Contacts of the helix formed by residues 563 - 584 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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561B LYS 4.1 1.0 + - - -
562B ILE* 1.3 78.8 - - - +
564B GLU* 1.3 63.9 + - - +
565B ALA* 3.7 8.6 + - - +
566B ASP* 3.0 37.3 + - - +
567B LYS* 3.1 20.3 + - - +
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Residues in contact with GLU 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560B GLY 5.9 1.4 + - - -
562B ILE* 3.7 6.9 + - - +
563B SER* 1.3 74.3 - - - +
565B ALA* 1.3 56.7 + - - +
567B LYS* 3.6 27.8 + - - +
568B LYS* 2.9 30.3 + - - +
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Residues in contact with ALA 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563B SER* 3.1 7.8 - - - +
564B GLU* 1.3 76.4 - - - +
566B ASP* 1.3 63.7 + - - +
568B LYS* 3.2 6.4 + - - +
569B LYS* 2.9 40.3 + - - +
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Residues in contact with ASP 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B ILE* 4.2 7.9 - - + +
563B SER* 3.0 24.4 + - - +
565B ALA* 1.3 76.0 - - - +
567B LYS* 1.3 65.5 - - - +
569B LYS* 3.1 21.2 + - - +
570B VAL* 2.9 27.7 + - - +
606B ILE* 3.5 34.2 - - + +
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Residues in contact with LYS 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553B VAL* 3.6 28.5 + - + +
554B GLU* 4.5 12.0 + - - +
555B ASP 5.9 0.2 + - - -
562B ILE* 3.9 22.9 - - + +
563B SER 3.1 18.1 + - - +
564B GLU* 3.6 29.4 + - - +
566B ASP* 1.3 77.2 - - - +
568B LYS* 1.3 57.1 + - - +
570B VAL* 3.3 5.7 + - - +
571B LEU* 2.9 55.3 + - + +
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Residues in contact with LYS 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564B GLU 2.9 19.5 + - - +
565B ALA* 3.7 6.3 - - - +
567B LYS* 1.3 74.1 - - - +
569B LYS* 1.3 65.0 + - - +
571B LEU* 4.5 7.4 - - + +
572B ASP* 2.9 60.2 + - - +
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Residues in contact with LYS 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565B ALA* 2.9 24.4 + - - +
566B ASP* 3.1 26.6 + - - +
568B LYS* 1.3 75.3 - - - +
570B VAL* 1.3 62.6 + - - +
572B ASP* 3.6 6.8 - - - +
573B LYS* 3.0 24.9 + - - +
602B VAL* 4.4 10.1 - - + +
606B ILE* 4.0 13.7 - - + -
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Residues in contact with VAL 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549B MET* 3.6 26.7 - - + -
553B VAL* 3.6 34.3 - - + -
566B ASP 2.9 16.5 + - - +
567B LYS 3.7 6.1 - - - +
569B LYS* 1.3 76.7 - - - +
571B LEU* 1.3 58.7 - - - +
573B LYS* 3.2 5.1 + - - +
574B CYS* 2.9 31.0 + - - -
602B VAL* 4.8 1.1 - - - -
603B CYS* 3.9 19.7 - - + +
606B ILE* 3.6 31.9 - - + -
607B ILE* 5.6 0.2 - - + -
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Residues in contact with LEU 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B LYS* 4.0 18.8 - - + -
553B VAL* 3.6 22.7 - - + -
554B GLU* 3.8 28.9 - - + +
567B LYS* 2.9 44.8 + - + +
568B LYS* 4.0 6.3 - - + +
570B VAL* 1.3 76.4 - - - +
572B ASP* 1.3 59.3 + - - +
574B CYS* 3.7 3.1 - - - +
575B GLN* 2.9 32.1 + - - +
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Residues in contact with ASP 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B LYS* 2.9 62.1 + - - +
569B LYS* 3.6 5.5 + - - +
571B LEU* 1.3 77.9 - - - +
573B LYS* 1.3 59.2 + - - +
575B GLN* 3.4 4.9 + - - +
576B GLU* 2.9 30.7 + - - +
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Residues in contact with LYS 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B LYS 3.0 17.3 + - - +
570B VAL 3.8 3.6 - - - +
572B ASP* 1.3 78.0 - - - +
574B CYS* 1.3 56.0 + - - +
576B GLU* 2.6 38.4 + - - +
577B VAL* 2.9 35.4 + - - +
598B GLU* 3.4 36.2 + - - +
599B LEU* 3.6 23.3 - - + +
602B VAL* 4.0 33.3 - - + +
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Residues in contact with CYS 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B ALA* 3.7 26.6 - - - +
549B MET* 3.8 26.2 - - - -
550B LYS* 3.8 21.3 - - + -
570B VAL* 2.9 23.5 + - - +
571B LEU* 3.7 6.7 - - - +
573B LYS* 1.3 77.6 - - - +
575B GLN* 1.3 56.6 + - - +
577B VAL* 3.3 4.9 + - - +
578B ILE* 2.9 36.6 + - + +
599B LEU* 4.1 14.6 - - - -
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Residues in contact with GLN 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B LYS* 5.4 8.6 - - - +
571B LEU 2.9 17.6 + - - +
572B ASP* 3.8 5.2 - - - +
574B CYS* 1.3 76.1 - - - +
576B GLU* 1.3 58.3 + - - +
578B ILE* 4.3 17.6 - - - +
579B SER* 2.9 38.3 + - - +
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Residues in contact with GLU 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572B ASP 2.9 17.8 + - - +
573B LYS* 2.6 43.5 + - - +
575B GLN* 1.3 77.1 - - - +
577B VAL* 1.3 56.6 + - + +
579B SER* 2.9 21.1 + - - +
580B TRP* 2.9 19.0 + - + +
595B LYS* 4.5 8.9 + - + +
598B GLU* 4.4 3.5 - - - +
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Residues in contact with VAL 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542B LEU* 3.8 29.8 - - + -
546B ALA* 3.9 17.5 - - + -
573B LYS* 2.9 27.0 + - - +
574B CYS* 3.3 6.3 + - - +
576B GLU* 1.3 76.7 - - + +
578B ILE* 1.3 56.4 + - - +
580B TRP* 3.3 7.8 + - - +
581B LEU* 2.9 32.4 + - + +
595B LYS* 3.9 27.1 - - + +
599B LEU* 4.1 24.9 - - + -
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Residues in contact with ILE 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B ALA* 4.5 13.7 - - + -
547B PHE* 3.7 50.5 - - + +
550B LYS* 4.2 20.0 - - + -
574B CYS* 2.9 24.2 + - + +
575B GLN* 3.8 19.3 - - - +
577B VAL* 1.3 73.9 - - - +
579B SER* 1.3 61.1 + - - +
581B LEU* 3.2 11.7 + - + +
582B ASP* 2.9 42.4 + - - +
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Residues in contact with SER 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575B GLN* 2.9 23.9 + - - +
576B GLU* 2.9 23.9 + - - +
578B ILE* 1.3 76.8 - - - +
580B TRP* 1.3 55.8 + - - +
582B ASP* 3.2 10.6 + - - +
583B ALA* 2.9 31.5 + - - +
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Residues in contact with TRP 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542B LEU* 3.9 8.7 - - + -
576B GLU* 2.9 20.8 + - + +
577B VAL* 3.3 9.0 - - - +
578B ILE 3.2 0.2 - - - -
579B SER* 1.3 77.5 + - - +
581B LEU* 1.3 69.0 + - + +
583B ALA* 3.1 2.5 + - - -
584B ASN* 2.7 61.5 + - + +
587B ALA* 3.8 20.6 - - + -
591B GLU* 4.0 32.8 - - + -
592B PHE* 3.6 31.2 - + - -
595B LYS* 3.7 39.0 - - + +
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Residues in contact with LEU 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539B LYS* 4.2 25.1 - - + +
542B LEU* 3.8 19.3 - - + -
543B GLU* 4.0 35.0 - - + +
546B ALA* 5.2 0.4 - - + -
547B PHE* 5.5 1.3 - - + -
577B VAL* 2.9 28.2 + - + +
578B ILE* 3.2 17.7 + - + +
580B TRP* 1.3 81.4 - - + +
582B ASP* 1.3 65.4 + - - +
583B ALA 3.3 0.5 + - - -
584B ASN 3.3 18.2 + - - +
585B THR* 3.9 6.8 + - - +
592B PHE* 3.8 28.3 - - + -
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Residues in contact with ASP 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578B ILE* 2.9 31.4 + - - +
579B SER* 3.2 10.9 + - - +
581B LEU* 1.3 80.6 - - - +
583B ALA* 1.3 58.9 + - - +
584B ASN 3.7 0.2 + - - -
585B THR* 3.9 14.9 - - - +
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Residues in contact with ALA 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579B SER 2.9 17.4 + - - +
580B TRP* 3.1 5.1 + - - +
582B ASP* 1.3 78.3 - - - +
584B ASN* 1.3 68.2 + - - +
585B THR* 3.8 2.0 + - - -
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Residues in contact with ASN 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539B LYS* 5.9 0.2 - - - -
580B TRP* 2.7 60.9 + - + +
581B LEU 3.3 7.1 + - - +
583B ALA* 1.3 91.1 - - - +
585B THR* 1.3 62.8 + - - +
586B LEU 3.1 5.8 + - - +
587B ALA* 3.2 27.9 + - + +
592B PHE* 4.3 8.1 - - - -
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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