Contacts of the helix formed by residues 203 - 215 (chain F) in PDB entry 5CEV
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 MET 203 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121F TYR* 3.7 20.4 - - + +
172F ILE* 4.6 8.3 - - + -
198F VAL* 4.1 12.3 + - + +
202F GLY* 1.3 71.7 - - - -
204F THR* 1.3 56.5 + - - +
206F VAL* 4.3 11.2 - - - -
207F MET* 2.9 52.9 + - + +
246F LEU* 3.4 36.1 - - + -
250F GLU* 3.7 45.3 + - + +
253F LEU* 4.3 13.0 - - + -
254F ALA* 4.6 2.0 - - + -
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Residues in contact with THR 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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199D ASP 3.5 3.7 + - - -
200D ARG* 3.2 51.4 + - + +
202F GLY 3.3 1.6 + - - -
203F MET* 1.3 77.3 - - - +
205F ARG* 1.3 58.3 + - - +
207F MET 3.3 0.2 + - - -
208F GLU* 2.8 54.1 + - - +
253F LEU* 3.4 9.9 - - - +
257F MET* 3.6 16.8 - - + +
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Residues in contact with ARG 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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201F LEU* 3.4 40.9 + - + +
202F GLY 3.3 2.2 + - - +
204F THR* 1.3 75.9 - - - +
206F VAL* 1.3 66.2 + - - +
208F GLU* 3.2 21.7 + - - +
209F GLU* 2.7 65.6 + - - +
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Residues in contact with VAL 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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172F ILE* 4.2 21.8 - - + -
193F TYR* 3.6 50.6 - - + -
197F GLU 4.0 17.3 - - - +
198F VAL* 4.1 13.7 - - + +
201F LEU* 4.2 5.8 - - + -
202F GLY 3.2 14.6 + - - +
203F MET* 3.7 13.7 - - - +
205F ARG* 1.3 80.1 - - - +
207F MET* 1.3 56.8 + - - +
209F GLU* 3.4 2.1 + - - +
210F THR* 2.9 35.3 + - - +
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Residues in contact with MET 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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119F ILE* 5.0 1.3 - - + -
121F TYR* 5.2 2.0 - - - -
172F ILE* 3.9 27.6 - - + -
203F MET* 2.9 33.6 + - + +
204F THR 3.8 3.4 - - - +
206F VAL* 1.3 73.8 - - - +
208F GLU* 1.3 60.5 + - - +
210F THR* 3.7 5.0 - - + -
211F ILE* 2.9 41.1 + - + +
254F ALA* 3.8 35.7 - - - +
257F MET* 3.8 18.8 - - + -
258F LEU* 3.4 42.6 - - + +
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Residues in contact with GLU 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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200D ARG* 5.0 8.1 + - - +
204F THR* 2.8 34.8 + - - +
205F ARG* 3.5 31.4 + - - +
207F MET* 1.3 76.8 - - - +
209F GLU* 1.3 59.1 + - + +
211F ILE* 3.4 5.6 + - - +
212F ALA* 3.0 30.4 + - - +
257F MET* 3.6 15.3 - - + +
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Residues in contact with GLU 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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191F LYS* 4.7 3.7 + - - -
193F TYR* 2.5 46.4 + - - +
201F LEU* 4.2 8.8 - - - +
205F ARG* 2.7 64.1 + - - +
206F VAL 3.7 1.3 - - - +
208F GLU* 1.3 77.1 - - - +
210F THR* 1.3 57.0 + - - +
212F ALA* 3.4 5.0 + - - +
213F TYR* 2.9 31.6 + - - +
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Residues in contact with THR 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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119F ILE* 3.8 28.9 - - + -
170F VAL* 3.4 38.5 - - + +
172F ILE* 3.7 15.5 - - + +
191F LYS* 5.3 0.4 - - - +
193F TYR* 3.4 9.9 + - - -
206F VAL 2.9 19.9 + - - -
207F MET* 3.7 9.0 - - + -
209F GLU* 1.3 75.1 - - - +
211F ILE* 1.3 65.7 + - - +
213F TYR* 3.4 4.8 + - - +
214F LEU* 3.1 26.0 + - + +
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Residues in contact with ILE 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 MET* 2.9 25.4 + - + +
208F GLU* 3.9 5.4 - - - +
210F THR* 1.3 75.6 - - - +
212F ALA* 1.3 59.1 + - - +
214F LEU* 4.2 0.3 - - - +
215F LYS* 2.9 51.1 + - - +
257F MET* 3.5 43.7 - - + +
258F LEU* 4.0 21.3 - - + -
261F ALA* 3.6 22.7 - - + -
263F ILE* 4.2 15.1 - - + +
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Residues in contact with ALA 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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208F GLU 3.0 18.6 + - - +
209F GLU* 3.7 6.5 - - - +
211F ILE* 1.3 79.3 - - - +
213F TYR* 1.3 62.8 + - - +
215F LYS* 4.1 5.0 - - - +
216F GLU* 3.0 31.7 + - - +
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Residues in contact with TYR 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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167F GLU* 2.6 40.9 + - - +
169F VAL 4.5 0.9 - - - -
170F VAL* 3.7 8.1 - - + -
189F GLY 5.3 2.8 + - - -
191F LYS* 3.6 48.4 + - + +
209F GLU 2.9 19.1 + - - +
210F THR* 3.5 4.5 - - - +
212F ALA* 1.3 78.9 - - - +
214F LEU* 1.3 80.7 + - + +
216F GLU* 3.5 8.8 - - - +
217F ARG* 2.9 62.0 + - - +
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Residues in contact with LEU 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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117F GLY* 4.5 0.4 - - - -
118F VAL 4.3 4.5 - - - +
119F ILE* 3.5 35.0 - - + -
168F HIS* 3.5 29.4 - - - +
170F VAL* 3.9 14.1 - - + -
210F THR* 3.1 16.5 + - + +
211F ILE 4.2 1.1 - - - +
213F TYR* 1.3 90.9 - - + +
215F LYS* 1.3 63.3 + - - +
216F GLU 2.9 5.2 - - - -
217F ARG* 3.0 11.4 + - + -
218F THR* 2.7 38.8 + - + +
221F VAL* 3.9 20.9 - - + -
263F ILE* 4.9 3.8 - - + -
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Residues in contact with LYS 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 ILE* 2.9 40.1 + - - +
212F ALA* 4.1 4.9 - - - +
214F LEU* 1.3 76.3 - - - +
216F GLU* 1.3 59.6 + - - +
217F ARG 3.4 1.0 + - - -
218F THR* 4.2 11.1 - - - +
221F VAL* 5.9 0.4 - - - -
261F ALA* 3.4 27.5 + - - +
263F ILE* 3.7 20.7 - - + +
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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