Contacts of the helix formed by residues 672 - 683 (chain V) in PDB entry 5IY8
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 TYR 672 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473V GLU* 4.1 19.3 - - + -
534V TYR* 4.8 10.4 + - - -
628V SER* 3.6 22.9 - - - +
629V HIS 3.3 23.3 + - - -
630V GLY* 4.7 4.9 - - - -
633V ARG* 3.5 30.7 - - - +
668V GLN* 3.5 21.3 + - + +
669V GLU* 3.3 20.2 - - - +
670V MET 3.1 1.2 + - - -
671V ALA* 1.3 76.5 - - + +
673V SER* 1.3 57.5 + - - +
674V THR 3.7 0.2 - - - -
675V LYS* 4.1 7.6 - - - +
676V ARG* 3.1 31.6 + - - +
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Residues in contact with SER 673 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509V GLU* 2.5 39.6 + - - +
511V TRP* 4.7 7.6 + - - -
628V SER* 5.3 0.2 + - - -
663V VAL* 4.4 4.0 - - - +
669V GLU 4.8 0.9 + - - -
670V MET* 3.2 21.5 + - - +
671V ALA 3.1 3.6 - - - -
672V TYR* 1.3 79.1 - - - +
674V THR* 1.3 61.6 + - - +
676V ARG* 3.7 1.5 + - - +
677V GLN* 2.8 35.6 + - - +
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Residues in contact with THR 674 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3922 ARG* 2.3 70.8 + - - +
670V MET 4.9 0.2 + - - -
671V ALA 4.3 5.4 + - - -
672V TYR 3.7 0.2 - - - -
673V SER* 1.3 73.7 - - - +
675V LYS* 1.3 55.5 + - - +
677V GLN* 3.9 1.1 - - - +
678V ARG* 3.2 54.6 + - - +
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Residues in contact with LYS 675 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473V GLU* 2.8 42.5 + - - +
475V ASP* 2.9 32.6 + - - -
633V ARG* 4.3 13.7 - - + +
671V ALA 5.0 2.4 + - - +
672V TYR* 4.1 11.2 - - - +
674V THR* 1.3 73.1 - - - +
676V ARG* 1.3 65.6 + - - +
678V ARG* 3.5 5.9 + - - +
679V PHE* 2.9 28.1 + - + +
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Residues in contact with ARG 676 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509V GLU* 2.7 38.8 + - - +
627V SER 4.1 3.4 + - - -
628V SER* 3.6 32.3 + - - +
633V ARG* 3.5 29.2 - - + +
636V GLU* 2.8 42.6 + - - +
659V PHE* 4.9 4.1 - - - -
661V SER* 3.6 27.6 + - - -
663V VAL* 4.3 1.8 - - - +
672V TYR* 3.1 25.1 + - - +
673V SER* 3.2 5.6 + - - +
675V LYS* 1.3 76.6 - - - +
677V GLN* 1.3 57.4 + - - +
679V PHE* 3.3 0.5 + - - -
680V LEU* 2.9 43.8 + - + +
687V PHE* 4.1 16.2 - - + -
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Residues in contact with GLN 677 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3882 THR* 3.1 51.2 - - - +
3892 ASP* 5.2 0.5 - - - -
3912 ILE* 4.8 8.5 - - + -
3922 ARG* 4.7 5.3 + - - +
673V SER* 2.8 21.5 + - - +
674V THR* 3.9 4.7 - - - +
676V ARG* 1.3 73.6 - - - +
678V ARG* 1.4 86.2 + - - +
680V LEU* 3.4 0.9 + - - +
681V VAL* 3.1 55.4 + - - +
687V PHE* 4.0 33.1 + - + +
689V VAL* 6.0 2.7 - - + -
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Residues in contact with ARG 678 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3892 ASP* 4.0 13.5 + - - +
3922 ARG* 2.8 31.1 - - - +
674V THR* 3.2 31.8 + - - +
675V LYS* 3.9 5.4 - - - +
677V GLN* 1.4 90.1 + - - +
679V PHE* 1.3 55.9 + - - +
681V VAL* 3.4 6.5 - - + +
682V ASP* 3.0 30.8 + - - +
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Residues in contact with PHE 679 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633V ARG* 3.2 44.0 - - + -
634V ARG* 3.4 45.5 - - + -
637V ALA* 3.7 23.3 - - + -
675V LYS* 2.9 23.8 + - + +
676V ARG* 3.8 1.6 - - - +
678V ARG* 1.3 71.4 - - - +
680V LEU* 1.4 70.2 + - + +
682V ASP* 3.6 6.3 + - + +
683V GLN* 3.0 67.3 + - + +
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Residues in contact with LEU 680 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507V CYS* 4.3 10.8 - - - -
633V ARG 4.9 3.1 - - - +
636V GLU* 5.4 5.8 - - + +
637V ALA* 4.8 10.8 - - + -
640V LEU* 4.7 10.8 - - + -
659V PHE* 5.4 4.9 - - + -
676V ARG* 2.9 37.4 + - + +
677V GLN 4.1 1.3 - - - +
679V PHE* 1.4 92.4 - - + +
681V VAL* 1.3 57.2 + - - +
683V GLN* 3.0 16.3 + - + +
684V GLY 3.0 0.3 + - - -
685V TYR* 3.0 59.0 + - + +
687V PHE* 3.8 28.0 - - + -
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Residues in contact with VAL 681 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3882 THR* 5.7 0.9 - - - -
677V GLN* 3.1 44.6 + - - +
678V ARG* 3.4 10.3 - - + +
680V LEU* 1.3 70.6 - - - +
682V ASP* 1.3 63.2 + - - +
684V GLY* 2.9 21.0 + - - -
685V TYR 3.7 19.5 - - - +
687V PHE* 3.8 19.1 - - + +
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Residues in contact with ASP 682 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493V TRP* 4.3 13.9 + - - -
634V ARG* 5.9 0.2 + - - -
678V ARG 3.0 21.0 + - - +
679V PHE* 3.7 8.5 - - + +
681V VAL* 1.3 79.3 - - - +
683V GLN* 1.3 68.6 + - - +
684V GLY* 3.2 1.7 + - - -
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Residues in contact with GLN 683 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490V GLU* 3.0 35.9 + - - +
491V ALA* 4.8 8.0 - - - +
493V TRP* 3.1 32.3 - - - +
634V ARG* 4.5 2.5 + - - +
637V ALA* 5.5 2.4 - - + +
679V PHE* 3.0 52.6 + - + +
680V LEU* 3.0 12.5 + - + +
682V ASP* 1.3 90.3 + - - +
684V GLY* 1.4 56.7 + - - +
685V TYR* 3.4 24.7 - - + -
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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