Contacts of the helix formed by residues 211 - 225 (chain C) in PDB entry 3H90
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 PRO 211 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209C ALA 4.6 0.9 - - - +
210C LEU* 1.3 87.6 - - + +
212C ASP* 1.3 66.6 + - - +
213C GLU* 4.4 6.7 - - + +
214C GLU* 2.8 47.5 + - + +
215C ARG* 3.1 8.0 + - - -
238C GLN* 4.8 3.6 - - - +
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Residues in contact with ASP 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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69A ASP* 5.5 2.8 - - - +
70A ASN* 6.0 0.2 + - - -
210C LEU 3.4 2.9 + - - -
211C PRO* 1.3 69.1 - - - +
213C GLU* 1.3 56.9 + - - +
215C ARG* 3.3 30.3 + - - +
216C GLN* 2.9 30.4 + - - +
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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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211C PRO* 2.8 10.5 + - + +
212C ASP* 1.3 74.4 - - - +
214C GLU* 1.3 67.9 + - + +
216C GLN* 3.1 8.7 + - - +
217C GLU* 3.1 43.1 + - - +
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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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210C LEU* 4.2 15.0 - - + +
211C PRO* 2.8 40.3 + - + +
213C GLU* 1.3 82.8 - - + +
215C ARG* 1.3 62.5 + - - +
217C GLU* 3.4 4.6 + - - +
218C ILE* 3.2 28.1 + - - +
238C GLN* 4.1 3.1 - - - +
243C ARG* 2.9 35.5 + - - -
275C PHE* 3.1 41.1 - - + -
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Residues in contact with ARG 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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69A ASP* 3.3 38.4 + - - -
70A ASN* 4.1 10.3 - - - +
209C ALA* 3.3 30.8 - - - +
210C LEU* 3.4 19.5 + - + +
211C PRO 3.1 9.1 + - - +
212C ASP* 3.4 32.5 + - - +
214C GLU* 1.3 79.8 - - - +
216C GLN* 1.3 60.7 + - - +
218C ILE* 3.4 11.4 + - - +
219C ILE* 3.2 30.7 + - + +
234C LEU* 3.7 27.0 - - + +
236C THR* 4.3 10.4 + - + +
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Residues in contact with GLN 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 ASP 2.9 17.0 + - - +
213C GLU* 3.6 8.1 - - - +
215C ARG* 1.3 75.3 - - - +
217C GLU* 1.3 53.6 + - - +
219C ILE* 3.0 28.5 + - - +
220C ASP* 2.8 65.6 + - - +
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Residues in contact with GLU 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* 3.1 44.7 + - - +
214C GLU* 3.5 9.3 - - - +
216C GLN* 1.3 76.6 - - - +
218C ILE* 1.3 52.5 + - - +
220C ASP* 3.3 8.1 + - - +
221C ILE* 2.8 40.8 + - - +
274C ARG* 2.7 44.7 + - - +
275C PHE* 3.9 22.0 - - + -
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Residues in contact with ILE 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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210C LEU* 4.1 9.0 - - + -
214C GLU 3.2 17.2 + - - +
215C ARG* 3.5 8.1 - - - +
217C GLU* 1.3 77.1 - - - +
219C ILE* 1.3 62.7 + - - +
221C ILE* 3.3 8.2 + - - +
222C VAL* 3.1 39.9 + - + +
234C LEU* 3.9 26.2 - - + -
236C THR* 4.1 16.6 - - + -
245C ILE* 3.8 35.9 - - + -
247C ILE* 4.9 2.5 - - + -
271C ILE* 4.4 13.0 - - + -
275C PHE* 3.6 19.1 - - + -
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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 ARG* 3.2 27.3 + - + +
216C GLN* 3.0 32.5 + - - +
218C ILE* 1.3 75.5 - - - +
220C ASP* 1.3 60.0 + - - +
222C VAL* 3.9 3.5 - - - +
223C THR* 3.0 44.2 + - + +
234C LEU* 4.8 14.8 - - + -
247C ILE* 5.9 2.9 - - + -
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Residues in contact with ASP 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 GLN* 2.8 51.4 + - - +
217C GLU* 3.6 8.5 - - - +
219C ILE* 1.3 72.4 - - - +
221C ILE* 1.3 66.2 + - + +
222C VAL 3.0 0.9 + - - -
223C THR* 4.1 4.9 + - - -
224C SER* 3.1 28.2 + - - -
274C ARG* 5.6 2.2 - - - +
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Residues in contact with ILE 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 GLU 2.8 29.3 + - - +
218C ILE* 3.6 9.2 - - - +
220C ASP* 1.3 73.4 - - + +
222C VAL* 1.3 61.4 + - - +
224C SER* 2.9 18.6 + - - -
225C TRP* 3.6 17.3 - - + -
267C VAL* 4.6 1.3 - - + +
270C ALA* 3.7 29.2 - - + +
271C ILE* 4.1 24.2 - - + +
274C ARG* 3.8 52.9 - - + +
275C PHE* 4.6 4.3 - - + -
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Residues in contact with VAL 222 (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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218C ILE* 3.1 20.1 + - + +
219C ILE* 3.9 3.6 - - - +
220C ASP 3.1 0.6 - - - -
221C ILE* 1.3 75.9 - - - +
223C THR* 1.3 69.5 + - + +
225C TRP* 3.0 16.6 + - - +
228C VAL* 3.3 19.5 - - + +
231C ALA* 3.6 30.7 - - + -
247C ILE* 4.1 17.7 - - + -
249C LEU* 3.7 17.9 - - + -
267C VAL* 3.6 24.9 - - + -
271C ILE* 4.1 13.0 - - + -
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Residues in contact with THR 223 (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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219C ILE* 3.0 35.0 + - + +
220C ASP* 3.7 6.1 + - - -
222C VAL* 1.3 81.1 - - + +
224C SER* 1.3 63.4 + - - +
225C TRP 3.4 4.7 + - - +
228C VAL* 4.2 12.5 - - - +
229C SER 5.8 0.3 - - - +
230C GLY* 6.0 0.9 - - - -
231C ALA* 5.0 12.8 - - + +
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Residues in contact with SER 224 (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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220C ASP 3.1 13.5 + - - -
221C ILE* 2.9 19.8 + - - -
223C THR* 1.3 78.6 + - - +
225C TRP* 1.3 70.5 + - - +
226C PRO* 3.5 4.3 - - - +
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Residues in contact with TRP 225 (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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221C ILE* 3.6 17.9 - - + +
222C VAL 3.0 15.4 + - - +
223C THR 4.0 1.6 - - - +
224C SER* 1.3 85.3 + - - +
226C PRO* 1.4 95.9 - - + +
227C GLY 3.5 10.6 + - - -
228C VAL* 3.5 18.8 + - + +
263C VAL* 4.7 3.8 - - + -
266C GLN* 2.7 49.7 + - + +
267C VAL* 3.6 25.1 - - + -
270C ALA* 3.3 34.1 - - + -
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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