Contacts of the helix formed by residues 207 - 212 (chain E) in PDB entry 5ZR1
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 GLY 207 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203E MET 5.4 2.2 + - - -
204E SER 4.8 2.7 + - - -
205E ARG* 3.2 2.2 - - - +
206E CYS* 1.3 79.3 - - - +
208E GLU* 1.3 58.6 + - - +
210E MET* 3.5 10.3 + - - +
211E GLU* 3.3 29.6 + - - +
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Residues in contact with GLU 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C LYS* 6.1 0.5 - - - -
204E SER 5.0 3.7 + - - +
205E ARG* 3.3 36.8 + - - +
207E GLY* 1.3 75.1 - - - +
209E LEU* 1.3 54.5 + - + +
210E MET 3.2 0.7 - - - -
211E GLU* 3.4 11.4 + - - +
212E ASP* 2.8 39.4 + - + +
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Residues in contact with LEU 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E ARG* 3.1 51.7 + - + +
206E CYS 4.3 1.6 - - - +
207E GLY 3.4 0.4 - - - -
208E GLU* 1.3 75.8 - - + +
210E MET* 1.3 60.3 + - - +
212E ASP* 4.1 8.8 - - + +
215E LEU* 3.5 23.3 - - - +
236E ALA* 4.0 29.6 - - + +
239E PHE* 4.2 12.8 - - + -
240E ILE* 4.4 6.7 - - + -
262E ILE* 4.0 16.4 - - + -
263E ASP* 6.4 0.9 - - - -
266E TRP* 3.6 49.6 + - + +
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Residues in contact with MET 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206E CYS* 3.3 22.0 + - + +
207E GLY* 3.5 9.1 + - - +
208E GLU 3.2 0.4 - - - -
209E LEU* 1.3 77.6 - - + +
211E GLU* 1.3 68.4 + - - +
212E ASP 3.1 17.6 - - - +
215E LEU* 4.7 7.4 - - + +
216E ARG* 4.2 15.9 + - - +
229E ASP* 4.9 12.3 - - + +
232E PHE* 4.7 22.7 - - + +
233E GLN* 3.6 48.2 - - + +
236E ALA* 5.6 1.1 - - + -
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Residues in contact with GLU 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E GLY* 3.3 18.8 - - - +
208E GLU* 3.4 15.2 + - - +
210E MET* 1.3 81.8 - - - +
212E ASP* 1.3 63.2 + - - +
213E SER* 3.5 2.4 + - - -
216E ARG* 3.1 32.8 + - - +
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Residues in contact with ASP 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208E GLU* 2.8 21.7 + - + +
209E LEU* 4.2 5.6 - - + +
210E MET 3.1 13.5 - - - +
211E GLU* 1.3 77.0 - - - +
213E SER* 1.3 72.4 + - - +
214E CYS* 3.3 17.2 + - - +
215E LEU* 3.9 1.7 + - - +
216E ARG* 3.4 12.5 + - - +
263E ASP* 4.8 6.4 - - - +
266E TRP* 3.1 37.6 + - + +
267E PRO* 5.0 4.5 - - - +
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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