 + - + +
480A GLN* 2.7 19.6 + - + +
482A ARG* 1.3 72.2 - - + +
484A VAL* 1.3 53.8 + - + +
486A TRP* 3.1 13.8 + - + +
487A LEU* 2.6 36.3 + - - +
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Residues in contact with VAL 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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63A VAL* 4.1 11.9 - - + -
423A LEU* 3.5 29.6 - - + -
452A LEU* 4.1 17.7 - - + -
471A ILE* 3.6 31.6 - - + -
473A PHE* 3.9 22.0 - - + -
480A GLN* 2.9 15.6 + - + +
481A LYS* 3.7 8.5 - - - +
483A LYS* 1.3 72.8 - - + +
485A GLN* 1.3 60.0 + - - +
487A LEU* 3.5 6.7 - - - +
488A MET* 2.8 30.4 + - - +
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Residues in contact with GLN 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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63A VAL* 3.6 19.3 - - + +
64A MET* 3.0 43.7 - - - +
481A LYS* 2.9 15.5 + - - +
482A ARG* 3.3 22.2 - - - +
484A VAL* 1.3 80.7 - - - +
486A TRP* 1.3 59.7 + - - +
488A MET* 4.1 0.5 - - - +
489A ARG* 3.4 35.5 + - - +
509A PHE* 4.4 18.6 - - + -
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Residues in contact with TRP 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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446A ARG* 3.8 41.7 - - - -
449A GLU* 3.4 29.8 - - + -
450A ALA* 4.2 15.0 - - + -
482A ARG 2.8 15.0 + - - +
483A LYS* 3.1 14.6 + - + +
485A GLN* 1.3 74.3 - - - +
487A LEU* 1.3 77.7 + - + +
489A ARG* 3.9 2.8 - - - +
490A THR* 2.3 55.9 + - + +
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Residues in contact with LEU 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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446A ARG* 3.6 30.7 - - + +
447A CYS* 3.7 13.0 - - - +
450A ALA* 4.1 8.1 - - + -
452A LEU* 3.2 33.9 - - + -
471A ILE* 3.7 23.3 - - + -
483A LYS 2.6 19.9 + - - +
484A VAL* 3.5 5.2 - - - +
486A TRP* 1.3 78.8 - - - +
488A MET* 1.3 57.0 + - - +
490A THR* 3.1 3.9 + - - -
491A LEU* 2.8 70.9 + - + +
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Residues in contact with MET 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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423A LEU* 4.2 20.2 - - + -
424A PHE 4.0 11.4 - - - +
425A PHE* 3.0 53.4 - - + -
426A SER 5.1 0.2 - - - +
471A ILE* 4.6 5.4 - - + -
484A VAL 2.8 20.2 + - - +
485A GLN 4.1 0.2 - - - +
487A LEU* 1.3 76.6 - - - +
489A ARG* 1.3 59.1 + - - +
491A LEU* 3.3 5.1 + - - +
492A ILE* 2.9 47.6 + - + +
502A GLU* 5.2 0.2 - - + -
506A HIS* 6.0 2.0 - - + +
509A PHE* 3.6 42.2 - - + -
513A ILE* 4.8 9.2 - - + -
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Residues in contact with ARG 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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64A MET* 5.1 7.3 - - - +
485A GLN* 3.4 24.8 + - - +
486A TRP* 4.2 3.6 - - - +
487A LEU 3.3 0.2 - - - -
488A MET* 1.3 79.7 - - - +
490A THR* 1.3 61.4 + - - +
492A ILE* 4.1 1.1 - - - -
493A ASP* 3.7 12.0 + - - +
508A ALA* 2.7 34.6 + - - +
509A PHE* 3.3 21.1 - - + +
512A GLN* 3.0 63.8 + - - +
560A LEU* 3.9 33.7 + - - +
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Residues in contact with THR 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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446A ARG* 3.6 42.6 - - - +
486A TRP* 2.3 54.1 + - + +
487A LEU* 3.5 4.5 - - - -
489A ARG* 1.3 74.2 - - - +
491A LEU* 1.3 55.7 + - - +
493A ASP* 3.1 8.8 + - - +
494A ASP* 2.8 34.9 + - - +
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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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425A PHE* 3.7 31.9 - - + -
442A VAL* 3.9 18.2 - - + +
443A THR* 3.6 49.8 - - + +
446A ARG* 4.0 9.0 - - + -
447A CYS* 4.9 1.6 - - - -
469A VAL* 5.4 0.4 - - + -
471A ILE* 5.3 2.9 - - + -
487A LEU* 2.8 53.4 + - + +
488A MET* 3.6 4.3 - - - +
490A THR* 1.3 68.5 - - - +
492A ILE* 1.3 67.4 + - - +
494A ASP* 2.8 5.6 + - - +
495A CYS* 2.8 28.4 + - - -
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Residues in contact with ILE 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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425A PHE* 3.7 5.8 - - + -
488A MET* 2.9 41.7 + - + +
490A THR 3.4 0.2 - - - -
491A LEU* 1.3 73.2 - - - +
493A ASP* 1.3 62.1 + - - +
496A ALA* 3.1 19.2 + - - +
500A TRP 4.8 0.3 - - - +
502A GLU* 3.3 20.1 - - - +
509A PHE* 3.9 16.8 - - + -
512A GLN* 3.6 40.8 - - + +
513A ILE* 3.8 35.4 - - + -
516A THR* 3.8 19.1 + - + +
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Residues in contact with ASP 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 ARG 3.7 12.0 + - - +
490A THR* 3.1 10.6 + - + +
492A ILE* 1.3 79.0 - - - +
494A ASP* 1.3 65.9 + - - +
496A ALA* 3.1 7.6 + - - +
497A ALA* 2.9 24.7 + - - +
512A GLN* 3.2 17.5 + - - +
516A THR* 5.1 2.8 + - - -
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Residues in contact with ASP 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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442A VAL* 3.8 21.1 - - + +
446A ARG* 2.6 53.2 + - - +
490A THR* 2.8 16.4 + - - +
491A LEU* 3.3 9.6 - - - +
493A ASP* 1.3 75.2 - - - +
495A CYS* 1.3 63.1 + - - +
497A ALA* 3.2 8.0 + - - +
498A ASN* 2.8 32.6 + - - +
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Residues in contact with CYS 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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425A PHE* 3.4 26.0 - - + -
427A PRO* 4.6 7.0 - - + -
439A GLN* 4.7 5.8 - - - -
442A VAL* 4.4 9.9 - - - -
443A THR* 4.8 0.9 - - - -
491A LEU* 2.8 27.4 + - - +
494A ASP* 1.3 76.6 - - - +
496A ALA* 1.3 58.9 + - - +
498A ASN* 3.1 2.0 + - - -
499A GLY 2.9 10.7 + - - -
500A TRP* 2.8 61.3 + - + +
502A GLU* 4.0 9.0 - - - +
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Residues in contact with ALA 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 ILE 3.1 14.3 + - - +
493A ASP* 3.1 12.4 + - - +
495A CYS* 1.3 75.9 - - - +
497A ALA* 1.3 57.1 + - - +
499A GLY* 2.8 20.8 + - - -
500A TRP 3.6 10.9 + - - +
516A THR* 4.0 24.5 - - + +
217B LEU* 4.6 10.2 - - + +
218B PRO* 4.9 0.9 - - + +
220B PRO* 3.5 7.8 - - - +
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Residues in contact with ALA 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 ASP 2.9 12.5 + - - +
494A ASP* 3.2 13.4 + - - +
496A ALA* 1.3 75.7 - - - +
498A ASN* 1.3 62.4 + - - +
499A GLY 3.4 0.4 - - - -
220B PRO* 3.4 21.5 - - - +
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Residues in contact with ASN 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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438A MET* 4.4 16.8 - - + +
442A VAL* 4.1 19.1 - - - +
494A ASP* 2.8 20.1 + - - +
495A CYS 3.1 4.6 + - - +
496A ALA 3.1 1.0 - - - -
497A ALA* 1.3 84.3 + - - +
499A GLY* 1.3 58.2 + - - +
500A TRP* 3.4 30.0 - - + -
220B PRO* 4.1 3.8 - - - -
237B LYS* 2.6 35.1 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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