Contacts of the helix formed by residues 664 - 675 (chain C) in PDB entry 5VOT
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 ILE 664 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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662C SER* 3.2 3.1 + - - +
663C LYS* 1.3 75.6 - - - +
665C ALA* 1.3 55.8 + - - +
666C VAL* 4.5 6.3 - - + -
667C PHE* 3.0 36.8 + - + +
668C ASP* 2.5 37.1 + - - +
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Residues in contact with ALA 665 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663C LYS 3.4 4.9 + - - -
664C ILE* 1.3 70.5 - - - +
666C VAL* 1.3 64.5 + - - +
668C ASP* 3.2 7.8 + - - +
669C LYS* 2.9 24.4 + - - +
761D LYS* 3.9 29.8 - - - +
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Residues in contact with VAL 666 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637C GLU* 4.0 24.5 - - + +
640C SER* 3.3 31.8 - - - +
664C ILE* 4.5 7.9 - - + -
665C ALA* 1.3 77.1 - - - +
667C PHE* 1.3 84.4 + - + +
669C LYS* 3.3 7.8 + - - +
670C MET* 2.9 39.0 + - - +
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Residues in contact with PHE 667 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636C ALA* 4.6 10.8 - - + -
658C PHE* 4.4 21.1 - + - -
659C PHE* 4.5 13.5 - + + +
662C SER* 3.2 27.1 - - - +
664C ILE* 3.0 21.6 + - + +
666C VAL* 1.3 88.0 - - + +
668C ASP* 1.3 61.1 + - - +
670C MET* 3.2 27.1 + - + +
671C TRP* 2.9 30.0 + - - +
727C LEU* 3.8 37.2 - - + -
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Residues in contact with ASP 668 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659C PHE 5.7 0.7 - - - -
662C SER* 4.7 13.4 + - - +
663C LYS* 5.0 3.1 - - - +
664C ILE 2.5 21.3 + - - +
665C ALA* 3.5 10.1 - - - +
667C PHE* 1.3 73.7 - - - +
669C LYS* 1.3 51.8 + - - +
671C TRP* 3.4 10.7 + - - +
672C THR* 2.6 45.0 + - - -
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Residues in contact with LYS 669 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640C SER* 4.0 27.4 - - - +
647C TYR* 6.0 0.4 - - - +
665C ALA 2.9 12.4 + - - +
666C VAL* 3.6 10.1 - - - +
668C ASP* 1.3 73.5 - - - +
670C MET* 1.3 61.6 + - - +
672C THR* 3.1 10.1 + - + -
673C TYR* 2.9 30.8 + - + +
769D ASP* 4.5 16.4 - - + -
770D LYS* 3.3 43.1 - - - +
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Residues in contact with MET 670 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636C ALA* 4.4 25.1 - - + +
639C LEU* 5.1 4.9 - - + -
640C SER* 4.1 11.9 - - - -
647C TYR* 3.5 42.2 - - + +
659C PHE* 4.4 16.6 - - + -
666C VAL* 2.9 23.7 + - - +
667C PHE* 3.2 37.9 + - + +
669C LYS* 1.3 76.8 - - - +
671C TRP* 1.3 61.8 + - - +
673C TYR* 3.2 3.3 + - - +
674C MET* 2.9 35.1 + - + +
703C LEU* 4.4 12.3 - - + -
727C LEU* 6.2 1.3 - - + -
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Residues in contact with TRP 671 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656C LYS* 3.7 48.5 - - + -
659C PHE* 3.7 33.9 - - + +
660C ARG* 3.6 42.4 + - + +
667C PHE 2.9 16.2 + - - +
668C ASP* 3.7 11.2 - - - +
670C MET* 1.3 75.8 - - - +
672C THR* 1.3 61.3 + - - +
674C MET* 3.6 16.4 - - + +
675C ARG* 2.9 80.1 + - + +
682C PHE* 4.5 9.6 - + - -
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Residues in contact with THR 672 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668C ASP* 2.6 34.1 + - - -
669C LYS* 3.1 11.6 + - + -
671C TRP* 1.3 77.7 - - - +
673C TYR* 1.3 61.2 + - - +
675C ARG* 3.2 26.3 + - - +
676C SER* 3.2 12.0 + - - -
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Residues in contact with TYR 673 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643C THR* 4.7 19.7 + - + -
645C ILE 5.6 0.4 - - - -
646C ALA* 4.8 22.1 - - + +
647C TYR* 4.3 34.5 - + - +
669C LYS* 2.9 14.8 + - + +
670C MET 3.7 5.8 - - - +
672C THR* 1.3 77.1 - - - +
674C MET* 1.3 64.6 + - + +
676C SER* 3.3 2.3 + - - -
677C ALA* 2.8 57.3 + - + +
681C VAL* 5.2 0.4 - - + -
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Residues in contact with MET 674 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647C TYR* 3.3 43.1 - - + +
648C GLY* 4.0 11.7 - - - -
649C THR* 4.5 8.1 - - - +
659C PHE* 3.8 32.3 - - + -
670C MET* 2.9 35.9 + - + +
671C TRP* 3.6 14.8 - - + +
673C TYR* 1.3 79.6 - - + +
675C ARG* 1.3 63.5 + - - +
676C SER 3.2 1.2 + - - -
677C ALA 3.7 5.2 + - - +
681C VAL* 3.2 32.5 + - + +
682C PHE* 4.0 11.8 - - + -
703C LEU* 4.5 8.7 - - + -
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Residues in contact with ARG 675 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671C TRP* 2.9 65.3 + - + +
672C THR* 3.2 24.8 + - - +
674C MET* 1.3 77.9 - - - +
676C SER* 1.3 61.8 + - - +
677C ALA 5.3 0.4 - - - -
682C PHE* 4.7 11.0 - - - -
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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