Contacts of the helix formed by residues 678 - 688 (chain A) in PDB entry 2VWK
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 PRO 678 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A GLY* 1.3 82.4 - - - +
679A HIS* 1.3 77.2 + - + +
680A VAL 3.5 0.2 - - - -
681A ALA* 3.4 6.6 + - - +
682A VAL* 3.2 24.6 + - - +
701A TYR* 3.7 34.5 - - + +
703A VAL* 4.3 3.6 - - + -
711A GLY* 3.1 18.3 - - - +
712A ASP* 4.6 3.8 - - - -
714A ALA* 3.4 24.9 - - + +
731A TYR* 4.6 15.5 - - + +
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Residues in contact with HIS 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A ASP* 6.1 0.7 - - - -
664A GLU* 2.8 43.3 + - - -
666A ILE* 5.1 0.2 - - + -
670A LEU* 4.1 29.6 - - + +
673A TYR* 3.5 46.9 - + + +
674A LYS* 5.3 3.8 + - - +
676A THR 5.4 0.8 + - - -
677A GLY* 3.2 5.8 + - - -
678A PRO* 1.3 90.4 - - + +
680A VAL* 1.3 67.4 + - + +
682A VAL* 3.1 7.5 + - - +
683A ALA* 2.9 22.7 + - - +
699A ILE* 4.7 7.0 - - + -
701A TYR* 4.1 5.1 + + - -
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Residues in contact with VAL 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A LEU 4.4 10.8 - - - +
671A LYS* 5.4 9.0 - - - +
673A TYR 4.8 7.0 - - - +
674A LYS 4.3 8.5 - - - +
675A ALA* 3.6 27.8 - - - +
677A GLY 4.1 3.7 + - - +
678A PRO 3.5 0.4 - - - -
679A HIS* 1.3 75.0 - - + +
681A ALA* 1.3 56.8 + - - +
683A ALA* 3.2 10.0 + - + +
684A LYS* 3.0 47.4 + - + +
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Residues in contact with ALA 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A GLY 4.8 0.8 + - - -
678A PRO 3.4 7.4 + - - +
679A HIS 3.2 0.4 - - - -
680A VAL* 1.3 76.7 - - - +
682A VAL* 1.3 63.4 + - - +
684A LYS* 3.5 12.6 + - - +
685A ARG* 3.2 29.2 + - + +
712A ASP 3.4 25.6 - - - +
713A ARG* 4.5 2.9 - - + -
714A ALA 3.6 18.2 - - - +
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Residues in contact with VAL 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLU* 6.1 0.7 - - + -
670A LEU* 4.4 9.2 - - + -
678A PRO 3.2 16.1 + - - +
679A HIS* 3.1 8.8 + - - +
681A ALA* 1.3 75.3 - - - +
683A ALA* 1.3 57.8 + - - +
685A ARG* 3.3 2.1 + - - +
686A LEU* 3.0 47.2 + - + +
699A ILE* 4.5 13.2 - - + -
700A SER 5.2 1.8 - - - +
701A TYR* 3.7 31.6 - - + -
714A ALA* 3.4 20.0 - - + +
715A ILE 4.3 0.9 - - - +
716A PRO* 4.2 16.8 - - + -
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Residues in contact with ALA 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A LEU* 3.7 35.4 - - + +
671A LYS* 4.2 16.4 - - + +
679A HIS 2.9 12.8 + - - +
680A VAL* 3.2 11.9 + - + +
682A VAL* 1.3 78.4 - - - +
684A LYS* 1.3 56.1 + - + +
686A LEU* 3.4 4.3 + - - +
687A ALA* 2.9 29.1 + - - +
691A ILE 5.0 0.7 - - - +
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Residues in contact with LYS 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680A VAL* 3.0 37.4 + - + +
681A ALA* 3.9 10.3 - - - +
682A VAL 3.3 0.2 - - - -
683A ALA* 1.3 73.7 - - + +
685A ARG* 1.3 62.9 + - + +
687A ALA* 3.3 6.3 + - - +
688A ALA* 3.0 31.2 + - - +
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Residues in contact with ARG 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681A ALA* 3.2 18.9 + - + +
682A VAL 3.8 0.7 - - - +
684A LYS* 1.3 78.1 - - + +
686A LEU* 1.3 57.8 + - - +
688A ALA* 3.9 5.7 + - - +
689A ARG* 3.3 18.2 + - - +
713A ARG* 5.4 6.3 - - - +
714A ALA 4.3 0.7 - - - +
715A ILE* 3.7 30.2 - - + +
716A PRO* 3.6 21.8 - - + -
719A GLU* 2.7 44.2 + - - +
725A HIS* 4.0 22.4 + - - -
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Residues in contact with LEU 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A GLU* 3.9 29.2 - - + -
670A LEU* 4.4 9.0 - - + -
682A VAL* 3.0 36.4 + - + +
683A ALA* 3.9 4.5 - - - +
685A ARG* 1.3 77.2 - - - +
687A ALA* 1.3 63.5 + - - +
688A ALA 3.3 0.2 - - - -
689A ARG* 3.0 21.3 + - - +
690A GLY 3.1 0.5 + - - -
691A ILE* 2.9 49.7 + - + +
693A ILE* 3.9 26.5 - - + -
699A ILE* 5.0 0.9 - - + -
716A PRO* 3.9 20.4 - - + -
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Residues in contact with ALA 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683A ALA 2.9 18.5 + - - +
684A LYS* 3.3 7.6 + - - +
686A LEU* 1.3 76.2 - - - +
688A ALA* 1.3 54.5 + - - +
690A GLY* 2.8 22.5 + - - -
691A ILE 3.7 12.0 + - - +
692A LYS* 6.1 2.0 - - + -
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Residues in contact with ALA 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684A LYS 3.0 16.9 + - - +
685A ARG* 4.1 9.4 - - - +
686A LEU 3.3 0.2 - - - -
687A ALA* 1.3 74.9 - - - +
689A ARG* 1.3 60.0 + - + +
690A GLY 3.3 0.7 - - - -
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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