Contacts of the helix formed by residues 459 - 472 (chain B) 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 SER 459 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457B GLN 3.6 0.2 + - - -
458B GLU* 1.3 71.7 - - - +
460B GLU* 1.3 60.5 + - - +
462B HIS* 2.8 29.3 + - - +
463B THR* 3.5 5.7 + - - -
534B ILE* 3.6 17.4 - - - +
535B SER 2.9 20.2 + - - -
536B MET* 3.5 19.6 - - - +
537B ALA* 4.6 0.4 - - - -
538B THR* 5.6 0.2 - - - -
542B ASP* 2.8 37.0 + - - +
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Residues in contact with GLU 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B GLU* 3.4 7.5 - - + +
459B SER* 1.3 81.3 + - - +
461B ARG* 1.3 54.9 + - - +
463B THR* 2.7 39.4 + - - +
464B ASP* 2.9 13.4 + - - +
479B ARG* 3.4 31.7 + - - +
486B ARG* 5.3 5.2 + - - -
536B MET* 5.8 0.8 - - + +
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Residues in contact with ARG 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ARG 5.3 2.2 + - - -
295B GLY 6.1 0.2 - - - +
297B PRO* 6.4 0.6 - - - +
457B GLN* 3.6 40.6 + - + +
458B GLU* 3.3 33.8 + - + +
459B SER 3.2 0.8 + - - -
460B GLU* 1.3 77.4 - - - +
462B HIS* 1.3 61.5 + - - +
464B ASP* 3.6 23.5 - - - +
465B VAL* 3.8 12.8 - - - +
509B ASP 4.8 0.4 + - - -
510B GLU* 3.1 65.1 + - - +
513B ASP* 4.0 15.7 + - - +
514B VAL* 4.4 10.4 - - + +
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Residues in contact with HIS 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B GLN* 3.3 21.3 - - + +
458B GLU 3.6 6.3 + - - -
459B SER 2.8 12.4 + - - +
461B ARG* 1.3 77.2 - - - +
463B THR* 1.3 60.9 + - - +
464B ASP 3.4 0.2 - - - -
465B VAL* 3.5 4.3 + - - +
466B ILE* 3.1 33.2 + - - +
514B VAL* 4.4 10.8 - - + -
518B PHE* 5.1 0.7 - + - -
532B TYR* 2.9 47.0 + + - -
534B ILE* 3.6 22.1 - - + +
542B ASP 4.6 1.7 + - - +
545B ALA* 4.8 9.9 - - + -
546B VAL* 2.9 26.5 - - + +
549B LEU* 4.2 16.4 - - + +
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Residues in contact with THR 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B SER* 3.6 10.4 + - - -
460B GLU* 2.7 27.0 + - - +
462B HIS* 1.3 75.0 - - - +
464B ASP* 1.3 56.5 + - - -
465B VAL 3.0 2.0 + - - -
466B ILE* 3.0 4.7 + - - +
467B ASP* 2.5 36.6 + - - +
478B TYR* 3.6 30.4 - - + -
479B ARG* 3.3 35.4 - - + +
486B ARG* 4.4 6.9 + - - +
542B ASP* 5.0 4.3 + - - -
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Residues in contact with ASP 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B GLU* 2.9 11.4 + - - +
461B ARG* 3.6 21.9 + - - +
463B THR* 1.3 76.1 - - - +
465B VAL* 1.3 60.9 + - - +
467B ASP* 4.0 3.4 - - - +
468B ALA* 3.2 24.3 + - - +
479B ARG* 2.6 40.7 + - - +
510B GLU* 3.9 17.7 - - - +
511B ILE* 3.6 22.5 - - + +
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Residues in contact with VAL 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B ARG 3.8 7.9 - - - +
462B HIS 3.5 7.9 + - - +
463B THR 3.0 0.6 - - - -
464B ASP* 1.3 75.6 - - - +
466B ILE* 1.3 65.0 + - - +
468B ALA* 3.1 3.9 + - - +
469B ILE* 2.8 40.2 + - + +
501B LEU* 5.7 4.3 - - + -
505B LEU* 5.6 1.1 - - + -
511B ILE* 3.5 26.9 - - + +
514B VAL* 3.3 39.0 - - + -
515B ILE* 5.2 8.5 - - + +
549B LEU* 3.7 26.7 - - + -
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Residues in contact with ILE 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B HIS 3.1 17.0 + - - +
463B THR* 3.0 3.4 + - - +
465B VAL* 1.3 75.5 - - + +
467B ASP* 1.3 63.5 + - - +
469B ILE* 3.1 21.7 + - + +
470B THR* 3.3 13.0 + - - +
478B TYR* 3.8 20.6 - - + -
489B TRP* 3.3 35.9 - - + -
490B LEU* 4.8 2.0 - - + -
545B ALA* 4.5 15.0 - - + +
548B LEU* 4.4 16.8 - - + -
549B LEU* 3.3 39.5 - - + -
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Residues in contact with ASP 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B THR* 2.5 25.2 + - + +
464B ASP* 4.0 5.1 - - - +
466B ILE* 1.3 71.7 - - - +
468B ALA* 1.3 54.5 + - - +
470B THR* 2.6 17.2 + - - -
471B THR* 2.7 27.7 + - - -
477B SER* 2.5 31.3 + - - -
478B TYR* 3.2 18.7 + - + +
479B ARG* 3.3 30.5 + - + +
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Residues in contact with ALA 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B ASP 3.2 16.7 + - - +
465B VAL* 3.1 6.8 + - - +
467B ASP* 1.3 78.1 - - - +
469B ILE* 1.3 58.3 + - + +
470B THR 3.1 4.9 - - - -
471B THR* 3.9 8.8 - - - -
472B HIS* 3.2 27.4 + - - +
505B LEU* 3.5 11.2 - - + +
506B PRO* 5.6 3.9 - - + +
511B ILE* 4.9 12.8 - - + -
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Residues in contact with ILE 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B VAL* 2.8 36.9 + - + +
466B ILE* 3.1 24.6 + - + +
468B ALA* 1.3 76.7 - - - +
470B THR* 1.3 59.1 + - + +
472B HIS* 4.6 0.7 - - - -
473B LEU* 3.3 24.6 - - + +
489B TRP* 4.7 5.6 - - + -
500B LEU* 3.1 52.3 - - + +
501B LEU* 4.5 9.0 - - + +
502B PRO* 4.4 6.3 - - + -
505B LEU* 3.5 31.4 - - + -
549B LEU* 5.8 0.4 - - + -
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Residues in contact with THR 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B ILE 3.3 8.2 + - - +
467B ASP 2.6 23.0 + - - -
469B ILE* 1.3 78.7 - - - +
471B THR* 1.3 66.8 + - - +
472B HIS 3.2 1.3 - - - -
473B LEU* 2.9 20.0 + - + +
475B ILE* 2.7 36.7 - - + +
476B GLY 3.4 13.3 + - - -
478B TYR* 3.6 10.4 + - + -
481B TRP* 4.2 8.7 - - + -
489B TRP* 3.4 41.3 - - + -
500B LEU* 6.2 0.2 - - + -
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Residues in contact with THR 471 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B ASP* 2.7 31.0 + - - -
468B ALA* 4.0 8.3 - - - -
470B THR* 1.3 81.4 + - - +
472B HIS* 1.3 57.5 + - - +
473B LEU 3.0 12.3 - - - +
474B GLY 4.6 1.6 - - - +
475B ILE 4.3 0.2 - - - -
476B GLY* 3.5 13.2 + - - -
477B SER* 4.4 4.2 - - - -
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Residues in contact with HIS 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B ALA 3.2 17.7 + - - +
469B ILE* 4.6 2.2 - - - -
470B THR 3.2 0.4 - - - -
471B THR* 1.3 78.7 - - - +
473B LEU* 1.3 66.7 + - + +
502B PRO* 3.5 28.7 - - + +
504B ASP* 2.6 48.6 + - - -
505B LEU* 3.6 13.6 + - + -
506B PRO* 3.6 14.0 - - + +
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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