Contacts of the helix formed by residues 522 - 543 (chain A) in PDB entry 4H1J
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 LYS 522 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520A SER 3.7 11.4 + - - +
521A LEU* 1.3 78.0 - - - +
523A VAL* 1.3 65.1 + - - +
524A LEU* 4.2 9.6 - - + +
525A THR* 3.2 25.9 + - - +
526A LEU* 3.4 13.8 + - - +
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Residues in contact with VAL 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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521A LEU 5.9 0.2 - - - +
522A LYS* 1.3 73.5 - - - +
524A LEU* 1.3 63.4 + - - +
526A LEU* 3.0 13.3 + - + +
527A VAL* 2.9 25.3 + - + +
619A LEU* 4.2 8.5 - - + -
621A PHE* 5.9 0.2 - - + -
649A LEU* 3.6 54.7 - - + +
651A PRO* 3.9 24.7 - - + -
686A GLU* 4.3 10.5 - - - +
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Residues in contact with LEU 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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522A LYS* 3.2 7.2 - - + +
523A VAL* 1.3 76.5 - - - +
525A THR* 1.3 57.2 + - - +
527A VAL* 3.3 7.3 + - + +
528A LEU* 2.9 27.5 + - - +
683A TYR* 3.5 55.1 - - + +
686A GLU* 3.8 12.6 + - + +
687A LYS* 3.5 38.1 - - + +
690A ALA* 4.7 15.3 - - + -
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Residues in contact with THR 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 LEU* 3.8 17.3 - - + -
522A LYS* 3.2 21.5 + - - +
524A LEU* 1.3 76.8 - - - +
526A LEU* 1.3 57.9 + - - +
528A LEU* 3.3 12.7 + - + +
529A TYR* 3.0 62.9 + - + +
560A PRO 4.2 6.3 - - - +
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Residues in contact with LEU 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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514A LEU* 3.5 31.0 - - + -
521A LEU* 4.5 10.3 - - + -
522A LYS 3.6 11.0 - - - +
523A VAL* 3.0 18.4 + - + +
525A THR* 1.3 73.8 - - - +
527A VAL* 1.4 64.4 + - - +
529A TYR* 3.5 4.5 + - + -
530A SER* 3.1 26.7 + - - -
618A ILE* 3.6 33.6 - - + +
619A LEU* 4.0 26.2 - - + +
621A PHE* 3.6 35.9 - - + -
649A LEU* 5.6 0.4 - - + -
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Residues in contact with VAL 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 VAL* 2.9 30.5 + - + +
524A LEU* 3.7 7.2 - - - +
526A LEU* 1.4 71.3 - - - +
528A LEU* 1.3 66.2 + - - +
530A SER* 3.3 7.1 + - - -
531A LEU* 3.0 22.7 + - + +
619A LEU* 5.1 1.1 - - + -
651A PRO* 4.7 1.6 - - + -
654A LEU* 4.2 23.1 - - + -
679A LEU* 4.3 11.2 - - + +
682A VAL* 3.9 12.1 - - + -
683A TYR* 3.8 37.0 - - + +
686A GLU* 4.3 15.5 - - + -
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Residues in contact with LEU 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 LEU 2.9 14.4 + - - +
525A THR* 3.4 15.7 - - + +
527A VAL* 1.3 75.1 - - - +
529A TYR* 1.3 69.3 + - + +
531A LEU* 3.2 12.2 + - + +
532A GLN* 3.0 57.1 + - + +
560A PRO 5.1 0.7 - - - +
561A GLU* 4.1 20.2 - - + +
683A TYR* 3.8 32.0 - - + +
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Residues in contact with TYR 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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510A LEU* 3.8 27.4 - - + -
513A TYR* 3.9 15.2 + + - -
514A LEU* 4.6 7.2 - - + -
521A LEU* 4.4 11.1 - - + +
525A THR* 3.0 39.5 + - + +
526A LEU* 3.9 9.4 - - + +
527A VAL 3.4 0.2 - - - -
528A LEU* 1.3 79.8 - - + +
530A SER* 1.4 61.8 + - - +
532A GLN* 3.3 14.0 + - - +
533A ILE* 3.1 28.9 + - - +
557A VAL* 5.0 0.8 - - + +
559A SER 4.5 1.1 + - - -
560A PRO* 2.6 40.6 + - - +
561A GLU 4.7 2.0 - - - -
562A CYS 4.6 4.3 - - - -
563A VAL* 3.7 31.6 - - + +
618A ILE* 4.4 13.9 - - + -
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Residues in contact with SER 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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526A LEU 3.1 13.7 + - - -
527A VAL* 3.3 11.9 + - - -
529A TYR* 1.4 76.1 - - - +
531A LEU* 1.3 56.7 + - - +
533A ILE* 3.4 1.1 + - - -
534A CYS 3.0 23.6 + - - -
611A PHE* 3.3 17.1 - - - -
615A MET* 3.8 34.1 - - - +
618A ILE* 3.9 15.6 - - - +
619A LEU* 4.1 11.3 - - - +
654A LEU* 5.2 2.2 - - - +
679A LEU* 4.2 6.5 - - - -
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Residues in contact with LEU 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 VAL 3.0 13.4 + - - +
528A LEU* 3.2 14.1 + - + +
530A SER* 1.3 74.1 - - - +
532A GLN* 1.3 59.7 + - + +
534A CYS* 3.3 2.5 + - + +
535A LYS* 3.0 56.2 + - + +
676A VAL* 3.6 20.9 - - + +
679A LEU* 3.7 23.3 - - + +
680A SER* 3.5 36.8 - - - +
683A TYR* 4.3 20.9 - - + -
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Residues in contact with GLN 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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485A HIS* 3.4 53.1 + - + +
528A LEU* 3.0 42.6 + - + +
529A TYR* 3.3 10.3 + - - +
531A LEU* 1.3 76.4 - - + +
533A ILE* 1.3 61.3 + - - +
535A LYS* 3.3 8.0 + - + +
536A ALA 3.2 16.6 + - - -
561A GLU 3.0 23.5 + - - +
562A CYS* 3.6 1.2 - - - -
563A VAL* 3.0 34.2 + - + +
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Residues in contact with ILE 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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485A HIS 4.4 3.4 - - - +
529A TYR 3.1 18.1 + - - +
530A SER* 3.9 4.3 - - - +
532A GLN* 1.3 74.3 - - - +
534A CYS* 1.3 59.7 + - - +
536A ALA* 3.2 5.8 + - - +
537A MET* 2.9 32.4 + - + +
550A ILE* 4.7 4.3 - - + -
555A ILE* 3.8 35.9 - - + -
563A VAL* 3.7 21.8 - - + -
564A LYS 4.2 0.7 - - - +
565A LEU* 3.9 43.3 - - + +
611A PHE* 3.8 22.2 - - + -
614A CYS* 5.2 0.9 - - - -
618A ILE* 5.3 4.0 - - + -
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Residues in contact with CYS 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 SER 3.0 18.3 + - - +
531A LEU* 3.6 6.1 - - - +
533A ILE* 1.3 76.7 - - - +
535A LYS* 1.3 51.0 + - - +
537A MET* 3.3 5.3 + - - +
538A ALA* 2.8 32.2 + - - +
611A PHE* 3.6 9.1 - - + -
672A PHE* 3.8 27.8 - - - +
675A LEU* 3.9 17.7 - - - -
676A VAL* 3.8 15.5 - - + -
679A LEU* 3.6 24.7 - - + -
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Residues in contact with LYS 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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483A HIS* 3.7 19.4 + - + +
485A HIS* 4.7 8.1 - - + +
531A LEU* 3.0 40.4 + - + +
532A GLN* 3.5 12.1 - - + +
533A ILE 3.2 0.2 - - - -
534A CYS* 1.3 72.4 - - - +
536A ALA* 1.3 64.0 + - - +
538A ALA* 3.3 4.4 + - - +
539A TYR* 3.1 17.5 + - - +
676A VAL* 4.0 32.8 - - + -
680A SER* 4.8 3.3 + - - -
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Residues in contact with ALA 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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483A HIS* 3.7 12.7 - - - -
485A HIS* 3.5 26.9 - - + +
486A ILE* 3.8 16.3 - - + +
532A GLN 3.2 10.2 + - - +
533A ILE* 3.2 10.9 + - - +
535A LYS* 1.3 74.7 - - - +
537A MET* 1.3 57.5 + - - +
539A TYR* 3.3 6.6 + - - +
540A LEU* 3.2 29.2 + - - +
565A LEU* 4.2 12.8 - - + -
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Residues in contact with MET 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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533A ILE* 2.9 25.6 + - + +
534A CYS* 3.7 1.1 - - - +
536A ALA* 1.3 74.1 - - - +
538A ALA* 1.4 53.5 + - - +
540A LEU* 3.2 20.6 + - + +
541A GLU* 2.8 35.3 + - - +
545A CYS 5.1 2.0 - - - +
547A HIS* 4.0 9.4 - - + +
550A ILE* 3.7 20.4 - - + -
565A LEU* 3.6 26.9 - - + -
604A THR* 5.9 0.7 - - + -
607A ASP* 3.3 26.2 - - - +
611A PHE* 4.9 1.1 - - + -
672A PHE* 3.6 48.1 - - + -
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Residues in contact with ALA 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 CYS 2.8 17.6 + - - +
535A LYS* 3.3 6.5 + - - +
537A MET* 1.4 73.9 - - - +
539A TYR* 1.4 63.3 + - - +
541A GLU* 3.5 4.7 + - - +
542A SER* 3.1 22.3 + - - -
672A PHE* 3.7 17.8 - - - +
673A THR* 4.1 18.1 + - + +
676A VAL* 3.9 18.6 - - + -
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Residues in contact with TYR 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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480A ASN 5.1 6.4 + - - -
481A LEU* 3.7 30.5 - - + +
482A ASP 6.3 0.2 - - - -
483A HIS* 3.9 26.0 - + + +
486A ILE* 4.2 9.9 - - + -
535A LYS 3.1 8.4 + - - +
536A ALA 3.5 8.1 - - - +
537A MET 3.2 0.4 - - - -
538A ALA* 1.4 77.2 - - - +
540A LEU* 1.3 65.1 + - + +
542A SER* 2.6 32.5 + - - -
543A ILE* 3.5 35.7 + - + +
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Residues in contact with LEU 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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481A LEU* 4.9 4.3 - - + -
486A ILE* 4.7 5.2 - - + -
536A ALA 3.2 11.6 + - - +
537A MET* 3.2 38.0 + - + +
539A TYR* 1.3 81.5 - - + +
541A GLU* 1.3 59.5 + - - +
543A ILE* 3.3 22.8 + - + +
545A CYS* 2.9 51.0 + - + +
546A VAL 5.7 0.4 - - - -
547A HIS* 4.8 5.6 - - + +
565A LEU* 4.3 8.7 - - + -
701A 0YH 3.8 42.0 - - + -
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Residues in contact with GLU 541 (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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537A MET* 2.8 17.7 + - + +
538A ALA* 3.5 4.5 - - - +
540A LEU* 1.3 76.6 - - - +
542A SER* 1.4 56.3 + - - +
544A ASN* 3.0 26.8 + - - +
545A CYS 4.3 5.6 + - - -
604A THR* 3.3 34.2 + - + +
608A VAL* 4.9 0.5 - - - +
671A ARG* 3.5 26.7 + - - +
672A PHE* 2.8 27.1 + - + +
673A THR* 2.6 39.4 + - - +
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Residues in contact with SER 542 (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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538A ALA 3.1 13.4 + - - -
539A TYR* 2.6 32.8 + - - -
541A GLU* 1.4 73.7 - - - +
543A ILE* 1.3 64.2 + - - +
544A ASN* 3.5 5.9 + - - -
671A ARG* 6.3 1.1 - - - +
673A THR* 5.6 2.0 + - - -
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Residues in contact with ILE 543 (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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481A LEU* 5.8 1.8 - - + -
539A TYR* 3.7 40.6 - - + +
540A LEU* 3.5 21.8 - - + +
542A SER* 1.3 84.8 + - - +
544A ASN* 1.3 72.5 + - - +
545A CYS* 3.2 28.6 + - - -
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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