Contacts of the helix formed by residues 519 - 540 (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 ASP 519 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517A SER 4.3 0.6 + - - -
518A LEU* 1.3 74.8 - - - +
520A LEU* 1.3 64.8 + - - +
521A ALA* 3.8 17.6 - - - +
522A SER* 3.0 31.8 + - - -
523A LEU* 3.4 14.6 + - - +
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Residues in contact with LEU 520 (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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519A ASP* 1.3 74.8 - - - +
521A ALA* 1.3 63.2 + - - +
523A LEU* 3.1 14.1 + - + +
524A ILE* 2.9 39.4 + - + +
616A LEU* 3.7 30.3 - - + -
646A ASN* 3.4 29.6 - - + +
648A PRO* 3.8 18.2 - - + -
683A GLU* 3.6 31.2 - - + +
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Residues in contact with ALA 521 (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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519A ASP* 3.2 17.2 - - - +
520A LEU* 1.3 76.4 - - - +
522A SER* 1.3 56.6 + - - +
524A ILE* 3.4 1.2 + - - -
525A LEU* 2.9 26.4 + - - +
680A LEU* 3.3 19.8 - - + +
683A GLU* 4.3 24.9 - - - +
684A LYS* 4.6 16.4 - - + +
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Residues in contact with SER 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A LEU* 4.3 25.0 - - - +
519A ASP* 3.0 25.2 + - - -
521A ALA* 1.3 73.6 - - - +
523A LEU* 1.3 58.7 + - - +
525A LEU* 3.3 12.0 + - - +
526A TYR* 3.0 43.9 + - - -
557A THR 4.9 3.7 + - - -
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Residues in contact with LEU 523 (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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511A LEU* 3.6 31.6 - - + -
518A LEU* 4.5 4.9 - - + -
519A ASP 3.8 10.3 - - - +
520A LEU* 3.1 18.9 + - + +
522A SER* 1.3 72.0 - - - +
524A ILE* 1.3 66.7 + - - +
526A TYR* 3.3 9.2 + - + -
527A ALA* 3.3 18.2 + - - +
615A ILE* 3.5 38.6 - - + +
616A LEU* 4.3 25.4 - - + +
618A HIS* 3.6 34.1 - - + +
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Residues in contact with ILE 524 (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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520A LEU* 2.9 31.6 + - + +
521A ALA 3.8 3.4 - - - +
523A LEU* 1.3 74.5 - - + +
525A LEU* 1.3 61.2 + - - +
527A ALA* 3.1 6.8 + - - +
528A TYR* 2.9 27.2 + - - +
616A LEU* 5.1 0.4 - - + -
648A PRO* 4.3 4.7 - - + -
651A LEU* 4.0 19.7 - - + -
676A LEU* 4.3 16.2 - - + +
679A ILE* 3.9 22.7 - - + -
680A LEU* 3.8 31.6 - - + +
683A GLU* 3.7 35.9 - - + -
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Residues in contact with LEU 525 (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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521A ALA 2.9 18.4 + - - +
522A SER* 3.5 10.5 - - - +
524A ILE* 1.3 76.4 - - - +
526A TYR* 1.3 66.7 + - + +
528A TYR* 3.2 7.5 + - + +
529A GLN* 2.9 57.4 + - + +
558A ASP* 3.9 28.0 - - + +
680A LEU* 3.7 28.6 - - + +
684A LYS* 6.2 2.0 - - - +
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Residues in contact with TYR 526 (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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507A LEU* 4.3 7.9 - - + -
510A PHE* 3.7 13.9 - + - -
511A LEU* 3.9 28.3 - - + -
518A LEU* 3.7 19.6 - - + +
522A SER* 3.0 33.8 + - - -
523A LEU* 3.7 15.7 - - + +
524A ILE 3.3 0.4 - - - -
525A LEU* 1.3 80.2 - - + +
527A ALA* 1.3 60.2 + - - +
529A GLN* 4.3 5.4 - - - -
530A LEU* 3.1 31.2 + - - +
554A VAL* 5.7 0.4 - - + -
556A ALA 4.9 1.3 - - - -
557A THR 2.7 32.1 + - - -
558A ASP* 4.5 2.2 - - - -
559A CYS 4.4 5.8 - - - -
560A VAL* 3.6 38.4 - - + +
615A ILE* 4.3 15.5 - - + -
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Residues in contact with ALA 527 (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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523A LEU 3.3 8.7 + - - +
524A ILE* 3.1 10.8 + - - +
526A TYR* 1.3 74.7 - - - +
528A TYR* 1.3 66.1 + - - +
530A LEU* 3.4 2.3 + - - +
531A SER* 2.9 20.3 + - - -
608A PHE* 3.4 12.9 - - - -
612A MET* 4.1 33.2 - - + -
615A ILE* 4.4 12.6 - - + +
651A LEU* 5.8 1.8 - - + -
676A LEU* 4.0 11.2 - - + -
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Residues in contact with TYR 528 (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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524A ILE 2.9 18.5 + - - +
525A LEU* 3.2 8.3 + - + +
527A ALA* 1.3 72.1 - - - +
529A GLN* 1.3 76.6 + - + +
531A SER* 2.6 26.3 + - - -
532A THR* 3.0 29.6 + - + +
673A LYS* 3.5 42.1 - - + +
676A LEU* 4.2 13.7 - - + +
677A SER* 3.8 25.0 + - - -
680A LEU* 4.4 22.0 - - + -
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Residues in contact with GLN 529 (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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482A HIS* 3.5 44.1 + - + +
525A LEU* 2.9 43.3 + - + +
526A TYR* 3.9 6.3 - - - +
528A TYR* 1.3 81.8 - - + +
530A LEU* 1.3 61.4 + - - +
532A THR* 2.6 27.3 + - - -
533A ALA 3.2 4.3 + - - -
558A ASP 3.0 23.1 + - - +
559A CYS* 3.4 3.7 + - - +
560A VAL* 3.1 33.0 + - + +
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Residues in contact with LEU 530 (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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482A HIS* 5.0 1.8 - - + +
507A LEU* 5.0 0.2 - - + -
526A TYR 3.1 17.5 + - - +
527A ALA 3.8 3.6 - - - +
529A GLN* 1.3 77.9 - - - +
531A SER* 1.3 59.0 + - - +
533A ALA* 3.1 6.6 + - - +
534A LEU* 2.9 36.5 + - + +
552A VAL* 3.7 44.9 - - + -
560A VAL* 3.8 12.3 - - + +
561A LYS* 4.3 2.0 - - - +
562A LEU* 4.2 28.5 - - + +
608A PHE* 3.9 12.1 - - + -
611A CYS* 4.3 8.1 - - - -
615A ILE* 3.9 23.6 - - + -
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Residues in contact with SER 531 (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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527A ALA 2.9 14.3 + - - -
528A TYR* 2.6 23.3 + - - -
530A LEU* 1.3 76.4 - - - +
532A THR* 1.3 56.5 + - - +
534A LEU* 3.8 5.5 - - - +
535A ALA* 2.9 30.1 + - - +
608A PHE* 3.8 16.0 - - - -
669A PHE* 4.4 4.8 - - - +
672A LEU* 4.7 3.4 - - - -
673A LYS* 3.4 30.2 - - - +
676A LEU* 3.7 15.1 - - - +
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Residues in contact with THR 532 (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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480A HIS* 3.3 26.3 + - - -
482A HIS* 3.6 7.9 - - + -
528A TYR* 3.0 46.4 + - + +
529A GLN* 2.6 19.2 + - - -
531A SER* 1.3 74.1 - - - +
533A ALA* 1.3 64.3 + - - +
535A ALA* 3.9 1.5 - - - +
536A TYR* 3.1 18.0 + - - +
673A LYS* 3.6 26.9 + - + -
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Residues in contact with ALA 533 (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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480A HIS* 3.6 11.2 - - - +
482A HIS* 3.5 28.5 - - + +
483A ILE* 3.9 12.6 - - + +
529A GLN 3.2 6.0 + - - +
530A LEU* 3.1 11.1 + - - +
532A THR* 1.3 81.9 + - - +
534A LEU* 1.3 58.0 + - - +
536A TYR* 3.3 6.2 - - - +
537A LEU* 3.1 30.3 + - - +
562A LEU* 4.0 11.9 - - + -
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Residues in contact with LEU 534 (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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530A LEU* 2.9 23.6 + - + +
531A SER 4.1 0.7 - - - +
533A ALA* 1.3 75.0 - - - +
535A ALA* 1.3 60.1 + - - +
537A LEU* 3.4 16.3 + - + +
538A GLU* 2.8 28.2 + - - +
544A HIS* 4.6 2.5 - - + -
547A ILE* 3.7 34.8 - - + -
562A LEU* 4.1 23.8 - - + -
604A ASP* 5.2 1.8 - - - +
608A PHE* 3.6 33.9 - - + -
669A PHE* 3.7 36.0 - - + -
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Residues in contact with ALA 535 (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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531A SER 2.9 19.1 + - - +
532A THR 3.9 2.7 - - - +
534A LEU* 1.3 74.3 - - - +
536A TYR* 1.3 58.8 + - - +
538A GLU* 3.3 6.2 + - - +
539A SER* 3.0 28.9 + - - -
669A PHE* 3.6 25.8 - - + +
670A THR* 4.3 7.8 + - - +
673A LYS* 3.9 28.0 - - - +
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Residues in contact with TYR 536 (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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477A GLN 4.0 4.3 + - - -
478A PHE* 3.5 33.6 - + + -
479A ASP* 2.9 38.5 + - - +
480A HIS* 3.6 24.7 - + + +
483A ILE* 3.9 16.4 - - + -
532A THR 3.1 14.9 + - - +
533A ALA 3.3 7.2 - - - +
535A ALA* 1.3 76.1 - - - +
537A LEU* 1.3 65.3 + - + +
539A SER* 2.7 26.2 + - - -
540A LYS* 3.3 41.4 - - + +
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Residues in contact with LEU 537 (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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478A PHE* 3.6 40.4 - - + -
483A ILE* 3.9 14.1 - - + -
533A ALA 3.1 16.6 + - - +
534A LEU* 3.4 19.7 + - + +
536A TYR* 1.3 73.7 - - + +
538A GLU* 1.3 65.9 + - - +
540A LYS* 3.1 11.0 + - - +
542A PHE* 3.0 43.0 + - + +
544A HIS* 4.1 12.3 - - + -
562A LEU* 4.1 16.4 - - + -
565A PHE* 3.9 23.1 - - + -
604A ASP* 5.8 0.7 - - - +
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Residues in contact with GLU 538 (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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534A LEU 2.8 21.4 + - - +
535A ALA* 3.3 5.9 + - - +
537A LEU* 1.3 72.2 - - - +
539A SER* 1.3 59.0 + - - +
541A ARG* 3.0 23.1 + - - +
542A PHE 4.8 1.3 - - - +
601A SER* 3.9 31.3 + - - +
605A VAL* 4.8 1.2 - - - +
668A ARG* 3.6 21.6 - - - +
669A PHE* 2.9 35.4 + - + +
670A THR* 3.1 33.4 + - - -
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Residues in contact with SER 539 (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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535A ALA 3.0 14.3 + - - -
536A TYR* 2.7 22.6 + - - -
538A GLU* 1.3 77.9 - - - +
540A LYS* 1.3 73.2 + - - +
541A ARG* 3.2 5.6 + - - +
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Residues in contact with LYS 540 (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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477A GLN 5.7 2.9 - - - +
478A PHE* 4.9 10.8 - - + -
536A TYR* 3.3 52.9 - - + +
537A LEU* 3.1 10.0 + - - +
539A SER* 1.3 88.7 + - - +
541A ARG* 1.3 69.4 + - - +
542A PHE* 4.4 10.4 - - + +
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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
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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