Contacts of the helix formed by residues 680 - 694 (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 680 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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662B ASN* 4.1 4.1 - - - +
678B ASP 3.9 2.4 + - - -
679B GLU* 1.3 71.4 - - - +
681B VAL* 1.3 65.5 + - - +
682B GLU* 3.1 19.5 + - - -
683B HIS* 2.9 31.6 + - - -
721B LEU* 4.1 14.4 - - - -
724B ASP* 2.6 27.6 + - - -
727B LEU* 3.4 22.7 - - - +
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Residues in contact with VAL 681 (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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662B ASN* 3.4 15.0 + - + +
665B LEU* 4.1 15.7 - - + -
666B ILE* 4.5 8.3 - - + -
672B LEU* 3.6 19.3 - - + +
673B ALA* 3.5 38.1 - - + +
676B TYR* 3.7 12.4 - - + -
678B ASP* 3.6 36.1 - - - +
679B GLU 3.7 4.0 - - - +
680B SER* 1.3 76.8 - - - +
681B LEU* 1.3 65.2 + - - -
683B HIS 3.4 0.5 + - - -
684B HIS* 3.1 18.7 + - - +
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Residues in contact with LEU 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657B HIS* 3.7 16.6 + - - -
658B PRO* 3.4 35.2 - - - -
660B VAL 3.5 17.5 - - - +
661B SER* 3.9 2.2 - - - -
662B ASN* 2.7 41.3 + - - +
665B LEU* 3.6 21.5 - - - +
672B LEU* 5.8 1.3 - - - +
681B VAL* 1.3 72.0 + - - +
682B GLU* 1.3 61.1 + - - +
684B HIS* 3.0 11.8 + - - +
685B HIS* 2.8 53.0 + - - -
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Residues in contact with GLU 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B ASN* 3.0 28.4 + - - -
680B SER* 3.1 16.6 + - - +
681B LEU* 1.3 84.3 + - - +
683B HIS* 1.3 64.0 + - - +
685B HIS* 3.3 11.6 + - + -
686B PHE* 3.0 23.9 + - - +
720B ILE* 3.5 23.7 - - - +
721B LEU* 4.0 15.8 - - + +
723B THR* 3.9 6.2 - - - +
724B ASP* 3.5 38.3 - - + +
902B ZN 4.1 11.4 - - - -
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Residues in contact with HIS 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B TYR* 3.6 43.4 + + + -
679B GLU* 3.1 22.3 + - - +
680B SER* 2.9 30.7 + - - +
682B GLU* 1.3 75.6 - - - +
684B HIS* 1.3 58.4 + - - +
686B PHE* 3.3 11.0 + - - +
687B ASP* 2.9 28.2 + - - +
717B LYS* 4.4 15.3 - - - -
721B LEU* 3.7 31.8 - - + +
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Residues in contact with HIS 684 (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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607B ARG* 5.2 0.8 + - - -
655B LEU 4.2 4.3 - - - -
656B ASP* 2.7 46.4 + - + +
658B PRO* 5.7 3.8 - - + -
672B LEU* 3.8 41.6 - - + +
676B TYR* 4.0 6.4 + - - -
681B LEU* 3.0 23.9 + - - +
683B HIS* 1.3 74.0 - - - +
685B HIS* 1.3 68.9 + + - +
687B ASP* 3.2 14.4 + - - +
688B GLN* 3.0 48.1 + - - +
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Residues in contact with HIS 685 (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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652B SER 4.0 5.2 - - - +
653B HIS 3.0 34.3 - - - +
654B ASP* 3.3 26.7 + - - -
655B LEU 2.8 31.9 + - - +
656B ASP 4.7 0.4 - - - -
657B HIS* 3.7 22.9 - + - -
658B PRO* 5.0 0.4 - - + -
681B LEU* 2.8 49.9 + - - -
682B GLU* 3.6 17.0 - - + +
684B HIS* 1.3 75.3 - + - +
686B PHE* 1.3 57.5 + - - +
688B GLN* 3.3 3.8 + - - +
689B CYS* 2.9 28.8 + - - +
720B ILE* 3.9 5.6 - - + -
902B ZN 4.1 1.6 - - - -
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Residues in contact with PHE 686 (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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682B GLU 3.0 16.1 + - - +
683B HIS* 3.6 11.2 - - - +
685B HIS* 1.3 74.9 - - - +
687B ASP* 1.3 65.7 + - - +
689B CYS* 3.1 4.5 + - + +
690B LEU* 2.9 62.5 + - + +
713B LEU* 4.3 9.2 - - + -
716B ILE* 4.2 8.1 - - + -
717B LYS* 3.6 65.5 - - + +
720B ILE* 3.9 24.6 - - + +
721B LEU* 5.6 2.5 - - + -
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Residues in contact with ASP 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675B MET* 6.0 1.2 - - - +
676B TYR* 4.1 17.4 + - - +
683B HIS 2.9 13.6 + - - +
684B HIS* 3.4 18.3 + - - +
686B PHE* 1.3 78.9 - - - +
688B GLN* 1.3 64.6 + - - +
690B LEU* 3.3 12.4 + - - +
691B MET* 3.0 28.5 + - - +
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Residues in contact with GLN 688 (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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605B ASN* 4.2 12.8 - - - +
655B LEU* 3.7 21.1 - - + +
656B ASP* 3.6 27.7 + - + +
684B HIS* 3.0 43.3 + - - +
685B HIS 3.5 7.2 - - - +
687B ASP* 1.3 79.2 + - - +
689B CYS* 1.3 66.3 + - - +
691B MET* 3.2 28.0 + - + +
692B ILE* 3.0 29.2 + - + +
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Residues in contact with CYS 689 (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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598B TRP* 5.2 0.6 + - - -
648B ILE* 4.1 5.6 - - - -
652B SER* 3.6 31.6 - - - -
655B LEU* 3.6 9.6 - - - +
685B HIS 2.9 14.7 + - - +
686B PHE* 3.3 10.3 - - + +
688B GLN* 1.3 77.6 - - - +
690B LEU* 1.3 58.9 + - - +
692B ILE* 3.3 3.3 + - - +
693B LEU* 3.0 50.4 + - - +
716B ILE* 4.0 22.7 - - - -
720B ILE* 3.9 7.6 - - + -
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Residues in contact with LEU 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B PHE* 2.9 55.7 + - + +
687B ASP* 3.5 15.5 - - - +
689B CYS* 1.3 76.2 - - + +
691B MET* 1.3 64.6 + - - +
693B LEU* 3.2 8.7 + - + +
694B ASN* 3.0 40.5 + - - +
709B TYR* 5.7 0.4 - - - +
713B LEU* 3.7 33.2 - - + -
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Residues in contact with MET 691 (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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605B ASN* 4.3 13.5 - - - +
687B ASP* 3.0 15.7 + - - +
688B GLN* 3.2 36.8 + - - +
690B LEU* 1.3 76.9 - - - +
692B ILE* 1.3 79.2 + - + +
694B ASN* 3.4 5.2 + - - +
695B SER* 2.8 36.8 + - - -
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Residues in contact with ILE 692 (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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598B TRP* 3.5 26.5 - - + +
601B SER* 3.7 31.0 - - - +
602B VAL* 4.0 9.0 - - + -
605B ASN* 3.7 26.2 - - + +
655B LEU* 3.9 28.3 - - + -
688B GLN* 3.0 18.1 + - + +
689B CYS* 3.9 4.0 - - - +
691B MET* 1.3 87.8 - - + +
693B LEU* 1.3 66.0 + - - +
695B SER* 3.1 16.7 + - - +
698B ASN* 3.3 16.2 - - + +
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Residues in contact with LEU 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B TRP* 3.6 23.1 - - + +
648B ILE* 4.6 3.8 - - + -
689B CYS* 3.0 40.0 + - - +
690B LEU* 3.7 8.1 - - + +
692B ILE* 1.3 77.8 - - - +
694B ASN* 1.3 61.8 + - - +
698B ASN 4.3 3.4 - - - -
699B GLN* 3.2 28.5 - - - +
700B ILE* 3.7 25.1 - - + -
701B LEU* 4.0 32.5 + - + +
709B TYR* 5.6 4.9 - - + +
713B LEU* 4.2 17.9 - - + -
716B ILE* 4.4 6.1 - - + -
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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
------------------------------------------------------------
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