Contacts of the helix formed by residues 656 - 675 (chain J) in PDB entry 1SOJ
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 GLU 656 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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657J VAL* 1.3 62.4 + - + +
658J SER* 3.5 7.6 - - - +
659J LEU* 4.1 13.2 + - - +
660J ASP* 3.2 25.2 + - - +
729K ASN* 5.9 3.6 - - - +
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Residues in contact with VAL 657 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656J GLU* 1.3 77.5 - - + +
658J SER* 1.3 60.9 + - - +
659J LEU 3.4 0.4 - - - -
660J ASP* 3.7 7.0 - - - +
661J LEU* 2.8 30.8 + - - +
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Residues in contact with SER 658 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656J GLU 3.5 4.4 - - - +
657J VAL* 1.3 79.0 - - - +
659J LEU* 1.3 60.8 - - - +
661J LEU* 3.4 6.1 + - - +
662J ILE* 3.2 22.9 + - - +
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Residues in contact with LEU 659 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656J GLU* 4.1 15.0 + - - +
658J SER* 1.3 78.6 - - - +
660J ASP* 1.3 60.2 + - - +
662J ILE* 3.7 5.9 + - - +
663J LEU* 3.3 22.9 + - - +
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Residues in contact with ASP 660 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656J GLU 3.2 19.5 + - - +
657J VAL* 3.9 8.1 - - - +
658J SER 3.3 0.4 - - - -
659J LEU* 1.3 78.2 - - - +
661J LEU* 1.3 60.2 + - - +
662J ILE 3.3 0.4 - - - -
663J LEU* 3.5 9.3 + - - +
664J VAL* 3.0 32.1 + - + +
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Residues in contact with LEU 661 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657J VAL 2.8 20.2 + - - +
658J SER* 3.7 7.6 - - - +
659J LEU 3.4 0.2 - - - -
660J ASP* 1.3 75.2 - - - +
662J ILE* 1.3 61.2 + - - +
664J VAL* 3.7 9.6 - - - +
665J GLU* 2.9 34.0 + - - +
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Residues in contact with ILE 662 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658J SER 3.2 16.3 + - - +
659J LEU* 3.9 7.4 - - - +
660J ASP 3.3 0.2 - - - -
661J LEU* 1.3 75.0 - - - +
663J LEU* 1.3 63.0 + - - +
664J VAL 3.2 1.8 - - - -
665J GLU* 3.3 18.0 + - - +
666J GLU* 3.2 28.9 + - - +
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Residues in contact with LEU 663 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659J LEU 3.3 16.0 + - - +
660J ASP* 3.7 9.4 - - - +
661J LEU 3.4 0.2 - - - -
662J ILE* 1.3 78.0 - - - +
664J VAL* 1.3 66.7 + - + +
666J GLU* 3.2 19.7 + - - +
667J TYR* 3.2 21.5 + - + +
701J TYR* 6.1 5.4 - - + -
705J GLN* 6.2 0.2 - - - +
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Residues in contact with VAL 664 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660J ASP* 3.0 23.3 + - + +
661J LEU* 3.7 11.7 - - - +
663J LEU* 1.3 81.1 - - + +
665J GLU* 1.3 59.4 + - + +
667J TYR* 3.1 11.2 + - + +
668J ASP* 2.8 49.6 + - - +
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Residues in contact with GLU 665 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661J LEU* 2.9 23.2 + - - +
662J ILE* 3.3 19.7 + - - +
664J VAL* 1.3 75.5 - - + +
666J GLU* 1.3 66.5 + - + +
668J ASP* 3.2 9.1 + - - +
669J SER* 2.8 29.2 + - - +
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Residues in contact with GLU 666 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662J ILE* 3.2 11.9 + - - +
663J LEU* 3.2 29.1 - - - +
665J GLU* 1.3 76.1 - - + +
667J TYR* 1.3 63.6 + - - +
669J SER* 3.1 7.9 + - - -
670J LEU* 2.9 26.8 + - - +
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Residues in contact with TYR 667 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663J LEU* 3.2 14.7 + - + +
664J VAL* 3.1 15.4 + - + +
666J GLU* 1.3 80.7 - - - +
668J ASP* 1.3 79.2 + - - +
670J LEU* 3.2 4.5 + - - +
671J ILE* 2.9 42.2 + - + +
701J TYR* 6.0 0.4 - + - -
702J THR* 3.7 35.7 - - + -
705J GLN* 3.5 31.8 - - + +
706J ASP* 3.4 33.3 + - - +
790J LYS* 5.0 5.5 - - - +
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Residues in contact with ASP 668 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664J VAL* 2.8 43.4 + - - +
665J GLU* 3.7 7.6 + - - +
667J TYR* 1.3 87.3 - - - +
669J SER* 1.3 56.5 + - - +
671J ILE* 3.9 5.5 - - - +
672J GLU* 3.0 29.6 + - - +
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Residues in contact with SER 669 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665J GLU* 2.8 18.8 + - - +
666J GLU* 3.3 11.5 - - - -
668J ASP* 1.3 73.0 - - - +
670J LEU* 1.3 62.2 + - - +
672J GLU* 3.0 8.8 + - - +
673J LYS* 2.8 56.4 + - - +
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Residues in contact with LEU 670 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666J GLU 2.9 18.7 + - - +
667J TYR* 3.7 4.3 - - - +
669J SER* 1.3 73.7 - - - +
671J ILE* 1.3 58.4 + - - +
673J LYS* 3.1 9.9 + - + +
674J MET* 2.8 57.4 + - + +
679J PHE* 4.1 4.9 - - + -
684J LEU* 3.7 31.6 - - + -
698J GLN* 4.7 9.6 - - + +
699J VAL* 4.6 13.2 - - + -
702J THR* 3.5 30.7 - - + +
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Residues in contact with ILE 671 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667J TYR* 2.9 53.3 + - + +
668J ASP* 3.9 6.1 - - - +
670J LEU* 1.3 74.7 - - - +
672J GLU* 1.3 54.8 + - - +
674J MET* 3.2 5.9 + - - +
675J SER* 2.7 37.9 + - - +
702J THR* 3.4 24.5 - - + -
703J LEU* 5.0 7.4 - - + -
706J ASP* 3.8 19.3 - - + +
750J TRP* 5.2 3.3 - - + -
791J SER* 3.4 29.2 - - - +
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Residues in contact with GLU 672 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765A ASN* 5.2 10.6 - - - +
668J ASP 3.0 20.1 + - - +
669J SER* 3.4 5.3 - - - +
671J ILE* 1.3 77.7 - - - +
673J LYS* 1.3 71.3 + - - +
675J SER* 3.3 20.9 + - - -
676J ASN* 5.1 1.9 - - - +
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Residues in contact with LYS 673 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669J SER* 2.8 43.0 + - - +
670J LEU* 3.5 10.3 - - + +
672J GLU* 1.3 86.8 + - - +
674J MET* 1.3 58.9 + - - +
675J SER 3.4 0.5 + - - -
676J ASN* 3.6 15.2 + - - +
679J PHE* 3.4 30.6 - - + +
680J PRO* 4.1 16.4 - - + +
683J GLU* 6.0 3.8 - - + +
684J LEU* 5.9 7.0 - - + -
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Residues in contact with MET 674 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670J LEU* 2.8 49.5 + - + +
671J ILE* 3.8 5.8 - - - +
673J LYS* 1.3 67.2 - - - +
675J SER* 1.3 52.7 + - - +
676J ASN 2.6 19.2 + - - +
679J PHE* 3.6 22.2 - - + -
699J VAL* 3.3 36.1 - - + -
702J THR* 4.8 6.5 - - - -
703J LEU* 4.0 21.3 - - + -
743J THR* 5.6 0.2 - - + -
747J HIS* 2.9 50.7 + - + -
750J TRP* 3.6 16.0 - - + -
751J TYR* 4.3 1.0 - - - -
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Residues in contact with SER 675 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671J ILE* 2.7 27.4 + - - +
672J GLU* 3.4 13.9 - - - -
673J LYS 3.2 1.6 - - - -
674J MET* 1.3 73.8 - - - +
676J ASN* 1.3 58.2 + - - +
750J TRP* 4.6 1.3 - - - -
751J TYR* 4.0 13.1 + - - -
755J ARG* 4.0 17.6 + - - +
791J SER* 3.8 24.5 + - - -
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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