Contacts of the helix formed by residues 461 - 477 (chain A) in PDB entry 2JKK
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 461 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A CYS* 3.4 1.0 - - - +
460A THR* 1.3 82.2 - - - +
462A ASP* 1.3 59.4 + - - +
463A SER* 3.1 21.8 + - - -
464A VAL* 3.4 17.9 + - - +
465A ARG* 3.0 40.5 + - - +
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Residues in contact with ASP 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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461A SER* 1.3 70.9 - - - +
463A SER* 1.3 56.0 + - - +
465A ARG* 2.6 37.1 + - - +
466A GLU* 2.8 37.9 + - - +
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Residues in contact with SER 463 (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 SER* 3.1 17.2 + - - -
462A ASP* 1.3 77.6 - - - +
464A VAL* 1.3 58.6 + - - +
466A GLU* 2.7 27.3 - - - +
467A LYS* 3.1 16.7 + - - +
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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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433A PHE* 3.9 18.8 - - + -
459A CYS* 3.9 33.0 - - + -
460A THR 5.6 0.7 - - - +
461A SER* 3.4 20.9 + - - +
462A ASP 3.3 0.2 - - - -
463A SER* 1.3 77.9 + - - +
465A ARG* 1.3 61.8 + - - +
467A LYS* 3.1 8.8 + - + +
468A PHE* 2.9 28.3 + - - +
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Residues in contact with ARG 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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456A CYS* 4.8 2.0 - - - -
459A CYS* 3.1 36.0 + - + +
460A THR* 3.8 4.8 - - - +
461A SER* 3.0 27.6 + - - +
462A ASP* 2.6 38.1 + - - +
464A VAL* 1.3 76.9 - - - +
466A GLU* 1.3 57.6 + - - +
468A PHE* 3.4 7.6 + - - +
469A LEU* 3.0 38.0 + - + +
491A THR 5.5 1.8 - - - -
493A ASN* 3.2 37.1 + - - +
495A VAL* 3.8 22.0 - - + -
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Residues in contact with GLU 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 ASP 2.8 20.7 + - - +
463A SER* 2.7 31.8 - - - +
465A ARG* 1.3 71.4 - - - +
467A LYS* 1.3 70.7 + - - +
469A LEU* 3.4 3.3 + - - -
470A GLN* 2.6 65.9 + - - +
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Residues in contact with LYS 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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432A GLN* 5.2 10.0 - - - +
433A PHE* 4.0 22.1 - - + -
463A SER* 3.1 18.2 + - - +
464A VAL* 3.1 7.6 + - + +
466A GLU* 1.3 95.5 + - - +
468A PHE* 1.3 64.1 + - - +
470A GLN* 3.6 15.2 + - - +
471A GLU* 3.9 10.0 + - - +
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Residues in contact with PHE 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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433A PHE* 3.5 37.2 - + + -
454A LYS* 3.5 47.1 - - + -
455A THR 3.7 16.8 - - - -
456A CYS* 3.5 19.5 - - + -
464A VAL 2.9 15.5 + - - +
465A ARG 3.6 3.6 - - - +
467A LYS* 1.3 77.5 - - - +
469A LEU* 1.3 61.1 + - - +
471A GLU* 3.1 24.7 + - - +
495A VAL* 3.6 40.6 - - + -
497A ILE* 3.4 32.3 - - + +
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Residues in contact with LEU 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 ARG* 3.0 24.8 + - + +
466A GLU* 4.7 1.8 - - - -
468A PHE* 1.3 69.9 - - - +
470A GLN* 1.3 70.3 + - - +
471A GLU 3.1 2.2 - - - -
472A ALA* 2.9 20.5 + - + +
473A LEU* 3.0 20.6 + - + +
489A VAL* 4.4 20.6 - - + -
491A THR* 4.2 22.0 - - + +
495A VAL* 3.4 34.5 - - + -
497A ILE* 4.3 18.2 - - + -
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Residues in contact with GLN 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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466A GLU* 2.6 60.3 + - - +
467A LYS* 3.8 9.0 - - - +
468A PHE 3.3 0.6 - - - -
469A LEU* 1.3 81.7 - - - +
471A GLU* 1.3 57.3 + - + +
473A LEU* 3.6 31.6 - - + +
474A THR* 3.0 31.6 + - - -
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Residues in contact with GLU 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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432A GLN* 4.9 3.8 - - - +
433A PHE* 3.4 33.3 - - - -
454A LYS* 2.8 41.3 + - - +
467A LYS 3.9 7.1 + - - +
468A PHE* 3.3 14.1 - - - +
469A LEU 3.1 0.8 - - - -
470A GLN* 1.3 79.3 - - - +
472A ALA* 1.3 59.6 + - - +
474A THR* 3.5 7.7 + - - -
475A MET* 3.3 27.2 + - - +
497A ILE* 4.4 1.1 - - + -
564A ASP* 5.0 1.1 - - - +
566A GLY* 3.6 29.7 + - - +
567A LEU* 5.6 0.5 - - - +
569A ARG* 5.9 0.2 - - - +
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Residues in contact with ALA 472 (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 LEU* 2.9 12.2 + - + +
471A GLU* 1.3 76.8 - - - +
473A LEU* 1.3 61.1 + - + +
475A MET* 3.1 5.4 + - - +
476A ARG* 2.9 30.1 + - - +
486A LEU* 3.7 14.2 - - + +
489A VAL* 3.6 30.5 - - + -
497A ILE* 3.8 25.2 - - + +
499A MET* 6.0 0.2 - - - -
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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 LEU* 3.0 38.5 + - + +
470A GLN* 3.3 30.9 + - + +
472A ALA* 1.3 76.9 - - + +
474A THR* 1.3 61.6 + - - +
476A ARG* 3.7 38.7 + - - +
477A GLN* 3.6 19.9 + - - +
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Residues in contact with THR 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 GLN 3.0 14.9 + - - -
471A GLU* 3.6 12.5 - - - -
473A LEU* 1.3 76.1 - - - +
475A MET* 1.3 62.3 + - - +
477A GLN* 3.2 22.6 + - - +
478A PHE* 3.2 17.5 - - + -
542A PHE* 4.1 31.6 - - + -
565A PHE* 4.2 21.1 - - + -
569A ARG* 4.5 4.7 - - - +
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Residues in contact with MET 475 (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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471A GLU 3.3 11.1 + - - +
472A ALA* 3.1 8.2 + - - +
474A THR* 1.3 75.6 - - - +
476A ARG* 1.3 65.2 + - - +
477A GLN 3.1 1.0 + - - -
478A PHE* 3.2 23.3 + - + +
483A ILE* 3.7 20.2 - - + -
484A VAL* 3.6 36.8 - - + +
485A LYS* 5.8 0.3 - - - -
486A LEU* 4.3 14.4 + - + +
499A MET* 3.8 15.5 - - + -
564A ASP* 3.3 19.5 - - - +
565A PHE* 3.5 51.8 - - + +
566A GLY 5.6 0.7 - - - +
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Residues in contact with ARG 476 (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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413A ARG 5.7 0.6 + - - -
415A TYR* 3.4 54.6 + - + +
472A ALA 2.9 15.8 + - - +
473A LEU* 3.7 33.0 + - - +
475A MET* 1.3 76.8 - - - +
477A GLN* 1.3 61.7 + - + +
478A PHE 3.2 4.9 + - - +
486A LEU* 3.8 17.2 - - + +
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Residues in contact with GLN 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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473A LEU 3.6 15.2 + - - +
474A THR* 3.2 24.0 + - - +
475A MET 3.0 1.2 - - - -
476A ARG* 1.3 78.2 - - - +
478A PHE* 1.3 79.3 + - + +
479A ASP* 5.4 0.7 - - - +
536A TYR* 4.0 5.4 + - - -
540A LYS* 5.7 3.5 - - - +
542A PHE* 4.6 6.3 - - - -
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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