Contacts of the helix formed by residues 203 - 215 (chain N) in PDB entry 5A31
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 LEU 203 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202N GLU* 1.3 66.4 - - - +
204N ASP* 1.3 64.5 + - - +
205N SER 3.4 0.4 - - - -
206N ARG* 3.4 17.3 - - + +
207N TYR* 3.0 25.6 + - - +
282N GLU* 5.2 4.3 - - + +
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Residues in contact with ASP 204 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202N GLU* 2.1 25.4 + - - +
203N LEU* 1.3 74.4 - - - +
205N SER* 1.3 57.8 + - - -
207N TYR* 3.5 15.8 - - + +
208N ALA* 2.9 29.5 + - - +
279N GLY* 5.3 4.8 - - - -
281N TYR 3.3 23.0 - - - +
282N GLU* 3.4 13.1 - - + +
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Residues in contact with SER 205 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202N GLU* 2.6 54.5 + - - -
204N ASP* 1.3 72.6 - - - +
206N ARG* 1.3 74.7 + - - +
208N ALA* 3.3 6.5 + - - +
209N ARG* 3.0 22.6 + - - +
283N ARG* 5.2 10.8 - - - +
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Residues in contact with ARG 206 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202N GLU 4.8 2.2 - - - +
203N LEU* 3.4 22.7 - - + +
205N SER* 1.3 87.8 + - - +
207N TYR* 1.3 64.9 + - - +
209N ARG* 2.9 10.8 + - - +
210N ARG* 2.8 40.4 + - + +
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Residues in contact with TYR 207 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203N LEU 3.0 11.8 + - - +
204N ASP* 3.5 18.4 - - + +
206N ARG* 1.3 77.1 - - - +
208N ALA* 1.3 67.0 + - - +
210N ARG* 3.2 15.6 + - + +
211N ARG* 2.9 57.6 + - + +
214N ARG* 6.2 1.6 - - - -
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Residues in contact with ALA 208 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204N ASP 2.9 14.0 + - - +
205N SER* 3.5 11.2 - - - +
207N TYR* 1.3 79.4 - - + +
209N ARG* 1.3 56.1 + - - +
211N ARG* 3.1 9.2 + - - +
212N TYR* 2.8 54.9 + - + +
276N ARG* 5.0 11.2 - - - +
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Residues in contact with ARG 209 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205N SER 3.0 11.5 + - - +
206N ARG* 2.9 14.7 + - - +
208N ALA* 1.3 70.8 - - - +
210N ARG* 1.3 63.7 + - + +
212N TYR* 3.2 17.3 + - - +
213N TYR* 3.0 30.2 + - + +
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Residues in contact with ARG 210 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206N ARG* 2.8 31.6 + - + +
207N TYR* 3.3 18.8 - - + +
209N ARG* 1.3 73.1 - - + +
211N ARG* 1.3 64.4 + - - +
213N TYR* 3.4 8.2 - - + +
214N ARG* 3.1 64.1 + - - +
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Residues in contact with ARG 211 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207N TYR* 2.9 54.2 + - + +
208N ALA* 3.1 12.8 + - - +
210N ARG* 1.3 75.0 - - - +
212N TYR* 1.3 63.6 + - + +
214N ARG* 3.1 26.5 + - - +
215N LEU* 2.8 59.2 + - + +
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Residues in contact with TYR 212 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208N ALA* 2.8 45.9 + - + +
209N ARG* 3.6 17.5 - - - +
211N ARG* 1.3 80.8 - - + +
213N TYR* 1.3 64.6 + - - +
215N LEU* 3.2 29.1 + - + +
272N ARG* 4.6 6.4 + - - -
275N ASP* 4.9 8.4 + - - -
276N ARG* 3.2 27.0 + - - -
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Residues in contact with TYR 213 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209N ARG* 3.0 18.2 + - + +
210N ARG* 3.4 12.8 - - + +
212N TYR* 1.3 77.7 - - - +
214N ARG* 1.3 75.4 + - + +
215N LEU 3.5 2.8 + - - -
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Residues in contact with ARG 214 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207N TYR* 6.2 1.6 - - - -
210N ARG* 3.1 60.2 + - - +
211N ARG* 3.1 26.6 + - - +
213N TYR* 1.3 87.3 - - + +
215N LEU* 1.3 63.7 + - + +
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Residues in contact with LEU 215 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211N ARG* 2.8 47.0 + - + +
212N TYR* 3.2 24.3 + - + +
213N TYR 4.3 2.9 - - - -
214N ARG* 1.3 82.0 - - + +
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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