Contacts of the helix formed by residues 567 - 582 (chain B) in PDB entry 5JO3
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 567 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565B GLU 4.0 0.6 + - - -
566B LEU* 1.3 76.7 - - - +
568B ASP* 1.3 65.0 + - - +
569B LEU* 3.5 9.5 + - - +
570B GLU* 2.9 38.5 + - - +
571B THR* 3.0 21.3 + - - +
616B ARG* 3.4 2.7 - - - +
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Residues in contact with ASP 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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539B GLU* 4.5 7.2 - - - +
567B SER* 1.3 72.9 - - - +
569B LEU* 1.3 63.4 + - - +
571B THR* 2.7 24.7 + - - -
572B ALA 3.1 5.7 + - - -
603B LYS* 3.1 32.8 + - - +
608B LYS* 5.3 8.8 + - - -
615B TRP* 4.7 2.3 - - - -
616B ARG* 2.9 27.6 + - - +
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Residues in contact with LEU 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B GLU* 5.0 8.4 + - + +
542B SER* 4.6 17.5 - - - +
543B LEU* 3.8 41.5 - - + +
546B ALA* 5.3 0.9 - - + -
567B SER* 3.5 8.8 + - - +
568B ASP* 1.3 77.6 - - - +
570B GLU* 1.3 60.8 + - + +
572B ALA* 3.1 6.0 + - + +
573B LEU* 2.9 40.6 + - + +
603B LYS* 4.2 2.7 - - - +
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Residues in contact with GLU 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B LEU* 5.2 5.9 - - + +
565B GLU 4.0 4.0 - - - +
566B LEU* 3.4 27.1 - - + +
567B SER* 2.9 45.4 + - - +
569B LEU* 1.3 77.5 - - + +
571B THR* 1.3 57.7 + - - +
573B LEU* 3.3 16.7 + - + +
574B CYS* 2.9 34.7 + - - -
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Residues in contact with THR 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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566B LEU* 4.1 9.0 - - + -
567B SER 3.0 14.0 + - - +
568B ASP* 2.7 19.1 + - - -
570B GLU* 1.3 76.1 - - - +
572B ALA* 1.3 57.2 + - - +
574B CYS* 3.4 0.8 + - - -
575B THR* 2.9 31.0 + - - -
615B TRP* 2.9 26.8 + - - -
616B ARG* 3.7 28.5 - - - +
619B PHE* 3.2 41.3 - - + -
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Residues in contact with ALA 572 (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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543B LEU* 3.7 30.1 - - + -
568B ASP 3.1 4.0 + - - +
569B LEU* 3.1 11.2 + - + +
571B THR* 1.3 75.1 + - - +
573B LEU* 1.3 58.8 + - - +
575B THR* 3.2 4.6 + - - -
576B ILE* 3.0 30.5 + - - +
599B ILE* 4.0 19.6 - - + +
600B LEU* 4.6 1.1 - - + -
603B LYS* 3.8 21.3 - - - +
615B TRP* 5.0 1.3 - - - -
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Residues in contact with LEU 573 (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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543B LEU* 3.8 17.5 - - + +
546B ALA* 3.7 29.6 - - + -
547B VAL 4.8 1.1 - - - +
548B VAL* 3.6 33.3 - - + +
549B PRO* 4.3 23.1 - - + -
554B LEU* 4.4 6.1 - - + -
569B LEU* 2.9 33.7 + - + +
570B GLU* 3.6 17.0 - - + +
572B ALA* 1.3 73.2 - - - +
574B CYS* 1.3 66.2 + - - +
576B ILE* 3.1 5.8 + - + +
577B ARG* 3.0 18.4 + - - +
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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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554B LEU* 3.9 31.1 - - - +
556B ILE* 3.8 27.2 - - + +
561B PHE* 4.6 0.2 - - - -
566B LEU* 4.0 16.6 - - - -
570B GLU 2.9 17.8 + - - -
571B THR 3.5 8.1 - - - +
573B LEU* 1.3 75.0 - - - +
575B THR* 1.3 57.2 + - - +
577B ARG* 3.2 3.3 + - - +
578B MET* 2.9 33.4 + - + +
619B PHE* 3.5 22.9 - - + -
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Residues in contact with THR 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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571B THR 2.9 15.0 + - - -
572B ALA 3.4 9.0 - - - -
573B LEU 3.2 0.4 - - - -
574B CYS* 1.3 73.6 - - - +
576B ILE* 1.3 65.2 + - - +
578B MET* 3.1 20.1 + - - +
579B PHE* 3.2 18.8 + - + -
599B ILE* 3.8 27.4 - - + -
615B TRP* 3.9 7.6 - - - -
619B PHE* 3.5 17.5 - - - -
651B LEU* 3.7 35.2 - - + +
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Residues in contact with ILE 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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543B LEU* 3.6 32.3 - - + +
548B VAL* 3.8 30.7 - - + -
572B ALA 3.0 14.6 + - - +
573B LEU* 3.1 8.3 + - + +
575B THR* 1.3 74.4 - - - +
577B ARG* 1.3 58.5 + - - +
579B PHE* 3.2 4.7 + - - +
580B THR* 2.8 41.6 + - - +
585B VAL* 5.7 0.4 - - + -
592B HIS* 4.3 14.1 - - + +
595B LEU* 4.3 15.7 - - + -
596B CYS* 3.7 22.9 - - - -
599B ILE* 3.5 20.0 - - + -
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Residues in contact with ARG 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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548B VAL* 2.9 39.8 + - + +
549B PRO 2.8 16.3 + - - +
550B SER* 3.8 7.9 - - - +
551B ALA* 3.7 19.1 - - + +
554B LEU* 3.8 11.0 - - + -
556B ILE* 3.7 15.9 - - + -
573B LEU 3.0 13.6 + - - +
574B CYS 3.5 8.1 - - - +
576B ILE* 1.3 77.2 - - - +
578B MET* 1.3 56.2 + - - +
580B THR* 3.5 21.7 - - - +
581B ASP* 2.9 61.2 + - - +
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Residues in contact with MET 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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556B ILE* 3.9 9.4 - - + -
574B CYS* 2.9 22.6 + - + +
575B THR* 3.1 13.7 + - + +
577B ARG* 1.3 76.5 - - - +
579B PHE* 1.3 62.5 + - - +
581B ASP 3.5 0.2 + - - -
582B LEU* 3.2 30.5 + - - +
619B PHE* 3.7 31.9 - - + -
622B ALA* 3.9 31.2 - - - +
623B GLN* 3.7 30.5 - - + +
626B PHE* 3.8 28.6 - - + -
647B LEU* 4.1 16.6 - - + -
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Residues in contact with PHE 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 THR* 3.2 27.9 + - + -
576B ILE 3.2 7.9 + - - +
578B MET* 1.3 78.8 - - - +
580B THR* 1.3 63.9 + - - +
582B LEU 3.6 2.9 + - - -
584B LEU* 3.0 46.8 + - + +
585B VAL* 3.8 14.4 - - + -
590B MET* 4.1 28.3 - - + -
595B LEU* 3.9 19.3 - - + -
598B TRP* 3.6 28.5 - + - -
644B LEU* 4.7 0.4 - - + -
647B LEU* 3.7 20.6 - - + +
648B ILE* 4.3 12.3 - - + -
651B LEU* 3.7 25.1 - - + -
700B ILE* 4.2 9.0 - - + -
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Residues in contact with THR 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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548B VAL* 5.6 0.2 - - - +
576B ILE* 2.8 28.5 + - - +
577B ARG* 3.5 31.1 - - - +
579B PHE* 1.3 77.2 - - - +
581B ASP* 1.3 60.6 + - - +
583B ASN* 3.1 19.2 + - - -
585B VAL* 3.9 20.1 + - + +
586B GLN* 6.2 0.2 - - - +
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Residues in contact with ASP 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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551B ALA* 3.4 25.1 + - - +
577B ARG* 2.9 48.7 + - - +
578B MET 4.0 0.2 - - - -
580B THR* 1.3 74.7 - - - +
582B LEU* 1.3 57.2 + - - +
583B ASN* 3.2 6.8 + - - +
626B PHE* 4.0 17.5 - - + -
630B LYS* 2.9 28.9 + - - +
635B GLN* 4.9 0.7 + - - -
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Residues in contact with LEU 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 MET 3.2 19.6 + - - +
580B THR 3.2 0.4 - - - -
581B ASP* 1.3 76.2 - - - +
583B ASN* 1.3 72.3 + - - +
584B LEU* 3.3 20.2 + - + +
626B PHE* 3.9 19.7 - - + -
629B LEU* 3.8 31.0 - - + -
630B LYS* 3.9 10.8 - - - +
635B GLN* 3.7 32.4 + - - +
643B ILE* 3.9 24.7 - - + +
647B LEU* 4.1 24.7 - - + -
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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