Contacts of the helix formed by residues 202 - 229 (chain Y) in PDB entry 5KHU
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 ALA 202 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201Y LEU* 3.8 27.6 - - - +
203Y LEU* 3.8 28.3 - - - +
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Residues in contact with LEU 203 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202Y ALA* 3.8 29.4 - - - +
204Y ASP* 3.8 27.8 - - - +
206Y ILE* 4.6 16.2 - - - +
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Residues in contact with ASP 204 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203Y LEU* 3.8 24.9 - - - +
205Y ALA* 3.8 29.6 - - - +
207Y LEU* 4.3 17.7 - - - +
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Residues in contact with ALA 205 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204Y ASP* 3.8 29.4 - - - +
206Y ILE* 3.8 24.7 - - - +
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Residues in contact with ILE 206 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203Y LEU* 4.6 14.6 - - - +
205Y ALA* 3.8 28.9 - - - +
207Y LEU* 3.8 25.4 - - - +
209Y LEU* 4.5 17.5 - - - +
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Residues in contact with LEU 207 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204Y ASP* 4.3 18.8 - - - +
206Y ILE* 3.8 24.9 - - - +
208Y GLY* 3.8 29.2 - - - +
210Y LEU* 4.5 15.9 - - - +
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Residues in contact with GLY 208 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207Y LEU* 3.8 29.2 - - - +
209Y LEU* 3.8 25.6 - - - +
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Residues in contact with LEU 209 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206Y ILE* 4.5 15.3 - - - +
208Y GLY* 3.8 28.9 - - - +
210Y LEU* 3.8 25.4 - - - +
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Residues in contact with LEU 210 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207Y LEU* 4.5 15.5 - - - +
209Y LEU* 3.8 29.4 - - - +
211Y SER* 3.8 26.5 - - - +
213Y SER* 4.5 17.0 - - - +
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Residues in contact with SER 211 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210Y LEU* 3.8 24.7 - - - +
212Y LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 212 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211Y SER* 3.8 28.5 - - - +
213Y SER* 3.8 24.7 - - - +
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Residues in contact with SER 213 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210Y LEU* 4.5 17.0 - - - +
212Y LEU* 3.8 29.2 - - - +
214Y VAL* 3.8 28.3 - - - +
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Residues in contact with VAL 214 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213Y SER* 3.8 26.7 - - - +
215Y LYS* 3.8 28.7 - - - +
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Residues in contact with LYS 215 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214Y VAL* 3.8 29.2 - - - +
216Y GLY* 3.8 24.7 - - - +
218Y GLU* 4.1 21.5 - - - +
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Residues in contact with GLY 216 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215Y LYS* 3.8 24.2 - - - +
217Y ALA* 3.8 29.4 - - - +
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Residues in contact with ALA 217 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216Y GLY* 3.8 29.4 - - - +
218Y GLU* 3.8 26.0 - - - +
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Residues in contact with GLU 218 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215Y LYS* 4.1 18.2 - - - +
217Y ALA* 3.8 27.4 - - - +
219Y VAL* 3.8 29.2 - - - +
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Residues in contact with VAL 219 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218Y GLU* 3.8 26.0 - - - +
220Y ALA* 3.8 29.2 - - - +
222Y MET* 4.6 14.8 - - - +
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Residues in contact with ALA 220 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219Y VAL* 3.8 26.0 - - - +
221Y SER* 3.8 29.4 - - - +
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Residues in contact with SER 221 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220Y ALA* 3.8 25.8 - - - +
222Y MET* 3.8 29.2 - - - +
224Y MET* 4.5 16.6 - - - +
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Residues in contact with MET 222 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219Y VAL* 4.6 16.6 - - - +
221Y SER* 3.8 29.2 - - - +
223Y THR* 3.8 26.0 - - - +
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Residues in contact with THR 223 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222Y MET* 3.8 24.7 - - - +
224Y MET* 3.8 29.6 - - - +
226Y VAL* 4.2 19.7 - - - +
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Residues in contact with MET 224 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221Y SER* 4.5 18.2 - - - +
223Y THR* 3.8 26.0 - - - +
225Y ASN* 3.8 28.0 - - - +
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Residues in contact with ASN 225 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224Y MET* 3.8 29.6 - - - +
226Y VAL* 3.8 25.8 - - - +
228Y GLN* 4.4 17.7 - - - +
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Residues in contact with VAL 226 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223Y THR* 4.2 18.4 - - - +
225Y ASN* 3.8 25.6 - - - +
227Y ILE* 3.8 29.2 - - - +
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Residues in contact with ILE 227 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226Y VAL* 3.8 29.2 - - - +
228Y GLN* 3.8 25.6 - - - +
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Residues in contact with GLN 228 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225Y ASN* 4.4 15.7 - - - +
227Y ILE* 3.8 26.0 - - - +
229Y THR* 3.8 29.4 - - - +
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Residues in contact with THR 229 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228Y GLN* 3.8 28.9 - - - +
230Y VAL* 3.8 28.3 - - - +
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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