Contacts of the helix formed by residues 207 - 221 (chain C) in PDB entry 1ORR
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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195C MET 5.3 3.1 - - - -
200C GLN* 3.8 22.4 - - - -
202C ALA* 3.3 7.1 - - - +
203C THR 4.7 0.2 - - - -
206C GLN* 1.3 82.6 - - - +
208C TRP* 1.3 61.1 + - - +
209C VAL 3.3 3.1 - - - -
210C GLY 3.3 3.1 + - - -
211C TRP* 2.8 32.3 + - - +
1400C NAD 5.9 1.3 - - - -
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Residues in contact with TRP 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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194C SER* 3.0 27.6 + - - -
207C GLY* 1.3 76.0 - - - +
209C VAL* 1.3 74.8 + - + +
211C TRP* 3.4 5.7 + - - +
212C PHE* 3.0 38.3 + + + -
235C GLN 5.8 0.2 - - - -
237C ARG* 3.8 16.1 - - + +
239C VAL* 3.7 25.1 - - + -
274C LEU* 4.1 24.9 - - + -
275C SER 4.4 1.1 - - - -
276C LEU* 4.0 24.2 - - + -
279C LEU* 3.4 37.5 - - + -
1401C CDP 3.4 68.1 - - + +
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Residues in contact with VAL 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C SER* 5.1 2.7 - - - -
195C MET 5.3 1.3 + - - +
196C TYR* 3.9 39.7 - - + -
207C GLY 3.3 0.6 - - - -
208C TRP* 1.3 113.9 - - + +
210C GLY* 1.3 61.9 + - - +
212C PHE* 3.5 2.4 + - - +
213C CYS* 3.2 26.0 + - - -
239C VAL* 3.9 18.2 - - + -
274C LEU* 6.0 0.4 - - + -
279C LEU* 4.3 10.2 - - + +
329C VAL* 4.3 19.3 - - + -
332C MET* 4.3 7.2 - - + -
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Residues in contact with GLY 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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200C GLN* 4.3 3.6 - - - +
202C ALA* 3.6 12.1 - - - -
207C GLY 3.3 6.5 + - - -
209C VAL* 1.3 77.3 - - - +
211C TRP* 1.3 60.1 + - - +
213C CYS* 3.1 6.0 + - - +
214C GLN* 2.9 33.5 + - - +
332C MET* 3.5 30.8 - - - +
336C THR* 4.4 1.2 + - - -
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Residues in contact with TRP 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ALA* 3.4 4.2 - - + +
203C THR* 3.5 29.6 - - - +
204C TYR* 3.6 36.1 - + + -
207C GLY 2.8 18.2 + - - +
208C TRP* 3.5 6.1 - - - +
210C GLY* 1.3 78.0 - - - +
212C PHE* 1.3 83.8 + + - +
214C GLN* 3.1 33.7 + - - +
215C LYS* 2.9 57.8 + - + +
227C PHE* 5.7 2.2 - - + +
228C THR 5.0 2.0 + - - -
1401C CDP 3.1 28.1 + + + -
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Residues in contact with PHE 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 TRP* 3.0 41.9 + + + +
209C VAL 3.9 0.4 - - - +
211C TRP* 1.3 94.4 - + - +
213C CYS* 1.3 59.6 + - - +
215C LYS* 3.5 13.0 - - + -
216C ALA 3.0 20.4 + - - -
227C PHE* 3.9 14.1 - + - -
228C THR 3.8 15.9 - - - -
229C ILE* 4.5 0.2 - - + -
276C LEU* 3.9 23.6 - - + -
279C LEU* 3.9 17.3 - - + -
280C PHE* 3.7 24.2 - + + -
283C LEU* 3.5 6.2 - - + +
291C MET* 3.3 11.3 - - + +
1401C CDP 3.5 35.2 - + - -
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Residues in contact with CYS 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 VAL* 3.2 25.1 + - - +
210C GLY* 3.1 10.7 + - - +
211C TRP 3.1 0.6 - - - -
212C PHE* 1.3 75.5 - - - +
214C GLN* 1.3 62.7 + - - +
216C ALA* 3.1 4.8 + - - +
217C VAL* 2.8 32.9 + - - +
279C LEU* 5.5 0.4 - - - -
283C LEU* 4.2 24.5 - - - -
329C VAL* 4.4 4.0 - - - -
332C MET* 3.8 26.7 - - - -
333C TYR* 4.1 11.4 - - - -
336C THR* 3.6 21.8 - - - +
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Residues in contact with GLN 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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200C GLN 5.2 1.6 + - - -
201C PHE* 4.4 1.6 - - - +
202C ALA* 3.0 45.9 + - - +
210C GLY* 2.9 14.8 + - - +
211C TRP* 3.3 30.5 - - - +
213C CYS* 1.3 77.2 - - - +
215C LYS* 1.3 68.1 + - - +
217C VAL* 3.0 3.0 + - - +
218C GLU* 2.8 36.0 + - + +
336C THR* 3.7 20.6 + - + +
339C ILE* 5.7 7.2 - - + +
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Residues in contact with LYS 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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211C TRP* 2.9 63.0 + - + +
212C PHE* 3.3 28.5 - - + +
213C CYS 3.0 0.2 - - - -
214C GLN* 1.3 83.6 - - - +
216C ALA* 1.3 61.9 + - - +
218C GLU* 3.1 35.7 + - - +
219C ILE* 3.2 27.5 + - - +
227C PHE* 3.9 34.8 - - + -
291C MET* 4.0 9.6 - - + -
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Residues in contact with ALA 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 PHE 3.0 11.7 + - - +
213C CYS 3.1 3.8 + - - +
215C LYS* 1.3 74.5 - - - +
217C VAL* 1.3 59.2 + - - +
219C ILE* 4.1 0.9 - - - -
220C LYS* 3.3 20.6 + - - +
283C LEU* 3.9 16.8 - - + -
287C CYS* 4.5 0.9 - - - -
289C ILE* 3.4 31.0 - - + +
291C MET* 3.5 19.7 - - + +
333C TYR* 4.0 16.0 + - + -
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Residues in contact with VAL 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 CYS 2.8 16.9 + - - +
214C GLN* 3.0 5.1 + - - +
216C ALA* 1.3 76.1 - - - +
218C GLU* 1.3 68.0 + - + +
220C LYS* 3.0 13.0 - - - +
221C ASN* 2.9 32.2 + - - +
223C ILE* 5.9 0.2 - - + -
333C TYR* 3.2 35.4 - - + +
336C THR* 3.5 24.9 - - + +
337C SER* 3.9 23.8 - - - +
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Residues in contact with GLU 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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214C GLN* 2.8 20.9 + - + +
215C LYS* 3.1 37.5 + - - +
217C VAL* 1.3 71.5 - - + +
219C ILE* 1.3 69.4 + - + +
221C ASN 2.7 15.1 + - - -
222C GLY 2.7 10.7 + - - -
223C ILE* 3.0 56.9 + - + +
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Residues in contact with ILE 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 LYS 3.2 17.9 + - - +
216C ALA 3.8 4.0 - - - +
218C GLU* 1.3 79.2 - - + +
220C LYS* 1.3 58.4 + - - +
222C GLY* 3.0 18.1 + - - +
223C ILE 4.5 11.2 - - - +
227C PHE* 4.4 13.7 - - + -
289C ILE* 3.5 27.4 - - + -
290C ASP 3.4 26.9 - - - +
291C MET* 3.6 25.6 - - + -
292C ARG 4.3 4.9 - - - +
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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 ALA 3.3 9.5 + - - +
217C VAL 3.0 14.3 + - - +
218C GLU 3.0 0.2 - - - -
219C ILE* 1.3 82.0 - - - +
221C ASN* 1.3 66.1 + - - +
222C GLY 3.3 0.8 + - - -
287C CYS* 2.3 42.5 + - + +
288C ASN* 3.4 20.3 + - - +
289C ILE* 3.3 18.1 - - + +
333C TYR* 3.4 15.7 - - - +
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Residues in contact with ASN 221 (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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217C VAL* 2.9 33.7 + - - +
218C GLU* 2.7 10.0 + - - +
220C LYS* 1.3 86.4 - - - +
222C GLY* 1.3 68.0 + - - +
223C ILE* 3.9 12.5 - - + +
337C SER* 5.7 0.8 + - - -
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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