Contacts of the helix formed by residues 649 - 664 (chain E) in PDB entry 1FSJ
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 649 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605E ARG 3.9 6.3 - - - -
606E ASN* 4.2 15.0 - - - -
607E LYS 3.8 4.3 - - - -
647E PHE* 3.3 1.7 - - - +
648E LYS* 1.3 82.2 - - - +
650E PHE* 1.3 65.7 + - - +
651E ASP* 3.4 10.9 + - - +
652E ASP* 3.1 32.6 + - - +
653E PHE 3.1 5.2 + - - -
714E TYR* 3.0 17.5 + - - -
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Residues in contact with PHE 650 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605E ARG* 2.8 50.0 + - + +
649E SER* 1.3 71.9 - - - +
651E ASP* 1.3 58.9 + - - +
653E PHE* 3.0 25.1 + + + +
654E ARG* 2.8 30.5 + - + +
701E LEU* 3.8 43.7 - - + -
703E HIS* 3.5 22.2 - + - -
713E VAL* 3.3 39.9 - - + -
714E TYR* 3.2 8.5 + + - -
719E ILE* 3.8 10.1 - - + -
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Residues in contact with ASP 651 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605E ARG 4.7 0.2 + - - -
606E ASN* 5.9 0.8 + - - +
649E SER* 3.1 10.1 + - - +
650E PHE* 1.3 80.2 - - - +
652E ASP* 1.3 61.6 + - - +
654E ARG* 2.8 43.4 + - - +
655E LYS* 3.2 21.0 + - - +
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Residues in contact with ASP 652 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646E GLU 4.9 0.3 - - - +
647E PHE* 3.7 14.5 - - + +
648E LYS* 3.0 50.5 + - - +
649E SER* 3.1 30.6 + - - +
651E ASP* 1.3 74.9 + - - +
653E PHE* 1.3 60.8 + - - +
655E LYS* 3.3 17.7 + - - +
656E ALA* 3.3 18.7 + - - +
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Residues in contact with PHE 653 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611E ALA* 4.2 6.7 - - + -
634E ILE* 4.9 3.8 - - + -
642E LEU* 3.9 18.6 - - + -
647E PHE* 3.7 34.4 - + + -
649E SER 3.1 2.2 + - - -
650E PHE* 3.0 28.1 + + - +
652E ASP* 1.3 75.2 - - - +
654E ARG* 1.3 67.4 + - - +
656E ALA* 3.2 3.3 + - - +
657E VAL* 3.0 43.2 + - + +
701E LEU* 4.1 7.6 - - + -
714E TYR* 3.8 29.4 - + + -
716E MET* 3.9 26.2 - - + -
719E ILE* 3.5 32.1 - - + -
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Residues in contact with ARG 654 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650E PHE* 2.8 15.8 + - + +
651E ASP* 2.8 45.3 + - - +
653E PHE* 1.3 77.3 - - - +
655E LYS* 1.3 72.0 + - - +
657E VAL* 3.2 11.2 + - - +
658E TRP* 3.2 30.8 + - + +
682E GLY 2.7 29.9 + - - -
683E TYR* 4.0 4.8 - - - +
684E SER* 3.1 36.2 + - - +
699E TYR 5.8 0.9 - - - -
701E LEU* 4.0 28.9 - - + +
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Residues in contact with LYS 655 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651E ASP* 3.2 10.0 + - - +
652E ASP* 3.4 19.7 - - - +
653E PHE 3.2 0.2 - - - -
654E ARG* 1.3 86.1 - - - +
656E ALA* 1.3 58.1 + - - +
658E TRP 3.4 0.5 + - - -
659E GLU* 3.0 47.0 + - - +
681E LYS 3.5 20.2 - - - -
682E GLY* 3.4 31.1 - - - +
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Residues in contact with ALA 656 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642E LEU* 3.8 15.7 - - + -
645E LYS* 5.3 1.3 - - - -
647E PHE* 3.5 32.1 - - + -
652E ASP 3.3 3.9 + - - +
653E PHE 3.2 6.8 + - - +
655E LYS* 1.3 78.3 - - - +
657E VAL* 1.3 64.9 + - - +
659E GLU* 3.9 12.1 - - - +
660E GLU* 3.0 29.3 + - - +
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Residues in contact with VAL 657 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622E TRP* 5.7 3.4 - - + -
634E ILE* 4.5 18.8 - - + -
635E PRO* 6.1 0.9 - - + -
638E ILE* 4.5 13.2 - - + +
642E LEU* 3.8 13.9 - - + -
653E PHE* 3.0 49.0 + - + +
654E ARG* 3.2 8.7 + - - +
656E ALA* 1.3 78.3 - - - +
658E TRP* 1.3 72.4 + - + +
660E GLU* 3.4 2.1 + - - +
661E VAL* 2.9 42.5 + - + +
701E LEU* 4.6 9.0 - - + -
721E VAL* 5.7 0.9 - - + -
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Residues in contact with TRP 658 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622E TRP* 4.3 14.8 - + - -
623E LEU* 4.5 9.9 - - + -
654E ARG* 3.2 36.0 + - + +
655E LYS 4.1 2.9 - - - +
657E VAL* 1.3 81.0 - - + +
659E GLU* 1.3 64.8 + - - +
661E VAL* 3.4 36.1 - - + +
662E SER* 3.0 21.3 + - - -
671E LEU* 5.8 0.4 - - + -
679E VAL* 3.6 18.1 - - + +
682E GLY 4.7 1.3 - - - +
683E TYR 3.9 13.9 - - - +
684E SER* 3.4 28.7 + - - -
685E PRO* 3.6 30.5 - - + -
699E TYR* 3.9 24.9 + + + -
701E LEU* 4.7 14.0 - - + +
721E VAL* 4.1 22.9 - - + -
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Residues in contact with GLU 659 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655E LYS* 3.0 46.1 + - - +
656E ALA* 3.9 11.4 - - - +
658E TRP* 1.3 76.4 - - - +
660E GLU* 1.3 61.4 + - + +
662E SER* 2.9 18.4 + - - -
663E LYS* 3.3 25.8 - - - +
679E VAL 3.7 7.0 - - - +
680E SER 4.0 10.5 - - - +
681E LYS* 4.1 2.8 - - - -
682E GLY* 3.7 19.7 + - - +
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Residues in contact with GLU 660 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638E ILE* 3.6 24.2 - - + +
641E LYS* 3.8 43.5 + - + +
642E LEU* 4.0 21.0 - - + +
656E ALA* 3.0 21.8 + - + +
657E VAL 3.9 1.6 - - - +
659E GLU* 1.3 73.7 - - + +
661E VAL* 1.3 67.1 + - - +
663E LYS* 3.1 36.5 + - - +
664E ASP* 3.3 12.0 + - - +
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Residues in contact with VAL 661 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622E TRP* 4.0 18.8 - - + -
623E LEU* 6.2 0.7 - - + -
638E ILE* 3.7 16.4 - - + +
657E VAL* 2.9 30.8 + - + +
658E TRP* 3.4 39.0 - - + +
660E GLU* 1.3 75.4 - - - +
662E SER* 1.3 61.5 + - - +
664E ASP* 3.0 29.3 + - - +
667E LEU* 4.1 24.9 - - + +
668E SER* 3.5 7.0 + - - +
671E LEU* 4.5 10.1 - - + -
679E VAL* 5.4 0.7 - - + -
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Residues in contact with SER 662 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658E TRP 3.0 6.7 + - - -
659E GLU 2.9 16.1 + - - -
661E VAL* 1.3 75.9 - - - +
663E LYS* 1.3 61.4 + - - +
664E ASP 3.2 0.4 + - - -
668E SER* 3.9 19.4 + - - -
676E LYS* 4.6 6.7 - - - +
679E VAL* 3.4 29.6 - - - -
680E SER* 3.4 26.3 - - - -
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Residues in contact with LYS 663 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641E LYS* 6.1 1.8 - - - +
659E GLU* 3.3 26.7 - - - +
660E GLU* 3.1 32.0 + - - +
661E VAL 3.1 1.2 - - - -
662E SER* 1.3 79.4 - - - +
664E ASP* 1.3 59.6 + - - +
665E PRO* 3.5 11.7 - - - +
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Residues in contact with ASP 664 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637E ARG* 2.8 42.9 + - - +
638E ILE* 5.1 2.2 - - + +
660E GLU 3.3 8.6 + - - +
661E VAL 3.0 9.1 + - - +
662E SER 4.7 0.4 - - - -
663E LYS* 1.3 77.9 - - - +
665E PRO* 1.3 65.1 - - - +
666E GLU* 3.0 26.2 + - - +
667E LEU* 3.3 24.8 + - + +
668E SER* 2.7 32.9 + - - -
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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
------------------------------------------------------------
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