Contacts of the helix formed by residues 207 - 220 (chain C) in PDB entry 1I3O
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 207 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174C HIS* 4.5 7.9 - - + +
205C ASP 5.1 1.1 - - - +
206C LEU* 1.3 74.4 - - - +
208C ARG* 1.3 68.3 + - - +
209C GLU* 3.2 15.1 + - - +
210C GLU* 2.9 42.7 + - - +
211C ILE* 2.8 22.4 + - - +
245C GLY* 4.1 2.5 - - - -
246C THR* 3.4 16.8 - - - +
247C ASN* 3.4 20.6 - - + +
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Residues in contact with ARG 208 (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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207C THR* 1.3 71.2 - - - +
209C GLU* 1.3 83.3 + - - +
211C ILE* 3.2 4.5 + - - +
212C VAL* 2.8 36.1 + - + +
245C GLY* 3.8 5.5 - - - -
247C ASN* 3.0 26.4 + - - +
254C GLY* 3.5 9.7 - - - +
255C PRO* 2.9 47.9 + - - +
256C VAL* 3.1 30.7 - - + +
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Residues in contact with GLU 209 (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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207C THR* 3.2 11.8 + - - +
208C ARG* 1.3 93.1 + - - +
210C GLU* 1.3 53.4 + - + +
212C VAL* 3.2 8.4 + - - +
213C GLU* 2.7 38.7 + - - +
247C ASN* 3.0 23.8 - - - +
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Residues in contact with GLU 210 (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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205C ASP 4.0 3.6 - - - +
206C LEU* 3.0 24.6 - - + +
207C THR* 2.9 45.5 + - - +
209C GLU* 1.3 78.1 - - + +
211C ILE* 1.3 53.8 + - - +
213C GLU* 3.5 16.3 - - - +
214C LEU* 2.6 37.2 + - - +
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Residues in contact with ILE 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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168C ILE* 3.9 29.2 - - + -
170C ASN* 4.0 23.6 - - - +
206C LEU* 3.8 16.6 - - + +
207C THR 2.8 17.9 + - - +
208C ARG* 3.5 8.7 - - - +
210C GLU* 1.3 72.4 - - - +
212C VAL* 1.3 68.2 + - + +
214C LEU* 3.0 6.4 + - - +
215C MET* 2.8 27.5 + - + +
243C ILE* 5.0 9.4 - - + -
244C PHE 4.4 3.8 - - - +
245C GLY* 4.0 13.2 - - - +
256C VAL* 5.2 5.2 - - + -
261C ILE* 3.7 32.3 - - + -
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Residues in contact with VAL 212 (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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208C ARG* 2.8 28.3 + - + +
209C GLU* 3.6 7.0 - - - +
211C ILE* 1.3 73.5 - - + +
213C GLU* 1.3 58.5 + - - +
215C MET* 3.4 2.1 + - - +
216C ARG* 2.9 41.5 + - - +
256C VAL* 4.2 14.1 - - + -
260C LYS* 4.0 29.2 - - + +
261C ILE* 5.6 2.9 - - + -
264C PHE* 3.5 30.5 - - + -
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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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209C GLU 2.7 21.2 + - - +
210C GLU* 3.5 16.3 - - - +
212C VAL* 1.3 72.9 - - - +
214C LEU* 1.3 67.3 + - - +
216C ARG* 3.2 13.9 + - - +
217C ASP* 2.9 40.9 + - - +
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Residues in contact with LEU 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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166C ILE* 4.0 11.9 - - + -
168C ILE* 4.5 3.8 - - + -
203C LYS* 3.6 43.5 - - + +
206C LEU* 3.8 15.7 - - + -
210C GLU 2.6 22.3 + - - +
211C ILE* 3.5 5.8 - - - +
213C GLU* 1.3 76.4 - - - +
215C MET* 1.3 83.6 + - + +
217C ASP* 3.2 6.5 + - + +
218C VAL* 2.9 42.7 + - + +
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Residues in contact with MET 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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166C ILE* 3.9 25.4 - - + -
168C ILE* 4.1 12.3 - - + -
211C ILE* 2.8 26.0 + - + +
212C VAL* 3.7 1.1 - - - +
214C LEU* 1.3 94.2 - - + +
216C ARG* 1.3 52.8 + - - +
218C VAL* 3.0 7.0 + - + +
219C SER* 2.7 38.1 + - - -
230C PHE* 5.0 0.7 - - - -
232C CYS* 3.9 17.0 - - - -
261C ILE* 3.5 32.3 - - + -
264C PHE* 3.7 20.0 - - + -
265C PHE* 4.1 22.2 - - + -
280C PHE* 5.3 0.2 - - - -
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Residues in contact with ARG 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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212C VAL* 2.9 36.9 + - - +
213C GLU* 3.5 11.6 - - - +
215C MET* 1.3 75.0 - - - +
217C ASP* 1.3 71.6 + - - +
219C SER* 2.5 23.3 + - - +
220C LYS* 3.3 40.9 - - - +
264C PHE* 3.4 33.3 - - + -
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Residues in contact with ASP 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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213C GLU* 2.9 36.6 + - - +
214C LEU* 3.6 10.4 - - + +
216C ARG* 1.3 86.1 - - - +
218C VAL* 1.3 59.7 + - + +
220C LYS* 2.8 30.0 + - - +
221C GLU* 3.4 7.9 + - - +
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Residues in contact with VAL 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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164C LEU* 3.5 31.9 - - + -
166C ILE* 4.3 15.5 - - + -
201C ARG* 4.9 3.1 - - - +
214C LEU* 2.9 38.9 + - + +
215C MET* 3.6 7.0 - - + +
217C ASP* 1.3 75.4 - - + +
219C SER* 1.3 61.0 + - - +
220C LYS 3.0 1.1 + - - -
221C GLU* 3.3 21.4 + - - +
224C HIS* 2.9 26.3 + - + +
230C PHE* 4.0 20.0 - - + -
265C PHE* 4.6 3.1 - - + -
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Residues in contact with SER 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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215C MET 2.7 16.7 + - - -
216C ARG* 2.5 27.5 + - - +
218C VAL* 1.3 72.9 - - - +
220C LYS* 1.3 63.2 + - - +
221C GLU 3.5 2.8 + - - +
264C PHE* 3.4 39.0 + - - +
265C PHE* 4.0 15.2 - - - -
269C ARG 4.4 3.9 + - - +
270C CYS* 3.4 26.6 - - - +
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Residues in contact with LYS 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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216C ARG* 3.3 41.6 - - + +
217C ASP* 2.8 15.3 + - - +
219C SER* 1.3 83.2 - - - +
221C GLU* 1.3 65.6 + - - +
269C ARG 6.0 0.9 - - - +
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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