Contacts of the helix formed by residues 659 - 672 (chain E) in PDB entry 1XFV
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 THR 659 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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658E PRO* 1.3 75.4 - - - +
660E SER* 1.3 71.8 + - - +
661E ALA* 4.2 4.0 - - - -
662E GLU* 2.8 30.6 + - - +
663E PHE* 2.9 20.6 + - - +
701E LEU* 4.2 2.0 - - - -
705E TYR* 3.8 28.9 - - + -
139S GLU* 4.3 19.9 + - + +
143S GLN* 5.4 6.1 - - - +
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Residues in contact with SER 660 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659E THR* 1.3 77.5 - - - +
661E ALA* 1.3 57.9 + - - +
663E PHE* 3.0 5.5 + - - +
664E ILE* 3.0 29.3 + - - +
698E ALA* 3.8 13.2 + - - +
701E LEU* 4.1 18.3 - - - +
702E SER* 3.5 30.1 - - - +
37S ARG 5.2 1.1 - - - -
38S SER* 2.7 38.5 + - - -
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Residues in contact with ALA 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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659E THR* 3.2 3.5 - - - -
660E SER* 1.3 76.9 - - - +
662E GLU* 1.3 64.0 + - - +
663E PHE 3.0 1.6 - - - -
664E ILE* 3.9 6.0 - - - +
665E LYS* 3.0 39.1 + - - +
38S SER 3.0 17.0 - - - +
39S LEU* 3.4 29.4 - - + +
40S GLY* 3.9 4.7 - - - +
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Residues in contact with GLU 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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653E LYS* 3.2 25.1 + - - +
658E PRO* 3.6 10.8 - - - +
659E THR* 2.8 33.6 + - - +
661E ALA* 1.3 78.8 - - - +
663E PHE* 1.3 61.0 + - - +
665E LYS* 3.6 16.9 - - + +
666E ASN* 3.0 45.5 + - - +
751E TYR* 5.7 0.2 - - - -
752E LEU* 6.0 0.3 - - - +
755E ARG* 2.8 32.9 + - - -
139S GLU* 4.4 5.9 - - - +
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Residues in contact with PHE 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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658E PRO* 5.0 3.1 - - + +
659E THR 2.9 11.2 + - - +
660E SER 3.0 11.2 - - - +
662E GLU* 1.3 75.8 - - - +
664E ILE* 1.3 72.3 + - + +
666E ASN* 2.9 15.2 + - - +
667E LEU* 3.2 34.1 + - + +
694E VAL* 4.2 14.8 - - + -
697E ILE* 4.0 24.7 - - + -
698E ALA* 4.3 14.4 - - + -
701E LEU* 3.7 20.0 - - + -
748E TYR* 3.1 39.3 - + - +
749E PHE* 4.1 20.6 - + - -
752E LEU* 3.6 18.4 - - + -
18S LEU* 5.9 0.4 - - + -
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Residues in contact with ILE 664 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660E SER* 3.0 14.7 + - - +
661E ALA* 3.7 4.9 + - - +
663E PHE* 1.3 76.9 - - + +
665E LYS* 1.3 66.6 + - - +
667E LEU* 3.0 15.1 + - + +
668E SER* 3.0 20.1 + - - -
698E ALA* 4.8 6.5 - - + -
11S GLU* 4.3 5.8 - - + +
14S GLU* 4.1 10.7 - - + +
15S ALA* 3.7 34.1 - - + +
18S LEU* 4.7 11.2 - - + -
19S PHE* 4.3 13.0 - - + -
38S SER* 3.6 39.0 - - - +
39S LEU* 4.1 9.9 - - + -
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Residues in contact with LYS 665 (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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661E ALA* 3.0 39.1 + - + +
662E GLU* 3.6 19.6 - - + +
664E ILE* 1.3 77.5 - - - +
666E ASN* 1.3 61.4 + - - +
668E SER* 3.1 10.9 - - - -
669E SER* 3.0 21.9 + - - -
11S GLU* 3.0 42.9 - - + +
39S LEU* 4.9 11.2 - - + -
82S GLU* 5.2 9.7 + - - -
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Residues in contact with ASN 666 (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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662E GLU* 3.0 32.2 + - - +
663E PHE 2.9 5.1 + - - +
665E LYS* 1.3 75.4 - - - +
667E LEU* 1.3 68.1 + - - +
669E SER* 3.2 9.3 - - - -
670E ILE* 3.2 28.5 + - - +
748E TYR* 3.1 49.2 + - + +
751E TYR* 5.7 1.3 - - - -
755E ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 667 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663E PHE* 3.6 37.5 - - + +
664E ILE* 3.0 11.6 + - + +
666E ASN* 1.3 72.4 - - - +
668E SER* 1.3 70.6 + - - +
670E ILE* 3.0 9.4 + - + +
671E ARG* 2.9 17.2 + - - +
678E VAL* 3.7 28.0 - - + -
679E TYR* 6.2 0.4 - - + -
694E VAL* 4.8 13.2 - - + -
745E TYR* 4.3 9.8 + - + -
748E TYR* 3.8 30.1 - - + -
749E PHE* 4.8 4.3 - - + -
14S GLU* 3.1 23.6 - - - +
18S LEU* 5.5 6.5 - - + -
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Residues in contact with SER 668 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664E ILE 3.0 11.7 + - - -
665E LYS 3.1 10.8 - - - -
667E LEU* 1.3 77.7 - - - +
669E SER* 1.3 66.5 + - - +
671E ARG* 3.0 16.3 + - - +
672E ARG* 3.1 6.6 + - - +
7S GLU* 4.3 1.2 + - - +
10S ALA* 3.1 14.3 - - - +
11S GLU* 3.0 46.4 + - - +
14S GLU* 3.3 20.1 + - - -
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Residues in contact with SER 669 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665E LYS 3.0 8.5 + - - -
666E ASN* 3.2 16.6 - - - -
668E SER* 1.3 78.2 + - - +
670E ILE* 1.3 58.8 + - - +
672E ARG* 2.8 33.4 + - - +
673E SER* 3.6 5.6 + - - -
7S GLU* 6.5 0.7 - - - -
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Residues in contact with ILE 670 (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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666E ASN* 3.2 19.1 - - + +
667E LEU* 3.0 8.1 + - - +
669E SER* 1.3 71.8 - - - +
671E ARG* 1.3 53.8 + - - +
673E SER* 2.9 13.0 + - - +
674E SER* 2.6 37.8 + - - +
744E GLU* 4.1 24.0 - - + +
745E TYR* 3.4 37.5 - - + -
748E TYR* 3.9 36.6 - - + -
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Residues in contact with ARG 671 (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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667E LEU 2.9 11.6 + - - +
668E SER 3.1 12.1 - - - +
670E ILE* 1.3 76.4 - - - +
672E ARG* 1.4 58.3 + - - +
674E SER 2.8 16.4 - - - +
675E ASN* 3.5 14.3 - - - +
676E VAL 4.2 2.2 - - - +
677E GLY* 3.1 35.7 - - - +
678E VAL* 3.8 5.1 - - - +
679E TYR* 3.9 29.9 + - - +
681E ASP 6.1 0.2 - - - +
745E TYR* 3.7 8.0 + - - +
10S ALA* 5.3 6.3 - - + +
13S LYS* 6.1 1.0 - - - +
14S GLU* 3.0 48.7 + - - +
17S SER* 5.9 3.0 - - - -
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Residues in contact with ARG 672 (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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668E SER 3.1 7.6 + - - +
669E SER* 2.8 15.8 + - - +
671E ARG* 1.4 77.9 - - - +
673E SER* 1.4 54.2 + - - +
675E ASN* 3.5 24.2 + - - +
6S GLU* 3.6 31.2 + - - +
7S GLU* 6.4 0.9 - - - -
10S ALA* 5.2 13.9 - - + +
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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