Contacts of the helix formed by residues 207 - 220 (chain C) in PDB entry 3E9B
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 GLY 207 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A ASP 5.9 1.1 - - - -
203C VAL 2.8 19.3 + - - -
204C ASP 5.0 2.0 - - - -
205C LYS 3.5 1.0 - - - -
206C LEU* 1.3 77.8 - - - +
208C ILE* 1.3 67.4 + - - -
209C GLY 3.0 4.9 + - - -
210C LYS 3.1 4.4 + - - -
211C VAL* 3.0 20.6 + - - +
256C GLU* 5.9 0.2 - - - -
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Residues in contact with ILE 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ASP* 3.7 23.5 + - + +
177C ILE* 4.8 2.0 - - + -
203C VAL* 4.0 10.7 + - + +
207C GLY* 1.3 71.2 - - - -
209C GLY* 1.3 65.8 + - - +
211C VAL* 3.4 20.4 - - + +
212C MET* 3.0 24.6 + - + +
252C LEU* 4.6 10.5 - - + -
256C GLU* 4.0 44.3 + - + +
259C TYR* 3.7 29.4 - - + -
260C ILE* 3.8 27.6 - - + -
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Residues in contact with GLY 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ASP 4.3 3.2 + - - -
205A LYS* 4.4 20.7 + - - -
207C GLY 3.0 1.6 + - - -
208C ILE* 1.3 86.0 - - - +
210C LYS* 1.3 60.6 + - - +
212C MET* 3.6 3.1 + - - +
213C GLU* 3.4 23.5 + - - +
259C TYR* 3.6 26.3 + - - -
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Residues in contact with LYS 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LYS 5.4 0.4 + - - -
206C LEU* 3.8 32.2 + - + +
207C GLY 3.1 3.0 + - - +
209C GLY* 1.3 73.2 - - - +
211C VAL* 1.3 65.6 + - - +
213C GLU* 3.2 37.5 + - - +
214C GLU* 3.0 65.3 + - - +
217C SER* 6.1 0.8 - - - -
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Residues in contact with VAL 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C ILE* 4.3 13.2 - - + -
198C PHE* 3.9 41.6 - - + -
202C GLU 4.0 6.1 - - - +
203C VAL* 3.9 27.8 - - + -
206C LEU* 4.3 4.9 - - + -
207C GLY 3.0 17.0 + - - +
208C ILE* 3.4 24.5 - - + +
209C GLY 3.2 0.2 - - - -
210C LYS* 1.3 77.7 - - - +
212C MET* 1.3 61.6 + - - +
214C GLU* 3.3 3.1 + - - +
215C THR* 2.9 34.5 + - + +
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Residues in contact with MET 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ILE* 4.6 1.8 - - + -
177C ILE* 3.8 25.4 - - + -
208C ILE* 3.0 19.8 + - + +
209C GLY 4.1 3.8 - - - +
210C LYS 3.3 0.4 - - - -
211C VAL* 1.3 77.8 - - - +
213C GLU* 1.3 63.1 + - - +
215C THR* 3.3 8.6 + - - +
216C PHE* 3.1 61.5 + - + -
259C TYR* 3.8 24.7 - - + -
260C ILE* 3.7 42.4 - - + +
263C GLU* 4.2 11.7 - - + -
264C ILE* 4.0 6.3 - - + -
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Residues in contact with GLU 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LYS* 4.5 14.1 + - - +
209C GLY 3.4 15.1 + - - +
210C LYS* 3.2 38.4 + - - +
212C MET* 1.3 79.2 - - - +
214C GLU* 1.3 58.1 + - - +
216C PHE* 3.9 6.7 + - - +
217C SER* 3.2 24.9 + - - -
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Residues in contact with GLU 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C LYS* 4.8 8.9 + - - -
198C PHE* 3.5 28.6 - - + -
206C LEU* 3.5 23.0 - - - +
210C LYS* 3.0 56.2 + - - +
211C VAL 3.8 0.4 - - - +
213C GLU* 1.3 77.1 - - - +
215C THR* 1.3 65.7 + - - +
217C SER* 3.5 7.6 - - - -
218C TYR* 2.9 24.1 + - - +
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Residues in contact with THR 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ILE* 4.3 6.5 - - - +
175C VAL* 3.6 24.5 - - + -
177C ILE* 3.9 15.7 - - + -
198C PHE* 3.4 25.6 - - + -
211C VAL 2.9 21.0 + - - +
212C MET* 3.3 12.9 + - - +
214C GLU* 1.3 74.8 - - - +
216C PHE* 1.3 74.1 + - - +
218C TYR* 3.1 6.3 + - - +
219C LEU* 2.9 36.4 + - - +
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Residues in contact with PHE 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ILE* 4.0 23.6 - - + -
212C MET* 3.1 38.5 + - + +
213C GLU* 4.1 5.8 - - - +
215C THR* 1.3 86.4 + - - +
217C SER* 1.3 57.7 + - - +
219C LEU* 5.1 2.5 - - + -
220C LEU* 2.9 54.2 + - + +
227C ILE* 4.4 5.8 - - + -
263C GLU* 3.7 38.4 - - + -
264C ILE* 3.8 9.4 - - + -
267C THR* 3.7 25.1 - - + -
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Residues in contact with SER 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C LYS* 6.1 0.7 - - - -
213C GLU 3.2 18.0 + - - -
214C GLU* 3.5 10.1 - - - -
215C THR 3.1 0.4 - - - -
216C PHE* 1.3 80.1 - - - +
218C TYR* 1.3 60.8 + - - +
221C GLY* 3.3 22.6 + - - +
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Residues in contact with TYR 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C ALA 3.4 6.8 + - - -
172C LYS* 3.1 50.3 - - + +
174C ILE 4.2 4.0 - - - -
175C VAL* 3.7 16.2 - - + -
194C GLY 4.4 5.7 + - - -
196C LYS* 3.6 45.6 + - + +
214C GLU 2.9 16.2 + - - +
215C THR* 3.5 6.1 - - - +
217C SER* 1.3 80.7 - - - +
219C LEU* 1.3 69.7 + - + +
220C LEU 3.6 0.2 + - - -
221C GLY* 4.0 4.0 + - - -
222C ARG 5.5 0.2 + - - -
225C ARG* 5.0 1.0 + - - -
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Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C CYS* 3.7 26.0 - - + -
120C VAL 3.9 6.1 - - - +
121C ILE* 3.8 28.5 - - + -
172C LYS 4.0 1.1 - - - +
173C ASP* 3.4 39.3 - - - +
174C ILE 3.8 0.4 - - - +
175C VAL* 3.4 32.8 - - + -
215C THR 2.9 19.3 + - - +
216C PHE* 5.1 2.2 - - + -
218C TYR* 1.3 82.2 - - + +
220C LEU* 1.3 61.7 + - + +
221C GLY 3.6 1.0 + - - -
222C ARG 5.4 0.5 + - - -
223C LYS 4.2 0.7 - - - +
225C ARG* 2.9 33.1 + - - +
227C ILE* 6.4 0.2 - - + -
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Residues in contact with LEU 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C CYS* 4.1 12.8 - - - -
216C PHE* 2.9 43.9 + - + +
217C SER* 5.2 0.2 - - - -
219C LEU* 1.3 87.6 - - + +
221C GLY* 1.3 63.4 + - - +
222C ARG 3.6 1.8 - - - -
223C LYS 3.5 17.7 + - - +
224C LYS* 3.8 24.1 + - + -
225C ARG* 3.7 39.0 - - + +
227C ILE* 4.3 7.0 - - + -
267C THR* 4.8 4.0 - - + -
269C LEU* 3.7 22.0 - - + -
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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