Contacts of the helix formed by residues 202 - 218 (chain F) in PDB entry 4GOO
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 THR 202 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200F SER* 3.5 16.6 - - - +
201F PHE* 1.3 76.5 - - - +
203F LEU* 1.3 61.3 + - - +
204F GLU* 3.4 28.1 - - + +
205F GLN* 2.9 34.5 + - - +
206F GLN* 2.9 33.2 + - - +
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Residues in contact with LEU 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F PRO* 4.1 31.6 - - + -
201F PHE 5.7 0.9 - - - +
202F THR* 1.3 75.6 - - - +
204F GLU* 1.3 69.4 + - - +
206F GLN* 3.2 10.7 + - - +
207F ALA* 2.8 29.8 + - - +
232F LEU* 4.6 14.6 - - + -
236F TRP* 4.2 20.4 + - + -
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Residues in contact with GLU 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202F THR* 3.4 26.1 - - + +
203F LEU* 1.3 86.9 + - - +
205F GLN* 1.3 57.3 + - + +
207F ALA* 3.4 7.1 + - - +
208F HIS* 2.9 27.7 + - - +
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Residues in contact with GLN 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F TYR* 3.4 31.2 + - - +
200F SER 3.8 3.2 + - - -
201F PHE* 3.5 26.9 - - + +
202F THR* 2.9 50.7 + - - +
204F GLU* 1.3 81.0 - - + +
206F GLN* 1.3 53.1 + - - +
208F HIS* 2.8 6.2 + - - +
209F LEU* 2.8 33.6 + - - +
301F 0Y2 4.1 10.7 + - - -
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Residues in contact with GLN 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F PRO* 4.3 4.8 - - + +
183F PRO 2.8 28.7 + - - -
184F TYR 3.8 1.5 + - - +
185F ALA* 3.5 12.8 - - - +
186F PRO* 5.2 0.7 - - - +
201F PHE* 3.6 23.4 - - + +
202F THR 2.9 17.7 + - - +
203F LEU* 3.5 11.8 - - - +
205F GLN* 1.3 77.0 - - - +
207F ALA* 1.3 60.5 + - - +
208F HIS 3.5 0.2 + - - -
209F LEU* 3.7 7.3 + - + +
210F ALA* 3.5 15.9 + - - +
227F ASN* 3.4 20.7 - - - +
236F TRP* 3.6 39.3 - - + +
237F TYR* 4.8 6.2 - - - +
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Residues in contact with ALA 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203F LEU 2.8 14.1 + - - +
204F GLU* 3.9 5.8 - - - +
206F GLN* 1.3 77.5 - - - +
208F HIS* 1.3 60.9 + - - +
210F ALA* 3.3 5.0 + - - +
211F GLU* 3.2 26.5 + - - +
236F TRP* 3.4 35.8 - - + +
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Residues in contact with HIS 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F TYR* 2.6 31.2 + + - +
166F ALA* 4.5 9.2 - - + +
204F GLU 2.9 13.5 + - - +
205F GLN* 2.8 12.9 + - - +
207F ALA* 1.3 74.4 - - - +
209F LEU* 1.3 64.6 + - - +
211F GLU* 3.0 20.6 + - + +
212F ILE* 2.9 39.9 + - + +
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Residues in contact with LEU 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F PHE* 3.8 22.2 - - + -
165F TYR* 4.0 18.8 - - + -
169F MET* 3.6 34.6 - - + +
180F CYS* 4.2 9.4 - - + -
182F PRO* 3.7 36.6 - - + -
201F PHE* 5.0 4.7 - - + -
205F GLN 2.8 11.5 + - - +
206F GLN* 3.7 12.8 - - + +
208F HIS* 1.3 75.1 - - - +
210F ALA* 1.3 63.7 + - - +
212F ILE* 3.1 6.4 + - - +
213F ALA* 3.0 22.4 + - - +
225F ILE* 4.5 15.5 - - + -
237F TYR* 5.0 3.8 - - + +
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Residues in contact with ALA 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206F GLN 3.5 3.9 + - - +
207F ALA 3.3 8.7 + - - +
208F HIS 3.2 0.6 - - - -
209F LEU* 1.3 78.6 - - - +
211F GLU* 1.3 56.7 + - - +
213F ALA* 3.1 8.2 + - - +
214F GLU* 2.9 31.9 + - - +
225F ILE* 4.7 3.8 - - - +
236F TRP* 3.3 31.9 - - + +
237F TYR* 3.8 14.6 - - + -
268F TYR* 3.6 16.6 + - - +
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Residues in contact with GLU 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207F ALA* 3.2 16.4 + - - +
208F HIS* 3.0 23.3 + - + +
210F ALA* 1.3 71.2 - - - +
212F ILE* 1.3 68.3 + - + +
213F ALA 2.9 1.6 - - - -
214F GLU* 2.8 31.8 + - - +
215F GLY* 3.0 10.0 + - - -
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Residues in contact with ILE 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F TYR* 3.7 28.0 - - + -
166F ALA* 3.9 18.2 - - + +
169F MET* 4.2 29.2 - - + -
170F ALA* 6.3 0.4 - - - -
208F HIS* 2.9 43.2 + - + +
209F LEU* 3.8 5.2 - - - +
211F GLU* 1.3 75.8 - - + +
213F ALA* 1.3 57.7 + - - +
215F GLY* 3.1 3.2 + - - +
216F LEU* 2.8 35.9 + - + +
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Residues in contact with ALA 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F MET* 4.6 6.6 - - + +
209F LEU 3.0 12.0 + - - +
210F ALA 3.3 10.1 - - - +
211F GLU 2.9 0.4 - - - -
212F ILE* 1.3 75.5 - - - +
214F GLU* 1.3 65.4 + - - +
216F LEU* 3.1 3.8 + - - +
217F VAL* 3.1 22.7 + - - +
223F VAL* 3.9 33.8 - - + +
225F ILE* 4.1 14.8 - - + -
268F TYR* 4.1 13.8 - - + -
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Residues in contact with GLU 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F ALA* 2.9 17.2 + - - +
211F GLU* 2.8 28.9 + - - +
213F ALA* 1.3 72.5 - - - +
215F GLY* 1.3 61.5 + - - +
217F VAL* 3.2 10.7 + - + +
218F GLU* 3.0 35.1 + - - +
236F TRP 4.7 10.2 - - - +
238F GLN* 5.5 1.7 - - - +
239F ARG* 3.7 43.0 + - + +
268F TYR* 4.0 15.2 - - + -
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Residues in contact with GLY 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211F GLU 3.0 11.4 + - - -
212F ILE* 3.6 4.3 - - - -
214F GLU* 1.3 76.9 - - - +
216F LEU* 1.3 64.6 + - - +
218F GLU* 3.3 10.0 + - - +
219F ARG* 3.3 27.2 + - - +
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Residues in contact with LEU 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F MET* 3.9 42.0 - - + +
170F ALA* 5.7 1.3 - - - -
172F ALA* 4.6 2.5 - - + +
178F VAL* 3.7 29.8 - - + -
212F ILE* 2.8 25.1 + - + +
213F ALA* 3.1 5.1 + - - +
215F GLY* 1.3 77.3 - - - +
217F VAL* 1.3 60.2 + - - +
219F ARG* 3.2 31.5 + - - +
221F ILE* 2.7 46.9 + - + +
223F VAL* 3.9 16.2 - - + -
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Residues in contact with VAL 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213F ALA 3.1 10.5 + - - +
214F GLU* 3.4 14.6 - - - +
216F LEU* 1.3 71.4 - - - +
218F GLU* 1.3 61.6 + - + +
219F ARG 2.9 3.8 - - - -
220F HIS* 2.6 30.0 + - - -
221F ILE 3.0 11.4 + - - +
223F VAL* 5.6 0.2 - - + -
268F TYR* 3.6 36.8 - - + +
269F LYS 3.5 33.0 - - - +
270F PRO* 3.6 10.0 - - + +
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Residues in contact with GLU 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214F GLU* 3.0 26.0 + - - +
215F GLY* 3.4 10.1 - - - +
217F VAL* 1.3 80.4 - - + +
219F ARG* 1.3 59.0 + - + +
220F HIS* 3.4 8.0 + - - -
239F ARG* 5.6 4.2 + - - -
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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