Contacts of the helix formed by residues 202 - 215 (chain B) in PDB entry 2AY6
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 202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B THR* 1.3 72.7 - - - +
203B ASP* 1.3 66.5 + - - +
205B TRP* 3.1 13.4 + - + +
206B ALA* 3.1 21.5 + - - +
235B GLU* 5.4 7.6 - - - +
238B ALA* 4.1 34.5 - - + +
239B GLY* 4.5 1.3 - - - +
242B LEU* 3.4 28.5 - - + -
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Residues in contact with ASP 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B THR* 3.1 12.2 + - - +
202B LEU* 1.3 81.8 + - - +
204B GLN* 1.3 64.8 + - + +
206B ALA* 3.2 9.0 + - - +
207B GLU* 3.1 21.2 + - - +
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Residues in contact with GLN 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B VAL* 5.2 5.3 + - - +
170B PHE* 3.4 50.5 - - + +
199B ASN 4.1 2.9 - - - +
200B LEU* 3.3 24.0 - - + +
201B THR* 2.9 47.4 + - - +
203B ASP* 1.3 79.0 - - + +
205B TRP* 1.3 56.1 + - - +
207B GLU* 3.1 5.6 - - - +
208B ILE* 2.9 33.3 + - - +
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Residues in contact with TRP 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B LEU* 4.0 30.3 - - + -
189B HIS 3.5 20.0 - - - -
190B GLY* 3.4 29.5 + - - -
200B LEU* 3.5 39.2 + - + +
201B THR 2.9 30.3 + - - -
202B LEU* 3.1 16.1 + - + +
204B GLN* 1.3 74.3 - - - +
206B ALA* 1.3 60.9 + - - +
208B ILE* 3.1 10.9 + - + +
209B ALA* 2.8 24.8 + - - +
221B ILE* 4.6 7.6 - - + -
239B GLY* 3.8 27.4 - - - +
240B THR 5.2 0.2 - - - -
242B LEU* 3.5 17.0 - - + +
243B ILE* 3.3 35.5 - - + +
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Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B LEU 3.1 12.0 + - - +
203B ASP* 3.5 11.0 - - - +
205B TRP* 1.3 75.6 - - - +
207B GLU* 1.3 60.8 + - - +
209B ALA 3.2 0.7 + - - -
210B SER* 2.9 17.2 + - - -
242B LEU* 3.6 18.5 - - + +
246B ARG* 2.6 35.4 + - - +
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Residues in contact with GLU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B PHE* 3.3 28.6 - - + -
174B LYS* 3.5 26.5 + - + +
203B ASP 3.1 10.5 + - - +
204B GLN 3.1 11.0 - - - +
206B ALA* 1.3 78.2 - - - +
208B ILE* 1.3 60.8 + - - +
210B SER* 3.1 24.5 + - - -
211B ILE* 3.3 12.4 + - + +
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Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B PHE* 3.3 29.4 - - + -
173B MET* 3.8 15.5 - - + -
174B LYS* 4.5 2.5 - - + -
177B LEU* 3.9 24.0 - - + -
188B LEU* 4.6 15.3 - - + -
200B LEU* 4.0 15.7 - - + -
204B GLN 2.9 18.7 + - - +
205B TRP* 3.1 15.9 + - + +
207B GLU* 1.3 73.7 - - - +
209B ALA* 1.3 59.4 + - - +
211B ILE* 3.3 15.7 + - + +
212B LEU* 3.0 43.6 + - + +
243B ILE* 5.4 0.9 - - + -
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Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B TRP 2.8 13.6 + - - +
206B ALA 3.2 9.6 + - - +
208B ILE* 1.3 76.4 - - - +
210B SER* 1.3 57.0 + - - +
212B LEU* 4.3 10.1 - - - -
213B GLU* 3.0 31.4 + - - +
242B LEU* 3.9 11.4 - - + -
243B ILE* 4.4 8.7 - - + -
246B ARG* 3.7 31.4 - - + +
247B ILE* 3.5 8.4 - - + +
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Residues in contact with SER 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B ALA 2.9 15.6 + - - -
207B GLU* 3.1 14.6 + - - -
208B ILE 3.1 0.4 - - - -
209B ALA* 1.3 74.5 - - - +
211B ILE* 1.3 66.4 + - - +
213B GLU* 3.6 8.0 - - - +
214B LYS* 3.1 27.5 + - - +
246B ARG* 3.1 19.7 + - - +
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Residues in contact with ILE 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B LYS* 3.8 48.2 - - + +
177B LEU* 3.9 35.4 - - + +
178B ALA* 3.9 10.3 - - + +
207B GLU* 3.3 14.3 + - + +
208B ILE* 3.3 16.7 + - + +
210B SER* 1.3 77.4 - - - +
212B LEU* 1.3 54.6 + - + +
214B LYS* 2.9 8.0 + - - +
215B THR* 2.8 41.0 + - + +
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Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B LEU* 5.8 3.8 - - + -
186B VAL* 4.0 21.8 - - + -
188B LEU* 4.8 4.5 - - + -
208B ILE* 3.0 37.9 + - + +
209B ALA* 3.7 5.4 - - - +
211B ILE* 1.3 77.4 - - + +
213B GLU* 1.3 56.6 - - - +
215B THR* 3.2 4.6 + - - -
216B GLY* 2.7 30.1 + - - -
217B ALA* 3.4 38.3 + - + +
219B PRO* 3.8 27.6 - - + -
243B ILE* 4.3 16.2 - - + -
247B ILE* 4.1 12.2 - - + +
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Residues in contact with GLU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ALA 3.0 15.6 + - - +
210B SER* 3.6 8.3 - - - +
212B LEU* 1.3 75.9 - - - +
214B LYS* 1.3 83.3 + - - +
216B GLY* 4.0 7.4 + - - +
246B ARG* 3.6 41.5 + - - +
247B ILE* 3.4 19.8 - - + +
248B PRO* 5.5 4.3 - - + -
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Residues in contact with LYS 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B SER* 3.1 18.0 + - - +
211B ILE* 2.9 8.1 + - - +
213B GLU* 1.3 102.5 + - - +
215B THR* 1.3 61.9 + - + +
216B GLY 3.5 0.2 - - - -
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Residues in contact with THR 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B LEU 4.0 10.9 + - - +
178B ALA* 3.7 18.6 - - - +
180B ALA 3.1 26.0 - - - +
181B LYS* 3.7 0.7 - - - -
182B LYS* 3.1 27.5 + - - +
211B ILE* 2.8 25.9 + - + +
212B LEU* 3.2 7.8 + - - +
214B LYS* 1.3 79.9 - - + +
216B GLY* 1.3 61.1 + - - +
217B ALA* 3.5 14.5 + - - +
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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