Contacts of the helix formed by residues 458 - 474 (chain A) in PDB entry 1JQO
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 GLU 458 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A ASP* 3.9 21.5 + - - +
295A GLY* 4.8 6.2 + - - -
457A GLN* 1.3 75.7 + - - +
459A SER* 1.3 65.5 + - - +
460A GLU* 4.2 15.8 - - - +
461A ARG* 3.1 38.8 + - + +
462A HIS* 4.1 0.7 + - - -
535A SER* 3.4 25.3 - - - +
536A MET* 4.6 17.3 - - + +
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Residues in contact with SER 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A GLN 3.3 1.8 + - - -
458A GLU* 1.3 67.7 - - - +
460A GLU* 1.3 55.9 + - - +
461A ARG 2.8 6.1 - - - -
462A HIS* 2.6 35.8 + - - +
463A THR* 2.9 10.5 + - - -
534A ILE* 3.2 25.4 - - - +
535A SER 3.2 8.5 + - - -
536A MET 4.8 2.6 + - - -
537A ALA* 3.8 14.8 - - - -
542A ASP* 3.5 35.2 + - - +
545A ALA* 5.5 0.7 - - - +
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Residues in contact with GLU 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A GLU* 3.2 17.9 + - - +
459A SER* 1.3 75.6 - - - +
461A ARG* 1.3 57.4 + - - +
463A THR* 3.4 17.8 + - - +
464A ASP* 3.2 28.4 + - - +
479A ARG* 2.7 39.1 + - - +
486A ARG* 5.5 2.3 + - - -
536A MET* 4.8 18.2 + - + +
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Residues in contact with ARG 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG 5.2 1.6 + - - -
295A GLY 5.8 0.8 - - - +
457A GLN* 3.2 41.8 + - + +
458A GLU* 3.1 29.3 + - + +
459A SER 2.7 0.8 + - - -
460A GLU* 1.3 75.5 - - - +
462A HIS* 1.3 66.9 + - + +
463A THR 3.0 1.6 - - - -
464A ASP* 3.0 26.6 + - - +
465A VAL* 3.1 18.2 + - - +
510A GLU* 3.2 54.3 + - - +
513A ASP* 4.1 11.5 + - - +
514A VAL* 4.7 10.4 - - + +
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Residues in contact with HIS 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A GLN* 3.8 32.3 - - + +
458A GLU 4.4 0.7 - - - -
459A SER* 2.6 28.0 + - - +
461A ARG* 1.3 74.8 - - + +
463A THR* 1.3 59.6 + - - +
465A VAL* 3.6 6.4 + - - +
466A ILE* 3.1 31.3 + - - +
514A VAL* 4.5 13.0 - - + -
518A PHE* 4.8 3.6 - + - -
532A TYR* 2.5 46.8 + + - -
534A ILE* 4.1 5.4 - - + +
545A ALA* 4.7 11.0 - - + -
546A VAL* 2.9 27.8 - - + +
549A LEU* 4.7 9.0 - - + -
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Residues in contact with THR 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A SER* 2.9 13.6 + - - -
460A GLU* 3.4 27.8 + - - +
461A ARG 3.0 0.2 - - - -
462A HIS* 1.3 75.2 - - - +
464A ASP* 1.3 58.8 + - - +
466A ILE* 3.3 1.2 + - - +
467A ASP* 2.8 33.1 + - - +
478A TYR* 4.0 26.6 - - + -
479A ARG* 3.0 33.2 - - + +
486A ARG* 4.2 16.3 + - - +
542A ASP* 4.4 8.1 + - - -
545A ALA* 6.0 0.4 - - - -
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Residues in contact with ASP 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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460A GLU* 3.2 12.5 + - - +
461A ARG* 3.0 23.1 + - - +
463A THR* 1.3 79.1 - - - +
465A VAL* 1.3 64.5 + - - +
467A ASP* 3.1 5.5 + - - +
468A ALA* 3.0 23.7 + - - +
479A ARG* 3.1 25.6 + - - +
510A GLU* 5.9 1.9 - - - +
511A ILE* 3.6 21.8 - - + +
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Residues in contact with VAL 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ARG 3.1 10.2 + - - +
462A HIS* 3.8 6.1 - - - +
464A ASP* 1.3 78.5 - - - +
466A ILE* 1.3 64.1 + - - +
468A ALA* 3.1 2.9 + - - +
469A ILE* 3.1 42.5 + - + +
501A LEU* 5.7 0.4 - - + -
505A LEU* 5.7 0.7 - - + -
511A ILE* 3.9 22.1 - - + +
514A VAL* 3.2 42.4 - - + -
515A ILE* 4.7 13.9 - - + -
549A LEU* 3.8 24.0 - - + -
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Residues in contact with ILE 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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462A HIS 3.1 18.1 + - - +
463A THR 3.9 2.5 - - - +
465A VAL* 1.3 78.4 - - - +
467A ASP* 1.3 61.8 + - - +
469A ILE* 3.4 11.8 + - + +
470A THR* 3.2 21.7 + - - +
478A TYR* 3.5 26.9 - - + -
489A TRP* 3.5 28.9 - - + -
490A LEU* 4.6 0.7 - - + -
545A ALA* 4.1 22.2 - - + +
548A LEU* 4.0 23.1 - - + -
549A LEU* 3.9 29.8 - - + -
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Residues in contact with ASP 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A THR 2.8 23.2 + - - +
464A ASP* 3.5 6.0 - - - +
466A ILE* 1.3 72.7 - - - +
468A ALA* 1.3 61.6 + - - +
470A THR* 2.9 12.1 + - - -
471A THR* 2.8 30.2 + - - -
477A SER* 2.8 28.2 + - - -
478A TYR* 3.0 27.1 + - + +
479A ARG* 3.1 30.3 - - + +
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Residues in contact with ALA 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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464A ASP 3.0 12.5 + - - +
465A VAL 3.6 7.6 - - - +
467A ASP* 1.3 80.4 + - - +
469A ILE* 1.3 58.0 + - - +
471A THR* 3.9 6.5 - - - -
472A HIS* 3.1 32.2 + - - +
505A LEU* 3.8 15.0 - - + +
506A PRO* 5.3 7.1 - - + +
511A ILE* 4.6 20.0 - - + -
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Residues in contact with ILE 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 VAL* 3.1 33.8 + - + +
466A ILE* 3.5 21.5 - - + +
467A ASP 3.2 0.2 - - - -
468A ALA* 1.3 77.4 - - - +
470A THR* 1.3 60.6 + - - +
472A HIS* 4.7 0.2 - - - -
473A LEU* 3.3 31.9 + - + +
489A TRP* 5.1 9.9 - - + -
500A LEU* 3.9 33.2 - - + +
501A LEU* 3.8 18.6 - - + -
502A PRO* 4.2 2.7 - - + -
505A LEU* 3.9 25.1 - - + -
549A LEU* 4.4 5.8 - - + -
552A GLU* 6.0 2.7 - - + -
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Residues in contact with THR 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ILE 3.2 12.8 + - - +
467A ASP 2.9 18.5 + - - -
469A ILE* 1.3 76.3 - - - +
471A THR* 1.3 67.1 + - - +
473A LEU 3.1 2.3 + - - -
474A GLY 3.0 17.8 + - - -
475A ILE* 3.2 27.6 + - + +
476A GLY 3.0 17.3 + - - -
478A TYR* 3.3 20.2 + - + -
481A TRP* 4.5 5.6 - - + -
489A TRP* 3.5 40.8 - - + -
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Residues in contact with THR 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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467A ASP* 2.8 33.9 + - - -
468A ALA* 3.9 7.0 - - - -
470A THR* 1.3 76.4 + - - +
472A HIS* 1.3 62.7 + - - +
474A GLY* 3.1 13.2 + - - -
475A ILE 5.0 0.7 - - - +
476A GLY 3.3 14.4 + - - +
477A SER* 4.4 4.7 - - - -
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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
----------------------------------------------------------
468A ALA 3.1 16.6 + - - +
469A ILE 4.0 3.1 - - - +
471A THR* 1.3 78.1 - - - +
473A LEU* 1.3 80.1 + - + +
474A GLY* 3.0 8.9 + - - -
502A PRO* 3.4 15.7 - - + -
504A ASP* 2.6 51.5 + - - -
505A LEU* 4.2 7.2 - - + -
506A PRO* 3.5 18.5 - - + +
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Residues in contact with LEU 473 (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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469A ILE* 3.3 25.9 + - + +
470A THR 3.1 4.9 + - - +
472A HIS* 1.3 84.2 - - + +
474A GLY* 1.3 63.4 + - - +
475A ILE* 4.3 20.8 - - + +
489A TRP* 6.2 0.4 - - + -
500A LEU* 3.3 29.8 - - + +
502A PRO* 3.4 34.3 - - + -
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Residues in contact with GLY 474 (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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470A THR 3.0 3.4 + - - -
471A THR 3.1 9.1 + - - -
472A HIS 3.0 6.2 + - - -
473A LEU* 1.3 80.5 - - - +
475A ILE* 1.3 67.9 + - - +
476A GLY 4.0 0.9 - - - -
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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
------------------------------------------------------------
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