Contacts of the helix formed by residues 559 - 564 (chain A) in PDB entry 1DY7
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 VAL 559 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A LEU* 3.2 30.7 - - + +
166A GLU* 3.8 8.7 - - + +
168A LEU* 2.9 27.5 + - + +
170A SER* 5.5 4.3 - - - +
204A LEU* 3.8 38.1 - - + +
208A GLY* 4.1 11.2 - - - +
211A LEU* 6.0 1.1 - - + -
225A LEU* 4.3 10.3 - - + -
557A PHE 3.5 2.6 + - - +
558A ASN* 1.3 72.8 - - - +
560A TYR* 1.3 58.6 + - - +
562A THR 3.8 0.3 - - - -
563A MET* 2.9 44.0 + - - +
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Residues in contact with TYR 560 (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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166A GLU* 3.1 53.2 + - + +
512A LYS* 3.6 35.4 - - + -
558A ASN* 3.2 5.3 + - - +
559A VAL* 1.3 76.5 - - - +
561A ASN* 1.3 73.4 + - - +
563A MET* 3.2 13.6 - - + +
564A THR* 2.8 56.9 + - + +
566A THR* 4.6 5.6 - - + -
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Residues in contact with ASN 561 (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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391A ARG* 4.4 5.7 + - - +
446A LYS* 6.3 0.7 - - - +
448A HIS* 4.1 12.3 + - - -
509A GLU* 4.2 13.6 - - - +
510A PHE* 3.0 27.3 + - - +
511A ASN 3.0 27.4 + - - +
512A LYS* 4.2 1.9 - - - -
558A ASN* 2.9 13.0 + - - +
560A TYR* 1.3 91.4 - - - +
562A THR* 1.3 57.9 + - - +
564A THR* 3.8 4.0 - - - -
565A ASP* 3.1 6.4 + - - -
566A THR* 2.9 50.2 + - - +
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Residues in contact with THR 562 (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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202A SER 4.0 9.6 - - - +
203A ARG* 4.0 33.7 - - - +
204A LEU* 4.0 23.1 - - + +
249A LYS* 3.0 21.8 + - - +
391A ARG* 4.5 11.6 + - - +
509A GLU* 3.8 4.5 + - - -
557A PHE* 3.5 18.0 - - + +
558A ASN 2.7 20.4 + - - -
559A VAL 3.9 1.8 - - - -
561A ASN* 1.3 76.8 - - - +
563A MET* 1.3 66.0 + - - +
564A THR 3.2 0.7 + - - -
565A ASP* 3.3 6.6 - - - +
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Residues in contact with MET 563 (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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166A GLU* 4.4 19.1 - - - +
204A LEU* 3.9 13.6 - - + +
205A SER 3.5 16.4 - - - +
206A ALA* 3.0 34.9 - - - +
207A SER* 3.4 7.9 - - - +
208A GLY* 3.4 25.6 - - - +
249A LYS* 3.6 20.0 - - - +
307A HIS* 5.7 0.9 - - - -
559A VAL* 2.9 23.9 + - - +
560A TYR* 3.2 26.9 - - + +
562A THR* 1.3 77.3 - - - +
564A THR* 1.3 67.5 + - + +
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Residues in contact with THR 564 (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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307A HIS* 3.9 9.8 - - - -
353A HIS* 3.6 11.3 + - - -
560A TYR* 2.8 51.3 + - + +
563A MET* 1.3 88.8 - - + +
565A ASP* 1.3 71.7 + - - +
566A THR* 2.6 27.9 + - - -
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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