Contacts of the helix formed by residues 453 - 471 (chain A) in PDB entry 1W6J
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 VAL 453 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A PHE 3.0 5.1 + - - -
444A PHE* 4.1 12.1 - - + +
451A TRP 3.7 5.6 - - - +
452A ILE* 1.3 84.7 - - - +
454A SER* 1.3 63.8 + - - +
455A ASP* 3.3 17.7 - - - +
456A CYS* 3.7 23.3 - - - -
457A THR* 2.8 29.0 + - - -
502A THR* 3.3 35.2 - - - +
503A TYR* 3.5 26.5 - - + +
1733A R71 4.1 10.3 - - + +
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Residues in contact with SER 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A VAL* 1.3 73.0 - - - +
455A ASP* 1.3 65.9 + - - +
458A ALA* 3.1 23.7 + - - +
490A LEU* 3.4 11.2 - - - +
493A MET* 3.7 30.6 - - - +
500A PHE* 4.7 6.5 - - - -
501A ALA 2.5 26.9 + - - -
502A THR* 2.8 16.9 + - - -
504A GLU 5.8 0.2 - - - -
533A CYS* 3.6 9.9 - - - +
537A VAL* 4.0 13.4 - - - +
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Residues in contact with ASP 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A TRP* 4.0 13.8 - - + -
453A VAL* 3.3 18.7 - - - +
454A SER* 1.3 76.5 + - - +
456A CYS* 1.3 67.1 + - - +
458A ALA* 3.4 6.4 + - - +
459A GLU* 3.0 36.2 + - + +
532A GLU* 5.0 3.4 - - - +
533A CYS* 3.7 19.9 + - - +
536A ALA* 4.1 18.8 - - + -
581A TRP* 5.5 0.3 - - - -
1733A R71 2.7 42.8 + - - -
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Residues in contact with CYS 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ILE* 4.8 5.3 - - + +
387A TRP* 3.7 26.2 - - + +
390A ALA* 5.3 0.5 - - - +
442A PHE* 3.6 12.1 - - - +
443A SER 3.6 18.2 - - - +
444A PHE* 3.5 33.2 - - - -
453A VAL* 3.5 14.9 + - - +
454A SER 3.4 0.4 - - - -
455A ASP* 1.3 90.7 + - - +
457A THR* 1.3 60.3 + - - +
459A GLU* 4.1 2.3 - - - +
460A ALA* 3.0 31.7 + - - +
1733A R71 4.7 0.7 - - - -
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Residues in contact with THR 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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441A GLY* 3.6 17.4 - - - -
442A PHE* 3.0 29.2 + - + -
452A ILE* 4.4 1.9 - - - +
453A VAL 2.8 23.8 + - - -
454A SER* 3.6 4.9 - - - -
456A CYS* 1.3 77.9 - - - +
458A ALA* 1.3 55.9 + - - +
460A ALA* 3.9 1.2 - - - +
461A LEU* 2.9 31.5 + - - +
486A ALA* 3.9 32.5 - - + +
489A VAL* 4.5 6.2 - - + +
490A LEU* 3.9 14.4 - - + -
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Residues in contact with ALA 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A SER 3.1 17.3 + - - +
455A ASP* 3.6 6.1 - - - +
456A CYS 3.3 0.2 - - - -
457A THR* 1.3 77.4 - - - +
459A GLU* 1.3 57.6 - - - +
461A LEU* 3.4 1.5 + - - +
462A LYS* 2.8 26.1 + - - +
490A LEU* 4.3 7.4 - - + +
536A ALA* 3.4 33.4 - - + +
537A VAL* 3.9 8.3 - - + -
540A ALA* 3.3 22.6 - - + +
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Residues in contact with GLU 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A TRP* 4.4 13.3 - - + -
390A ALA* 3.7 13.5 - - + +
391A PHE* 3.7 26.5 - - + -
394A GLN* 2.7 36.7 + - - +
455A ASP* 3.0 22.8 + - + +
456A CYS* 4.2 3.6 - - - +
458A ALA* 1.3 72.6 - - - +
460A ALA* 1.3 60.7 + - - +
462A LYS* 3.2 20.3 + - - -
463A ALA* 2.9 30.3 + - - +
536A ALA* 3.4 25.4 - - + +
539A GLN* 5.4 1.0 + - - -
591A PHE* 4.4 9.7 - - - -
714A TRP* 5.2 0.3 - - - -
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Residues in contact with ALA 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ILE* 4.5 9.9 - - + -
390A ALA* 3.8 10.7 - - + +
418A LEU* 4.2 6.5 - - + +
442A PHE* 3.5 39.5 - - + -
456A CYS 3.0 19.7 + - - +
459A GLU* 1.3 74.0 - - - +
461A LEU* 1.3 60.1 + - - +
463A ALA* 3.4 2.3 + - - +
464A VAL* 3.0 37.3 + - - +
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Residues in contact with LEU 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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442A PHE* 4.5 5.0 - - + -
457A THR 2.9 19.7 + - - +
458A ALA 3.5 3.8 - - - +
460A ALA* 1.3 73.9 - - - +
462A LYS* 1.3 59.6 + - - +
464A VAL* 3.3 4.9 + - - +
465A LEU* 2.9 48.6 + - + +
483A LEU* 3.4 34.8 - - + +
486A ALA* 3.8 22.7 - - + -
487A VAL* 4.0 22.9 - - + -
490A LEU* 4.5 11.2 - - + -
540A ALA* 4.4 25.8 - - + +
541A LEU 5.3 0.2 - - - +
544A PHE* 4.7 2.7 - - + -
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Residues in contact with LYS 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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394A GLN* 2.7 30.9 + - - +
458A ALA 2.8 16.5 + - - +
459A GLU* 3.2 26.9 + - - +
461A LEU* 1.3 72.9 - - - +
463A ALA* 1.3 57.5 + - - +
465A LEU* 3.5 9.0 + - - +
466A LEU* 2.8 44.0 + - + +
536A ALA 5.1 2.2 - - - -
539A GLN* 3.1 41.9 + - + +
540A ALA* 3.7 24.8 - - - +
543A TYR* 4.7 11.3 - - + -
714A TRP* 4.9 5.3 - - - -
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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
----------------------------------------------------------
390A ALA* 3.7 21.1 - - - +
393A ILE* 3.8 19.5 - - + +
394A GLN* 4.4 8.0 - - + +
418A LEU* 4.0 14.1 - - + -
459A GLU 2.9 19.0 + - - +
460A ALA 3.7 4.3 - - - +
461A LEU 3.3 0.2 - - - -
462A LYS* 1.3 74.9 - - - +
464A VAL* 1.3 63.9 + - - +
466A LEU* 3.4 4.0 + - - +
467A LEU* 3.0 28.5 + - - +
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Residues in contact with VAL 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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415A HIS* 4.1 9.9 - - + +
418A LEU* 4.1 22.9 - - + -
419A ARG 5.4 0.2 - - - +
442A PHE* 5.0 3.6 - - + -
460A ALA 3.0 22.2 + - - +
461A LEU* 3.7 5.6 - - - +
463A ALA* 1.3 76.3 - - - +
465A LEU* 1.3 62.6 + - - +
467A LEU* 3.3 8.1 + - + +
468A GLN* 3.0 52.7 + - - +
478A ILE* 3.7 30.7 - - + -
483A LEU* 4.1 16.8 - - + -
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Residues in contact with LEU 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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461A LEU* 2.9 39.4 + - + +
462A LYS* 3.7 2.5 - - - +
464A VAL* 1.3 77.0 - - - +
466A LEU* 1.3 62.1 + - - +
468A GLN* 3.4 7.1 + - + +
469A GLU* 3.1 24.6 + - - +
483A LEU* 3.9 31.4 - - + -
540A ALA 4.5 4.5 - - - +
543A TYR* 3.5 31.2 - - + -
544A PHE* 3.9 27.6 - - + +
547A ARG* 5.3 11.8 + - + +
548A PHE* 4.1 17.9 - - + -
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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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394A GLN* 4.0 32.8 - - + +
397A LEU* 3.7 20.6 - - + -
462A LYS* 2.8 32.8 + - + +
463A ALA* 3.7 3.1 - - - +
465A LEU* 1.3 72.2 - - - +
467A LEU* 1.3 58.1 + - - +
469A GLU* 3.5 0.7 + - - +
470A LYS* 3.0 56.1 + - + +
543A TYR* 3.5 33.9 - - + +
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Residues in contact with LEU 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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393A ILE* 3.7 37.9 - - + -
397A LEU* 4.2 11.2 - - + -
411A LEU* 3.9 26.9 - - + +
415A HIS* 3.7 37.5 - - + +
418A LEU* 5.7 0.4 - - + -
463A ALA 3.0 17.9 + - - +
464A VAL* 3.6 5.4 - - - +
466A LEU* 1.3 76.5 - - - +
468A GLN* 1.3 57.1 + - - +
471A CYS* 2.7 64.1 + - + +
474A VAL* 4.8 5.8 - - + +
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Residues in contact with GLN 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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415A HIS* 3.0 27.6 - - + -
464A VAL* 3.0 28.6 + - - +
465A LEU* 4.0 6.5 - - + +
467A LEU* 1.3 73.8 - - - +
469A GLU* 1.3 64.1 + - - +
471A CYS 4.4 5.8 - - - +
474A VAL* 5.0 1.3 - - + -
477A HIS* 3.3 43.5 + - + +
478A ILE* 2.9 39.3 - - - +
483A LEU* 4.3 11.1 - - - +
547A ARG* 4.3 16.4 + - - +
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Residues in contact with GLU 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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465A LEU 3.1 16.3 + - - +
466A LEU 3.9 2.2 - - - +
468A GLN* 1.3 78.9 - - - +
470A LYS* 1.3 73.1 + - + +
471A CYS 3.6 1.0 + - - -
543A TYR* 2.6 33.3 + - - +
546A LYS* 4.3 15.2 + - - -
547A ARG* 3.9 36.7 - - - +
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Residues in contact with LYS 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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397A LEU* 4.5 17.2 + - + -
402A HIS* 3.8 50.7 + - + +
403A HIS* 5.5 1.7 - - - -
466A LEU* 3.0 41.4 + - + +
467A LEU 4.5 0.2 - - - +
469A GLU* 1.3 94.8 - - + +
471A CYS* 1.3 61.4 + - - +
472A PRO* 3.8 7.4 - - - +
543A TYR* 5.4 0.2 - - - -
721A GLN* 5.3 9.3 + - - +
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Residues in contact with CYS 471 (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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397A LEU* 4.4 3.4 - - - -
402A HIS* 3.8 26.0 - - - -
411A LEU* 4.5 9.2 - - - -
467A LEU* 2.7 47.3 + - - +
468A GLN 4.4 7.0 - - - +
469A GLU 3.6 1.2 - - - -
470A LYS* 1.3 76.7 - - - +
472A PRO* 1.3 69.2 - - + +
473A HIS* 3.6 0.9 - - + +
474A VAL* 3.5 29.7 + - + +
477A HIS* 4.6 6.4 + - - -
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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