Contacts of the helix formed by residues 563 - 584 (chain A) in PDB entry 4PO2
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 563 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561A LYS 4.2 1.0 + - - -
562A ILE* 1.3 79.3 - - - +
564A GLU* 1.3 64.3 + - - +
565A ALA* 3.8 7.3 + - - +
566A ASP* 3.0 33.0 + - - -
567A LYS* 3.0 21.2 + - - +
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Residues in contact with GLU 564 (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 LYS* 4.8 12.6 - - - +
562A ILE* 3.8 3.9 + - - +
563A SER* 1.3 72.7 - - - +
565A ALA* 1.3 58.1 + - - +
567A LYS* 3.4 31.0 + - - +
568A LYS* 2.9 28.9 + - - +
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Residues in contact with ALA 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A SER* 3.2 8.4 - - - +
564A GLU* 1.3 77.1 - - - +
566A ASP* 1.3 62.8 + - - +
568A LYS* 3.1 10.4 + - - +
569A LYS* 2.9 36.3 + - - +
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Residues in contact with ASP 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A ILE* 3.6 17.8 - - + +
563A SER* 3.0 21.8 + - - +
565A ALA* 1.3 77.6 - - - +
567A LYS* 1.3 60.7 + - - +
569A LYS* 3.1 20.8 + - - +
570A VAL* 2.9 34.0 + - - +
606A ILE* 3.7 32.3 - - + +
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Residues in contact with LYS 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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553A VAL* 3.5 31.9 + - + +
554A GLU* 4.5 13.1 + - - +
559A LYS* 5.5 9.7 - - - +
562A ILE* 3.5 20.7 - - + +
563A SER 3.0 17.0 + - - +
564A GLU* 3.5 31.8 + - - +
566A ASP* 1.3 77.1 - - - +
568A LYS* 1.3 56.9 + - - +
570A VAL* 3.3 4.9 + - - +
571A LEU* 2.9 57.5 + - + +
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Residues in contact with LYS 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 GLU 2.9 14.5 + - - +
565A ALA* 3.3 11.9 - - - +
567A LYS* 1.3 74.5 - - - +
569A LYS* 1.3 66.6 + - + +
571A LEU* 4.0 5.8 - - - +
572A ASP* 2.9 56.7 + - - +
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Residues in contact with LYS 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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565A ALA* 2.9 19.3 + - - +
566A ASP* 3.1 29.0 + - - +
568A LYS* 1.3 76.0 - - + +
570A VAL* 1.3 64.0 + - - +
572A ASP* 3.7 4.9 - - - +
573A LYS* 3.0 26.3 + - - +
602A VAL* 4.2 17.5 - - + +
606A ILE* 4.5 6.5 - - + -
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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
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549A MET* 3.8 19.5 - - + +
553A VAL* 3.6 38.6 - - + -
562A ILE* 4.5 2.5 - - + -
566A ASP 2.9 18.8 + - - +
567A LYS 3.6 7.0 - - - +
569A LYS* 1.3 76.1 - - - +
571A LEU* 1.3 58.3 + - - +
573A LYS* 3.8 1.8 - - - +
574A CYS* 2.9 46.6 + - - -
599A LEU* 4.8 0.3 - - - +
602A VAL* 4.5 6.7 - - + -
603A CYS* 4.1 14.1 - - - -
606A ILE* 3.7 22.7 - - + -
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Residues in contact with LEU 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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550A LYS* 3.6 33.4 - - + +
553A VAL* 3.6 23.1 - - + -
554A GLU* 4.0 15.0 - - + +
567A LYS* 2.9 49.2 + - + +
568A LYS* 4.0 6.1 - - - +
570A VAL* 1.3 75.3 - - - +
572A ASP* 1.3 61.2 + - - +
574A CYS* 3.4 3.8 + - + +
575A GLN* 2.9 30.0 + - - +
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Residues in contact with ASP 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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568A LYS* 2.9 57.7 + - - +
569A LYS* 3.7 4.4 - - - +
571A LEU* 1.3 78.3 - - - +
573A LYS* 1.3 62.7 + - - +
575A GLN* 3.2 7.1 + - - +
576A GLU* 2.9 22.4 + - - +
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Residues in contact with LYS 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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569A LYS 3.0 17.5 + - - +
570A VAL 3.8 1.6 - - - +
572A ASP* 1.3 75.6 - - - +
574A CYS* 1.3 57.9 + - - +
576A GLU* 3.2 38.6 + - - +
577A VAL* 2.9 36.7 + - + +
598A GLU* 4.2 33.5 + - - +
599A LEU* 3.6 24.9 - - + +
602A VAL* 3.8 27.7 - - + +
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Residues in contact with CYS 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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546A ALA* 3.7 24.6 - - + +
549A MET* 3.7 21.1 - - - -
550A LYS* 4.0 14.4 - - + -
570A VAL* 2.9 32.1 + - - +
571A LEU* 3.6 7.4 - - - +
573A LYS* 1.3 77.7 - - - +
575A GLN* 1.3 56.6 + - - +
577A VAL* 3.3 4.7 + - - +
578A ILE* 2.9 41.2 + - + +
599A LEU* 4.1 17.9 - - - -
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Residues in contact with GLN 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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550A LYS* 5.9 2.8 - - - -
571A LEU 2.9 16.8 + - - +
572A ASP* 3.6 6.5 - - - +
574A CYS* 1.3 76.5 - - - +
576A GLU* 1.3 59.7 + - - +
578A ILE* 3.3 19.3 + - - +
579A SER* 2.9 41.0 + - - +
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Residues in contact with GLU 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A ASP 2.9 12.9 + - - +
573A LYS* 3.2 44.5 + - - +
575A GLN* 1.3 78.2 - - - +
577A VAL* 1.3 56.9 + - - +
579A SER* 3.4 6.2 + - - -
580A TRP* 2.9 28.9 + - + +
595A LYS* 4.7 9.5 + - + +
598A GLU* 4.3 8.0 - - - +
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Residues in contact with VAL 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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542A LEU* 3.7 31.6 - - + -
546A ALA* 4.2 15.7 - - + -
573A LYS* 2.9 26.4 + - + +
574A CYS* 3.3 6.7 + - - +
576A GLU* 1.3 76.1 - - + +
578A ILE* 1.3 57.5 + - - +
580A TRP* 3.3 8.6 + - - +
581A LEU* 2.9 31.5 + - + +
595A LYS* 3.9 26.2 - - + +
599A LEU* 4.1 27.1 - - + +
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Residues in contact with ILE 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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546A ALA* 4.2 22.2 - - + -
547A PHE* 4.9 24.2 - - + -
550A LYS* 4.9 17.5 - - + -
574A CYS* 2.9 26.6 + - + +
575A GLN* 3.7 20.6 - - - +
577A VAL* 1.3 73.2 - - - +
579A SER* 1.3 60.7 + - - +
581A LEU* 3.2 13.3 + - + +
582A ASP* 2.9 43.7 + - - +
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Residues in contact with SER 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 GLN* 2.9 34.5 + - - +
576A GLU* 3.6 6.2 - - - -
578A ILE* 1.3 75.8 - - - +
580A TRP* 1.3 63.7 + - - +
582A ASP* 3.2 7.8 + - - +
583A ALA* 2.9 25.9 + - - +
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Residues in contact with TRP 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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542A LEU* 3.9 8.1 - - + -
576A GLU* 2.9 16.0 + - + +
577A VAL* 3.3 11.2 + - - +
579A SER* 1.3 75.7 - - - +
581A LEU* 1.3 84.2 + - + +
583A ALA* 3.2 2.2 + - - -
584A ASN* 2.7 61.7 + - + +
587A ALA* 3.7 18.8 - - + -
591A GLU* 4.1 33.4 - - + -
592A PHE* 3.5 38.8 - + - -
595A LYS* 3.6 39.9 - - + +
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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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539A LYS* 4.4 23.7 - - + +
542A LEU* 3.8 24.2 - - + -
543A GLU* 3.7 43.1 - - + +
546A ALA* 5.2 0.4 - - + -
577A VAL* 2.9 22.3 + - + +
578A ILE* 3.2 17.2 + - + +
580A TRP* 1.3 81.2 - - + +
582A ASP* 1.3 67.3 + - - +
584A ASN 3.2 19.1 + - - +
585A THR* 3.9 6.4 + - - +
592A PHE* 3.8 28.5 - - + -
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Residues in contact with ASP 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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543A GLU* 5.0 7.3 - - - +
578A ILE* 2.9 34.0 + - - +
579A SER* 3.7 7.3 - - - +
581A LEU* 1.3 80.0 - - - +
583A ALA* 1.3 58.0 + - - +
584A ASN 3.7 0.3 + - - -
585A THR* 4.0 14.4 - - - +
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Residues in contact with ALA 583 (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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579A SER 2.9 16.9 + - - +
580A TRP* 3.9 4.0 - - - +
582A ASP* 1.3 79.8 - - - +
584A ASN* 1.3 69.7 + - - +
585A THR* 3.9 2.1 + - - -
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Residues in contact with ASN 584 (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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539A LYS* 5.7 0.3 - - - -
580A TRP* 2.7 61.1 + - + +
581A LEU 3.2 7.7 + - - +
583A ALA* 1.3 89.5 - - - +
585A THR* 1.3 64.1 + - - +
586A LEU 3.2 3.8 + - - +
587A ALA* 3.4 26.5 + - + +
592A PHE* 4.2 8.7 - - - -
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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