Contacts of the helix formed by residues 664 - 674 (chain A) in PDB entry 2DGV
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 664 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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662A ASP 3.2 15.0 - - - +
663A PHE* 1.3 76.6 - - - +
665A TRP* 1.3 66.9 + - - +
666A LYS* 3.9 7.2 + - - +
667A MET* 3.6 29.1 + - + +
668A LEU* 3.1 22.5 + - - +
683A ILE* 3.6 8.3 - - - +
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Residues in contact with TRP 665 (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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664A THR* 1.3 76.2 - - - +
666A LYS* 1.3 124.4 + - + +
668A LEU* 2.9 8.6 + - - +
669A LYS* 2.9 48.7 + - + +
681A ALA* 3.9 27.1 - - + +
682A ASP* 4.0 20.2 - - - +
683A ILE* 3.5 13.9 - - + +
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Residues in contact with LYS 666 (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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664A THR* 3.9 6.9 + - - +
665A TRP* 1.3 126.3 - - + +
667A MET* 1.3 66.2 + - + +
669A LYS* 3.3 2.2 + - + +
670A ASP* 3.2 41.2 + - - +
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Residues in contact with MET 667 (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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662A ASP* 4.5 6.1 - - + +
663A PHE* 4.0 30.3 - - + +
664A THR* 3.6 35.3 + - + +
665A TRP 3.2 0.4 - - - -
666A LYS* 1.3 78.6 - - + +
668A LEU* 1.3 57.3 + - - +
670A ASP* 3.5 4.6 + - - +
671A LYS* 2.8 43.7 + - - +
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Residues in contact with LEU 668 (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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656A VAL* 4.4 10.1 - - + -
659A LEU* 4.4 7.2 - - + -
663A PHE* 3.4 27.2 - - + -
664A THR 3.1 15.3 + - - +
665A TRP 2.9 7.5 + - - +
667A MET* 1.3 75.7 - - - +
669A LYS* 1.3 64.7 + - - +
671A LYS* 3.3 3.3 - - - +
672A PHE* 3.2 36.8 + - + +
681A ALA* 4.3 3.1 - - + -
682A ASP 3.3 34.5 - - - +
683A ILE* 3.8 9.9 - - + -
694A GLY* 4.5 0.9 - - - -
695A VAL 3.6 19.7 - - - +
696A VAL* 3.7 18.8 - - + +
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Residues in contact with LYS 669 (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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665A TRP* 2.9 30.7 + - + +
666A LYS* 3.5 7.9 - - + +
667A MET 3.1 0.2 - - - -
668A LEU* 1.3 72.4 - - - +
670A ASP* 1.3 62.4 + - - +
671A LYS 2.6 4.6 + - - -
672A PHE* 2.6 29.2 + - - +
673A ASN* 2.7 38.7 + - - +
677A HIS* 5.1 4.9 + - - -
678A VAL* 3.2 38.3 + - + -
679A LEU 4.5 7.6 - - - +
681A ALA* 3.7 21.5 - - + -
696A VAL* 5.4 0.4 - - - -
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Residues in contact with ASP 670 (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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666A LYS* 3.2 31.9 + - - +
667A MET* 4.2 3.8 - - - +
669A LYS* 1.3 91.1 + - - +
671A LYS* 1.3 60.7 + - - +
673A ASN* 3.3 29.1 + - - +
674A GLU* 4.1 6.8 + - - +
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Residues in contact with LYS 671 (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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663A PHE* 3.8 28.4 - - + -
667A MET* 2.8 26.9 + - - +
668A LEU* 3.3 9.4 - - - +
669A LYS 2.6 4.9 + - - -
670A ASP* 1.3 76.5 - - - +
672A PHE* 1.3 62.2 + - + +
674A GLU* 4.1 13.7 + - - +
711A MET* 3.0 31.3 - - + +
714A MET* 3.7 19.5 - - + -
716A LEU* 3.8 19.7 - - - +
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Residues in contact with PHE 672 (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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654A ILE* 3.0 29.2 - - + -
656A VAL* 3.7 25.1 - - + -
659A LEU* 6.1 0.9 - - + -
663A PHE* 5.9 0.7 - + - -
668A LEU* 3.2 35.8 + - + +
669A LYS 2.6 12.6 + - - +
671A LYS* 1.3 77.2 - - + +
673A ASN* 1.3 62.9 + - - +
674A GLU 3.1 2.7 - - - -
675A CYS* 3.1 15.0 + - + +
678A VAL* 3.7 15.7 - - + -
696A VAL* 3.7 13.2 - - + -
698A PHE* 3.5 24.4 - + + -
707A ALA* 4.0 6.3 - - + -
711A MET* 3.3 46.0 - - + -
714A MET* 4.6 6.1 - - + -
721A ILE* 4.8 0.7 - - + -
723A VAL* 4.0 7.0 - - + -
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Residues in contact with ASN 673 (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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669A LYS* 2.7 63.0 + - - +
670A ASP* 3.4 22.5 - - + +
671A LYS 3.3 0.4 - - - -
672A PHE* 1.3 76.5 - - - +
674A GLU* 1.3 66.2 + - - +
675A CYS 2.9 0.3 + - - -
676A GLY* 2.5 28.3 + - - +
677A HIS* 5.1 3.3 - - - -
678A VAL* 3.3 16.6 + - - +
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Residues in contact with GLU 674 (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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670A ASP 4.1 5.3 + - - +
671A LYS 4.2 14.8 - - - +
672A PHE* 3.1 0.6 - - - +
673A ASN* 1.3 78.9 - - - +
675A CYS* 1.3 62.6 + - - +
710A MET* 4.9 12.1 - - + +
711A MET* 5.7 2.7 - - + -
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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