Contacts of the helix formed by residues 204 - 216 (chain F) in PDB entry 6O81
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 HIS 204 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203F ILE* 1.3 77.7 - - - +
205F PRO* 1.3 75.1 - - + +
206F ALA* 3.2 29.9 + - + +
207F MET* 3.2 9.1 + - + -
208F VAL* 2.8 28.3 + - - +
235F GLN* 3.5 24.2 + - + -
236F VAL* 3.5 32.6 + - + +
239F ASP* 3.6 33.5 - - + +
255F LYS* 5.5 4.0 - - - -
259F TYR* 3.4 22.8 - - + -
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Residues in contact with PRO 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200F SER* 3.8 17.7 - - - +
204F HIS* 1.3 101.5 - - + +
206F ALA* 1.3 57.1 + - - +
208F VAL* 3.3 12.8 - - + +
209F ARG* 2.9 33.0 + - - +
1J MET* 5.1 3.4 - - - +
2J GLU* 3.6 50.7 - - + +
122J ARG* 5.4 0.2 + - - -
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Residues in contact with ALA 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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204F HIS* 3.2 17.7 + - + +
205F PRO* 1.3 78.3 - - - +
207F MET* 1.3 58.2 + - - +
209F ARG* 3.4 12.8 + - - +
210F LEU* 2.9 28.4 + - - +
232F ALA* 3.9 17.2 - - - +
235F GLN* 3.7 29.6 - - + -
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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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203F ILE* 3.9 12.6 - - + -
204F HIS* 3.2 21.5 + - + +
206F ALA* 1.3 80.3 - - - +
208F VAL* 1.3 57.4 + - - +
210F LEU* 3.3 15.5 + - - +
211F GLY* 2.9 23.6 + - - -
229F LEU* 4.9 0.4 - - - -
232F ALA* 4.6 5.4 - - + +
233F LEU* 4.0 16.2 - - + -
236F VAL* 3.7 23.8 - - + -
259F TYR* 3.7 30.1 - - + +
260F MET* 3.9 21.8 - - + -
262F PHE* 4.2 2.4 - - + -
263F LEU* 3.7 31.5 - - + +
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Residues in contact with VAL 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193F THR* 3.8 23.6 - - + -
196F MET* 3.9 10.8 - - + -
200F SER* 3.6 18.6 - - - +
203F ILE* 4.0 5.6 - - + +
204F HIS 2.8 19.5 + - - +
205F PRO* 3.3 15.3 - - + +
207F MET* 1.3 71.6 - - - +
209F ARG* 1.3 61.9 + - - +
211F GLY 3.8 0.2 - - - -
212F LEU* 2.9 32.1 + - + +
262F PHE* 3.7 30.7 - - + -
122J ARG* 4.1 18.4 - - - +
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Residues in contact with ARG 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205F PRO* 2.9 20.6 + - - +
206F ALA* 3.6 10.7 - - - +
207F MET 3.3 0.2 - - - -
208F VAL* 1.3 76.3 - - - +
210F LEU* 1.3 59.0 + - - +
212F LEU* 3.7 5.6 - - - +
213F GLN* 3.0 40.9 + - - +
2J GLU* 4.1 17.8 + - - +
100J ASP* 4.9 5.5 + - - -
121J PHE* 3.7 15.6 + - - -
122J ARG* 2.9 51.8 + - + +
125J ASP* 3.0 39.3 + - - +
126J ALA 5.5 0.2 + - - -
208J LYS* 5.4 7.0 - - - +
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Residues in contact with LEU 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 ALA 2.9 17.9 + - - +
207F MET* 3.3 7.6 + - - +
209F ARG* 1.3 77.4 - - - +
211F GLY* 1.3 57.4 + - - +
213F GLN* 3.3 26.4 - - - +
214F TYR* 2.9 62.7 + - + -
228F ALA* 3.5 24.7 - - + +
229F LEU* 3.7 23.3 - - + -
232F ALA* 3.9 13.9 - - + -
263F LEU* 3.8 29.2 - - + -
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Residues in contact with GLY 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 14.0 + - - -
208F VAL 3.8 1.8 - - - -
209F ARG 3.3 0.2 - - - -
210F LEU* 1.3 76.5 - - - +
212F LEU* 1.3 57.5 + - - +
214F TYR* 3.6 4.6 - - - +
215F SER* 2.9 31.4 + - - -
262F PHE* 4.5 2.7 - - - -
263F LEU* 3.8 18.3 - - - +
266F CYS* 3.6 23.2 - - - -
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Residues in contact with LEU 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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191F SER* 5.3 9.9 - - - +
193F THR* 3.7 29.6 - - + +
208F VAL* 2.9 26.4 + - + +
209F ARG 3.7 4.3 - - - +
211F GLY* 1.3 78.9 - - - +
213F GLN* 1.3 61.3 + - - +
215F SER* 3.5 3.6 + - - -
216F GLN* 3.3 34.3 + - - +
262F PHE* 4.9 4.0 - - + -
266F CYS* 5.3 2.5 - - - -
119J ASP* 3.7 42.8 - - + +
122J ARG* 3.8 26.7 - - + +
123J ALA* 3.9 13.7 - - + -
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Residues in contact with GLN 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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209F ARG* 3.0 31.1 + - - +
210F LEU* 3.3 35.8 - - - +
212F LEU* 1.3 74.8 - - - +
214F TYR* 1.3 60.1 + - + +
216F GLN 4.4 1.1 - - - -
218F LEU* 3.4 35.9 + - + -
219F VAL* 3.4 26.7 + - + +
228F ALA* 3.9 14.1 - - - +
122J ARG 5.2 0.2 - - - +
123J ALA* 3.6 23.7 - - - +
125J ASP* 5.6 5.0 - - - +
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Residues in contact with TYR 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 LEU* 2.9 47.6 + - + +
211F GLY* 3.6 5.6 - - - +
212F LEU 3.2 0.2 - - - -
213F GLN* 1.3 81.8 - - + +
215F SER* 1.3 63.9 + - - +
216F GLN 3.3 0.2 - - - -
217F GLY* 3.4 11.8 + - - -
219F VAL* 4.0 22.0 - - + +
225F ARG* 2.4 69.9 + - + +
228F ALA* 4.7 0.7 - - + -
229F LEU* 3.5 9.9 - - - +
263F LEU* 4.1 14.8 - - + -
266F CYS* 5.2 2.0 - - + -
267F ARG* 3.3 32.6 + - + +
269F LEU* 5.5 0.4 - - + -
273F MET* 3.6 26.4 - - + -
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Residues in contact with SER 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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170F ARG* 3.4 23.4 + - - -
187F SER 4.9 1.7 + - - -
188F ARG* 3.3 24.5 + - - +
190F ASN 4.7 1.0 + - - -
191F SER* 4.6 11.9 + - - -
211F GLY 2.9 17.7 + - - -
212F LEU* 3.5 4.9 + - - -
214F TYR* 1.3 77.3 - - - +
216F GLN* 1.3 63.2 + - - +
217F GLY 3.4 0.5 + - - -
266F CYS* 3.8 26.2 - - - -
267F ARG* 4.9 2.7 - - - +
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Residues in contact with GLN 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188F ARG* 3.8 30.8 + - - +
191F SER* 5.3 9.0 + - - +
212F LEU* 3.3 16.3 + - - +
214F TYR 3.3 0.2 - - - -
215F SER* 1.3 78.5 - - - +
217F GLY* 1.3 60.3 + - - +
218F LEU* 3.9 17.2 - - + +
119J ASP* 4.8 10.9 + - - +
120J LEU* 6.0 1.4 - - - +
123J ALA* 3.5 31.4 - - - +
124J TYR* 3.7 27.8 + - - +
165J LYS* 5.3 5.5 - - - +
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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