Contacts of the helix formed by residues 202 - 217 (chain V) in PDB entry 1O1F
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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2857 CYS 3.6 2.5 - - - +
2877 ILE* 0.6 285.9 - - + +
2907 ARG* 2.2 61.5 - - - +
201V VAL* 1.3 73.1 - - - +
203V THR* 1.4 52.1 + - - -
205V GLU* 2.9 17.8 + - - +
206V ARG* 3.1 11.2 + - - +
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Residues in contact with THR 203 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2867 ASP* 2.3 34.8 - - - +
2877 ILE* 1.4 36.1 - - - +
2887 ASP* 1.3 76.2 + - + +
62V ARG* 3.7 25.6 + - + +
202V THR 1.4 66.7 - - - -
204V ALA* 1.3 54.0 + - - -
205V GLU 3.2 0.4 - - - -
206V ARG* 3.7 11.7 - - - +
207V GLU* 3.3 24.3 + - - +
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Residues in contact with ALA 204 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2877 ILE* 2.8 32.3 - - + +
2887 ASP* 2.7 19.6 + - - +
2917 LYS* 5.6 4.7 - - + -
203V THR* 1.3 74.0 - - - +
205V GLU* 1.3 62.7 + - - +
207V GLU* 4.6 3.1 - - - -
208V ILE* 3.6 11.6 + - - +
243V PRO* 3.5 31.9 - - + +
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Residues in contact with GLU 205 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2877 ILE* 3.0 29.2 - - + +
2907 ARG* 5.3 2.8 + - - -
199V SER 4.2 3.9 - - - +
200V PHE* 3.4 33.5 - - + -
201V VAL* 3.5 17.8 - - + +
202V THR* 2.9 15.9 + - - +
204V ALA* 1.3 85.5 - - - +
206V ARG* 1.3 66.7 + - - +
208V ILE* 3.1 22.0 - - - +
209V VAL* 3.7 2.9 + - - +
242V LEU* 3.7 23.8 - - + +
243V PRO* 4.4 5.2 - - - +
244V ASP* 5.1 3.1 - - - +
246V GLN* 5.6 1.2 - - - +
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Residues in contact with ARG 206 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62V ARG* 4.4 13.1 - - - +
183V ARG* 6.1 3.0 - - - +
186V THR* 4.6 12.0 - - - +
187V ASP* 3.4 32.2 + - - -
190V MET* 3.7 27.2 - - + +
200V PHE* 4.2 3.2 - - - +
201V VAL 5.9 0.4 - - - +
202V THR 3.1 7.8 + - - +
203V THR* 3.7 15.3 - - - +
205V GLU* 1.3 77.1 - - - +
207V GLU* 1.3 66.1 + - - +
209V VAL* 3.0 30.2 + - - +
210V ARG* 5.1 0.8 - - - +
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Residues in contact with GLU 207 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2887 ASP* 4.1 10.7 - - - +
59V GLN* 3.8 12.6 - - - +
62V ARG* 2.9 38.5 + - - +
203V THR 3.3 13.6 + - - +
204V ALA* 5.1 2.2 - - - -
205V GLU 3.4 0.2 - - - -
206V ARG* 1.3 82.4 - - - +
208V ILE* 1.3 57.4 + - + +
210V ARG* 3.1 39.6 + - - +
211V ASP* 3.8 1.9 + - - +
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Residues in contact with ILE 208 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200V PHE* 5.4 3.4 - - + -
204V ALA 3.6 14.8 + - - +
205V GLU* 3.1 19.9 - - - +
207V GLU* 1.3 76.0 - - - +
209V VAL* 1.4 58.6 + - - +
210V ARG 3.1 2.2 - - - -
211V ASP* 3.0 10.9 + - + +
212V ILE* 2.9 33.2 + - + +
240V TYR* 3.2 40.2 - - + +
242V LEU* 4.4 13.7 - - + -
243V PRO* 3.9 29.6 - - + -
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Residues in contact with VAL 209 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186V THR* 3.6 22.4 - - + +
189V LEU* 3.5 21.6 - - + +
190V MET* 3.2 49.1 - - + +
193V LEU* 4.1 13.2 - - + -
200V PHE* 5.1 5.8 - - + -
205V GLU 3.7 2.4 + - - +
206V ARG* 3.0 25.3 + - - +
208V ILE* 1.4 78.4 - - - +
210V ARG* 1.3 59.1 + - - +
212V ILE* 3.2 12.1 + - - +
213V LYS* 3.0 24.8 + - - +
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Residues in contact with ARG 210 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16V LEU* 6.1 2.8 - - - +
186V THR* 3.7 31.9 - - + +
206V ARG* 6.2 0.4 - - - +
207V GLU* 3.1 24.2 + - - +
209V VAL* 1.3 82.4 - - + +
211V ASP* 1.3 60.8 + - - +
213V LYS* 3.4 12.6 - - - +
214V GLU* 2.8 68.6 + - - +
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Residues in contact with ASP 211 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207V GLU 3.8 1.1 + - - +
208V ILE* 3.0 19.4 + - + +
210V ARG* 1.3 82.7 + - - +
212V ILE* 1.3 60.3 + - - +
214V GLU* 4.0 14.0 - - - +
215V LYS* 2.7 64.2 + - - +
240V TYR* 2.9 20.7 + - - +
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Residues in contact with ILE 212 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189V LEU* 3.7 17.3 - - + -
193V LEU* 4.2 24.2 - - + -
200V PHE* 5.1 7.6 - - + -
208V ILE* 2.9 20.5 + - + +
209V VAL* 3.2 12.8 + - - +
211V ASP* 1.3 74.3 - - - +
213V LYS* 1.4 60.6 + - - +
215V LYS 3.2 1.2 + - - -
216V LEU* 2.9 41.9 + - + +
217V CYS* 3.7 2.6 + - - -
240V TYR* 3.9 39.9 - - + -
242V LEU* 5.2 1.1 - - + -
248V ILE* 4.3 16.2 - - + -
250V ILE* 4.5 16.2 - - + -
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Residues in contact with LYS 213 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157V ASP* 5.8 0.4 + - - -
182V GLY* 2.8 24.6 + - - +
185V LEU* 4.1 2.7 - - + -
186V THR* 2.7 41.8 + - - +
189V LEU* 3.5 17.5 - - + +
209V VAL 3.0 8.9 + - - +
210V ARG* 3.4 21.4 - - - +
212V ILE* 1.4 73.5 - - - +
214V GLU* 1.3 77.0 + - - +
217V CYS* 3.0 31.2 + - - +
257V CYS* 4.2 13.9 - - - -
303V THR* 5.1 1.2 + - - -
306V TYR* 3.7 32.3 + - + +
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Residues in contact with GLU 214 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210V ARG* 2.8 56.3 + - - +
211V ASP* 4.2 10.3 - - - +
212V ILE 3.3 0.2 - - - -
213V LYS* 1.3 94.7 + - - +
215V LYS* 1.3 64.8 + - + +
217V CYS 4.3 5.9 + - - +
306V TYR* 5.6 4.5 - - - -
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Residues in contact with LYS 215 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211V ASP* 2.7 53.0 + - - +
212V ILE* 4.1 0.9 - - - +
214V GLU* 1.3 78.3 - - + +
216V LEU* 1.3 73.1 + - + +
217V CYS 4.9 0.9 - - - +
218V TYR* 4.8 6.9 - - - -
240V TYR* 4.1 15.4 + - + -
254V ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 216 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212V ILE* 2.9 26.6 + - + +
215V LYS* 1.3 85.5 - - + +
217V CYS* 1.3 62.6 + - - +
218V TYR* 3.3 5.1 - - - -
238V LYS* 3.8 45.8 - - + +
239V SER 5.8 0.9 - - - +
240V TYR* 3.9 33.0 - - + +
250V ILE* 4.6 11.4 - - + -
254V ARG* 2.9 43.0 + - + +
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Residues in contact with CYS 217 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189V LEU* 4.6 7.4 - - - -
212V ILE* 4.6 2.7 - - - -
213V LYS* 3.0 36.5 + - - +
214V GLU 4.6 4.0 - - - +
215V LYS 4.9 0.7 - - - +
216V LEU* 1.3 72.8 - - - +
218V TYR* 1.3 73.1 + - - +
250V ILE* 6.2 0.2 - - - -
254V ARG* 2.9 27.8 - - - +
257V CYS* 4.2 19.3 - - - -
258V PRO* 4.1 3.4 - - + -
306V TYR* 4.0 21.6 - - + -
307V PRO* 3.4 17.7 - - - +
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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