Contacts of the helix formed by residues 558 - 583 (chain A) in PDB entry 3K57
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 558 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A HIS* 1.3 76.4 - - - +
559A GLU* 1.3 59.8 + - - +
560A GLU* 3.4 8.5 + - - +
561A GLU* 3.0 26.6 + - - +
562A ALA* 2.8 28.9 + - - +
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Residues in contact with GLU 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A HIS 5.4 0.3 - - - +
558A SER* 1.3 73.5 - - - +
560A GLU* 1.3 62.2 + - - +
562A ALA* 3.5 1.6 + - - +
563A ALA* 3.1 25.1 + - - +
594A TYR* 5.2 0.3 + - - -
597A HIS* 2.7 44.4 + - - +
599A CYS* 4.1 6.6 - - - +
621A ILE* 5.9 0.2 - - - +
622A GLN* 3.5 45.2 + - + +
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Residues in contact with GLU 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A SER* 3.2 7.4 + - - +
559A GLU* 1.3 80.0 - - - +
561A GLU* 1.3 61.7 + - - +
563A ALA* 3.4 6.2 + - - +
564A LYS* 3.2 52.6 + - - +
567A ARG* 4.6 2.9 + - - +
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Residues in contact with GLU 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A ALA 5.4 0.7 - - - +
557A HIS* 3.4 32.3 + - + -
558A SER* 3.0 21.9 + - - +
560A GLU* 1.3 74.6 - - - +
562A ALA* 1.3 64.8 + - - +
564A LYS* 3.3 19.8 + - - +
565A ILE* 3.2 35.0 + - - +
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Residues in contact with ALA 562 (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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416A LEU* 3.8 13.1 - - + +
553A LEU* 4.3 14.6 - - + -
557A HIS* 4.6 4.0 - - + -
558A SER 2.8 21.6 + - - +
559A GLU 3.9 1.1 - - - +
561A GLU* 1.3 74.9 - - - +
563A ALA* 1.3 62.4 + - - +
565A ILE* 3.3 4.2 + - - +
566A GLY* 3.0 19.2 + - - -
594A TYR* 4.0 2.4 + - - -
597A HIS* 3.5 42.4 - - + +
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Residues in contact with ALA 563 (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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559A GLU 3.1 17.8 + - - +
560A GLU* 3.8 4.7 - - - +
562A ALA* 1.3 75.4 - - - +
564A LYS* 1.3 65.4 + - - +
566A GLY* 3.3 0.9 + - - -
567A ARG* 3.0 46.7 + - - +
594A TYR* 3.6 26.1 + - + +
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Residues in contact with LYS 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A GLU* 3.2 46.9 + - - +
561A GLU* 3.7 22.7 - - - +
562A ALA 3.3 0.4 - - - -
563A ALA* 1.3 75.3 - - - +
565A ILE* 1.3 58.2 + - + +
567A ARG* 3.4 23.0 + - - +
568A ALA* 2.9 31.5 + - - +
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Residues in contact with ILE 565 (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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416A LEU* 4.3 2.0 - - + -
539A TYR* 3.7 37.5 - - + +
553A LEU* 4.1 18.8 - - + -
557A HIS* 3.8 31.0 - - + +
561A GLU* 3.2 27.4 + - - +
562A ALA 3.6 6.1 - - - +
563A ALA 3.2 0.2 - - - -
564A LYS* 1.3 75.6 - - + +
566A GLY* 1.3 61.0 + - - +
568A ALA* 3.2 6.7 + - - +
569A LEU* 2.8 45.3 + - + +
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Residues in contact with GLY 566 (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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416A LEU* 3.6 19.7 - - - +
418A LEU* 4.4 4.0 - - - -
562A ALA 3.0 11.3 + - - -
563A ALA 3.3 2.9 + - - -
565A ILE* 1.3 75.9 - - - +
567A ARG* 1.3 62.6 + - - +
569A LEU* 3.2 5.0 + - - +
570A VAL* 3.0 28.8 + - - +
594A TYR* 3.8 20.2 - - - -
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Residues in contact with ARG 567 (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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560A GLU* 4.6 3.0 + - - +
563A ALA* 3.0 44.5 + - - +
564A LYS* 3.8 24.3 - - - +
566A GLY* 1.3 74.7 - - - +
568A ALA* 1.3 66.3 + - - +
570A VAL* 3.3 11.4 - - + +
571A GLN* 3.1 23.4 + - - +
594A TYR* 4.3 16.8 - - + -
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Residues in contact with ALA 568 (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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564A LYS 2.9 18.5 + - - +
565A ILE* 3.6 6.7 - - - +
567A ARG* 1.3 78.2 - - - +
569A LEU* 1.3 59.3 - - + +
571A GLN* 3.3 9.8 + - - +
572A HIS* 2.9 29.0 + - - +
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Residues in contact with LEU 569 (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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416A LEU* 4.6 6.5 - - + -
418A LEU* 4.2 20.6 - - + -
534A ILE* 4.5 15.7 - - + -
537A GLN* 3.9 33.0 - - + +
539A TYR* 4.1 20.4 - - + -
551A VAL* 4.4 16.6 - - + -
565A ILE* 2.8 38.5 + - + +
566A GLY 3.6 3.6 - - - +
568A ALA* 1.3 75.6 - - + +
570A VAL* 1.3 66.0 + - - +
572A HIS* 3.2 6.6 + - + +
573A VAL* 2.9 29.3 + - + +
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Residues in contact with VAL 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LEU* 3.7 24.0 - - + -
566A GLY 3.0 15.1 + - - +
567A ARG* 3.3 17.3 - - + +
569A LEU* 1.3 74.7 - - - +
571A GLN* 1.3 62.9 + - + +
573A VAL 3.3 0.2 + - - -
574A ASN* 2.9 38.7 + - - +
592A LEU* 3.5 35.7 - - + +
593A GLU* 3.8 17.9 - - - -
594A TYR* 3.8 7.9 - - + +
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Residues in contact with GLN 571 (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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567A ARG 3.1 18.6 + - - +
568A ALA* 3.5 8.7 + - - +
570A VAL* 1.3 79.2 - - + +
572A HIS* 1.3 71.8 + - - +
574A ASN* 4.1 4.7 - - - +
575A ALA* 3.1 32.1 + - - +
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Residues in contact with HIS 572 (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 LEU* 4.1 26.6 + - + +
536A ALA* 6.0 0.6 - - - +
537A GLN* 3.6 45.6 + - + +
568A ALA 2.9 17.2 + - - +
569A LEU* 3.2 8.3 + - + +
571A GLN* 1.3 85.0 - - - +
573A VAL* 1.3 70.1 + - + +
575A ALA* 3.5 4.2 + - - +
576A TRP* 3.2 27.0 + + + +
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Residues in contact with VAL 573 (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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420A TYR* 3.4 25.4 - - - +
530A THR* 4.4 9.2 - - + -
533A LEU* 4.1 33.7 - - + -
534A ILE* 4.6 10.3 - - + -
569A LEU* 2.9 21.2 + - + +
570A VAL 3.8 3.6 - - - +
572A HIS* 1.3 79.8 - - + +
574A ASN* 1.3 65.5 + - - +
576A TRP* 3.1 4.7 + - - +
577A TRP* 3.1 32.3 + - + +
592A LEU* 4.0 22.7 - - + -
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Residues in contact with ASN 574 (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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420A TYR* 4.5 1.4 - - - -
570A VAL* 2.9 26.2 + - - +
571A GLN* 4.1 4.2 - - - +
573A VAL* 1.3 75.6 - - - +
575A ALA* 1.3 61.9 + - - +
577A TRP* 3.5 8.1 + - - +
578A ALA* 3.0 22.3 + - - +
588A SER* 5.0 1.6 + - - -
590A LEU 3.9 7.8 - - - +
591A GLU* 3.7 17.6 - - - +
592A LEU* 2.7 51.8 + - - +
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Residues in contact with ALA 575 (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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571A GLN* 3.1 32.1 + - - +
572A HIS* 3.8 5.2 - - - +
574A ASN* 1.3 72.8 - - - +
576A TRP* 1.3 55.9 + - - +
578A ALA* 3.2 7.8 + - - +
579A GLU* 2.8 37.3 + - - +
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Residues in contact with TRP 576 (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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529A GLN* 3.5 42.8 - - + -
533A LEU* 3.8 38.6 - - + +
572A HIS* 3.2 18.2 + + + +
573A VAL 3.1 8.9 + - - +
575A ALA* 1.3 80.6 - - - +
577A TRP* 1.3 85.1 + + - +
579A GLU* 3.2 19.2 + - - +
580A THR* 2.8 61.9 + - + +
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Residues in contact with TRP 577 (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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420A TYR* 2.9 23.5 + + - -
431A PHE* 5.6 3.4 - + - -
525A GLN* 4.8 9.2 - - + -
526A ILE* 3.8 39.7 - - + -
529A GLN* 3.8 31.4 - - + -
530A THR* 4.3 1.3 + - - -
533A LEU* 4.9 0.6 - - + +
573A VAL* 3.1 38.1 + - + +
574A ASN* 3.8 8.7 - - - +
576A TRP* 1.3 92.7 - + - +
578A ALA* 1.3 66.7 + - - +
580A THR* 3.7 7.4 - - - -
581A LEU* 2.9 41.9 + - + +
588A SER* 3.7 17.3 - - - +
590A LEU* 3.5 31.8 - - + +
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Residues in contact with ALA 578 (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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574A ASN 3.0 14.1 + - - +
575A ALA* 3.2 11.2 + - - +
577A TRP* 1.3 76.0 - - - +
579A GLU* 1.3 62.4 + - - +
581A LEU* 4.4 0.2 - - - +
582A GLN* 3.1 30.4 + - - +
588A SER* 3.9 16.3 + - - +
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Residues in contact with GLU 579 (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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575A ALA 2.8 19.9 + - - +
576A TRP* 3.5 20.4 + - - +
578A ALA* 1.3 75.2 - - - +
580A THR* 1.3 71.7 + - - +
582A GLN* 3.8 9.2 - - - +
583A LYS* 3.5 47.7 + - - +
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Residues in contact with THR 580 (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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576A TRP* 2.8 74.1 + - + +
577A TRP* 3.4 12.8 + - - -
579A GLU* 1.3 80.2 - - + +
581A LEU* 1.3 64.5 + - - +
583A LYS* 3.4 24.0 + - + +
584A GLN* 3.6 18.7 + - - +
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Residues in contact with LEU 581 (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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430A THR* 3.7 16.2 - - + -
431A PHE* 3.7 26.9 - - + -
577A TRP* 2.9 30.2 + - + +
578A ALA 4.4 0.4 - - - +
580A THR* 1.3 77.7 - - - +
582A GLN* 1.3 60.0 + - - +
584A GLN* 2.9 41.5 + - - +
586A LEU* 3.0 39.8 + - + +
588A SER* 3.6 26.5 - - - +
590A LEU* 4.0 17.9 - - + -
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Residues in contact with GLN 582 (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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578A ALA* 3.1 21.3 + - - +
579A GLU* 3.8 8.7 - - - +
580A THR 3.3 0.2 - - - -
581A LEU* 1.3 77.1 - - - +
583A LYS* 1.3 59.3 + - + +
584A GLN 3.0 0.4 - - - -
585A ARG* 2.9 21.3 + - - +
586A LEU 3.5 12.0 + - - +
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Residues in contact with LYS 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A GLU* 3.5 40.2 + - - +
580A THR* 3.4 15.1 + - + +
581A LEU 3.2 0.6 - - - -
582A GLN* 1.3 78.9 - - + +
584A GLN* 1.3 59.5 + - + +
585A ARG* 3.3 5.3 + - - +
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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
------------------------------------------------------------
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