Contacts of the helix formed by residues 567 - 582 (chain B) in PDB entry 1JQO
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 ARG 567 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536B MET* 3.7 45.6 - - + +
538B THR* 3.1 19.0 - - - +
566B GLU* 1.3 80.5 - - + +
568B LEU* 1.3 68.4 + - - +
569B ALA* 3.1 11.7 - - + +
570B ASP* 2.4 56.2 + - - +
571B LEU* 2.9 21.2 + - - +
603B ASP* 5.4 4.5 - - + +
607B ASP* 3.8 12.6 - - - +
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Residues in contact with LEU 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B GLU 3.9 1.4 + - - -
567B ARG* 1.3 70.2 - - - +
569B ALA* 1.3 65.2 + - - +
571B LEU* 3.1 11.9 + - + +
572B GLN* 3.0 49.6 + - + +
604B SER* 4.9 2.4 + - - +
607B ASP* 2.9 25.3 + - - +
608B ALA* 3.3 29.6 - - + -
612B SER* 5.2 4.0 - - - -
613B ALA* 5.6 2.9 - - - -
616B GLN* 3.6 25.4 - - + +
725B THR* 4.8 10.3 - - + +
729B ARG* 5.9 4.3 - - - +
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Residues in contact with ALA 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B ARG* 4.2 10.7 - - + +
568B LEU* 1.3 81.7 - - - +
570B ASP* 1.3 65.9 + - - +
572B GLN* 3.5 13.6 + - - +
573B SER* 2.9 23.7 + - - -
607B ASP* 4.4 1.0 + - - -
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Residues in contact with ASP 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B ALA 3.6 19.0 - - - +
538B THR* 3.3 13.3 - - - +
565B PHE* 4.1 15.7 - - + -
566B GLU 4.4 1.0 + - - -
567B ARG* 2.4 71.5 + - - +
569B ALA* 1.3 74.7 - - - +
571B LEU* 1.3 56.0 + - - +
573B SER* 2.8 8.4 + - - -
574B ALA* 2.6 36.8 + - - +
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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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565B PHE* 3.9 18.1 - - + +
566B GLU 4.6 0.7 - - - +
567B ARG 2.9 13.5 + - - +
568B LEU* 3.1 13.4 + - + +
570B ASP* 1.3 74.3 - - - +
572B GLN* 1.3 64.7 + - - +
574B ALA* 3.2 19.5 - - + +
575B PRO* 3.3 6.4 - - - +
599B VAL* 3.5 28.9 - - + -
604B SER* 3.1 28.7 - - - +
613B ALA* 5.1 1.1 - - - +
616B GLN* 4.0 25.8 + - + -
617B LEU* 4.1 15.7 - - + +
620B ALA* 3.7 25.9 - - + +
624B MET* 6.0 0.7 - - + -
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Residues in contact with GLN 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B LEU* 3.0 45.9 + - + +
569B ALA* 3.7 11.1 - - - +
571B LEU* 1.3 75.1 - - - +
573B SER* 1.3 58.2 + - - +
575B PRO* 3.3 17.0 - - - +
616B GLN* 3.8 21.5 - - - +
623B GLU* 5.3 1.7 - - - +
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Residues in contact with SER 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B THR 4.6 7.8 + - - -
569B ALA 2.9 13.9 + - - -
570B ASP* 2.8 21.5 + - - -
572B GLN* 1.3 77.0 - - - +
574B ALA* 1.3 65.0 + - - +
575B PRO* 3.3 0.7 - - - -
576B ALA* 2.8 27.5 + - - +
577B SER* 3.3 9.3 + - - -
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Residues in contact with ALA 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B PHE* 3.4 35.7 - - + -
570B ASP 2.6 18.5 + - - +
571B LEU* 3.2 15.0 - - + +
573B SER* 1.3 71.0 - - - +
575B PRO* 1.3 71.8 - - + +
576B ALA 2.9 1.6 + - - -
577B SER* 2.9 6.3 + - - -
578B VAL* 2.9 27.7 + - - +
620B ALA* 5.6 0.9 - - + -
624B MET* 4.1 9.2 - - + -
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Residues in contact with PRO 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B LEU 3.3 5.8 - - - +
572B GLN* 3.3 17.9 - - - +
573B SER 3.4 0.9 - - - -
574B ALA* 1.3 95.6 - - + +
576B ALA* 1.3 60.2 + - - +
578B VAL* 4.0 7.2 - - + +
579B GLU* 3.3 19.8 + - - +
620B ALA* 4.2 12.8 - - - +
623B GLU* 3.8 42.4 - - + +
624B MET* 4.4 7.1 - - - +
627B VAL* 3.5 16.9 - - + +
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Residues in contact with ALA 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B GLN 5.3 0.2 + - - -
573B SER* 2.8 17.0 + - - +
575B PRO* 1.3 77.1 - - - +
577B SER* 1.3 57.3 + - - +
579B GLU* 2.7 31.6 + - - +
580B ARG* 2.8 14.3 + - - +
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Residues in contact with SER 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B THR 3.2 22.4 + - - -
539B ALA* 5.0 0.9 - - - -
540B PRO* 3.8 26.8 - - - +
565B PHE* 4.2 16.3 - - - -
573B SER* 3.3 11.8 + - - -
574B ALA* 2.9 9.3 + - - -
576B ALA* 1.3 76.7 - - - +
578B VAL* 1.3 63.8 + - - -
580B ARG* 2.9 5.1 + - - +
581B LEU* 2.9 30.8 + - - +
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Residues in contact with VAL 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B PRO* 6.1 1.3 - - + -
565B PHE* 4.0 15.5 - - + -
574B ALA 2.9 15.7 + - - +
575B PRO 4.0 5.6 - - - +
577B SER* 1.3 74.5 - - - +
579B GLU* 1.3 61.9 + - - +
581B LEU* 3.6 10.4 + - - +
582B PHE* 3.2 52.1 + - + -
595B GLN* 5.5 2.5 - - + -
597B VAL* 5.1 5.8 - - + -
624B MET* 3.6 37.5 - - + -
627B VAL* 4.2 7.4 - - + -
635B LEU* 4.7 6.7 - - + -
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Residues in contact with GLU 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 PRO 3.3 11.6 + - - +
576B ALA* 2.7 18.0 + - - +
578B VAL* 1.3 73.6 - - - +
580B ARG* 1.3 61.7 + - - +
582B PHE* 3.1 13.5 + - - +
583B SER* 2.8 20.6 + - - +
627B VAL* 3.6 16.4 - - + +
630B ARG* 2.7 34.5 + - - -
631B TYR* 2.7 32.3 + - + +
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Residues in contact with ARG 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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484B ASP* 5.7 3.4 + - - -
487B GLN* 3.6 23.6 + - - +
540B PRO* 3.3 30.3 - - + -
576B ALA 2.8 14.5 + - - +
577B SER* 2.9 9.6 + - - +
579B GLU* 1.3 73.7 - - - +
581B LEU* 1.3 53.3 - - - +
583B SER* 2.6 50.9 + - - -
584B VAL* 3.4 12.9 + - + +
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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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540B PRO* 3.5 38.4 - - + +
543B VAL* 3.7 36.8 - - + -
544B LEU* 4.4 14.4 - - + -
563B PRO* 4.8 9.2 - - + -
565B PHE* 6.3 0.7 - - + -
577B SER* 2.9 22.4 + - - +
578B VAL* 3.9 8.7 - - - +
580B ARG* 1.3 76.9 - - - +
582B PHE* 1.3 61.9 + - + +
583B SER 3.2 0.9 + - - -
584B VAL* 3.5 11.7 + - + +
587B TYR* 3.4 49.3 - - + +
588B MET 4.5 0.2 + - - -
595B GLN* 5.6 3.4 - - - +
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Residues in contact with PHE 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 VAL* 3.2 39.0 + - + -
579B GLU 3.1 8.0 + - - +
580B ARG 3.1 1.2 - - - -
581B LEU* 1.3 80.3 - - + +
583B SER* 1.3 59.3 + - - +
584B VAL 3.6 0.4 - - - -
587B TYR* 4.9 4.9 - + - -
588B MET* 3.1 44.9 - - + +
591B ILE* 5.1 0.4 - - + -
595B GLN* 3.7 37.0 - - + -
627B VAL* 3.9 14.4 - - + -
628B ALA* 3.9 22.4 - - + -
631B TYR* 3.9 30.5 - + + -
633B VAL* 3.8 24.7 - - + -
635B LEU* 5.3 0.9 - - + -
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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