Contacts of the helix formed by residues 662 - 666 (chain A) in PDB entry 1D0N
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 MET 662 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LYS* 3.8 30.3 - - - +
642A LEU* 5.3 0.4 - - - +
660A GLU* 3.2 22.9 + - + +
661A PHE* 1.3 77.7 - - - +
663A GLN* 1.3 58.6 + - - +
664A GLU* 3.0 37.2 - - + +
665A ASP* 3.0 38.7 + - - +
666A LEU 4.1 1.2 + - - -
733A PHE* 3.4 13.8 - - - -
735A GLY* 6.2 2.5 - - - +
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Residues in contact with GLN 663 (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 MET* 1.3 71.8 - - - +
664A GLU* 1.3 70.9 + - - +
665A ASP 3.1 0.2 - - - -
666A LEU* 3.2 23.3 + - + +
733A PHE* 3.4 12.6 - - + +
735A GLY* 3.4 14.2 + - - +
736A TRP* 3.2 46.9 - - + +
737A ASP* 2.9 42.7 + - - +
740A TYR* 3.5 32.4 - - + +
741A TRP* 3.7 15.5 - - + -
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Residues in contact with GLU 664 (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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208A PHE* 3.3 22.7 - - - -
211A LEU* 5.0 5.6 - - + +
212A LYS* 4.9 6.4 + - - +
215A GLN* 6.0 4.7 - - - +
662A MET* 3.0 46.2 - - + +
663A GLN* 1.3 90.6 + - - +
665A ASP* 1.3 64.1 + - - +
666A LEU 3.2 2.0 + - - +
735A GLY* 4.2 9.6 - - - +
740A TYR* 3.7 37.4 + - + +
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Residues in contact with ASP 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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135A LYS* 3.2 26.9 + - - +
168A ARG 5.4 0.9 - - - +
169A ARG* 4.4 11.6 + - - +
208A PHE* 4.1 10.3 - - - -
212A LYS* 3.4 22.2 + - - -
642A LEU* 4.9 5.1 - - + +
657A VAL* 3.8 26.5 - - + +
660A GLU 4.3 0.3 - - - +
661A PHE* 5.2 0.5 - - - -
662A MET* 3.0 28.8 + - - +
664A GLU* 1.3 78.7 - - - +
666A LEU* 1.3 62.2 + - + +
667A ALA 3.1 7.6 + - - -
672A MET* 3.7 14.1 - - + +
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Residues in contact with LEU 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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208A PHE* 4.9 0.9 - - - -
642A LEU* 4.3 8.7 - - + -
662A MET 4.5 0.4 - - - +
663A GLN 3.2 17.5 + - - +
664A GLU 3.2 3.9 - - - +
665A ASP* 1.3 78.4 - - - +
667A ALA* 1.3 63.4 + - - +
668A THR* 3.2 8.7 + - - +
672A MET* 4.0 24.9 - - + -
683A TRP* 3.8 42.3 - - + +
729A PHE* 4.5 5.2 - - + -
733A PHE* 4.1 27.8 - - + -
736A TRP* 3.6 35.9 - - + -
740A TYR* 5.9 0.5 - - - -
741A TRP* 4.3 9.9 + - + -
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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