Contacts of the helix formed by residues 208 - 219 (chain C) in PDB entry 3UGV
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 ASP 208 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207C LEU* 1.3 75.0 - - - +
209C MET* 1.3 57.7 + - - +
210C ALA* 2.9 13.0 + - - +
211C GLU* 2.8 47.3 + - - +
212C ALA* 2.9 26.0 + - - +
231C VAL* 3.9 2.7 - - - -
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Residues in contact with MET 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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208C ASP* 1.3 76.1 - - - +
210C ALA* 1.3 57.9 + - - +
212C ALA* 3.3 2.5 + - - +
213C MET* 3.0 57.5 + - + +
231C VAL* 4.1 10.5 - - + +
235C ASN* 3.7 23.1 - - - +
238C GLY* 3.6 35.9 - - - +
241C GLN* 4.5 11.0 - - + -
242C LEU* 4.0 22.9 - - + -
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Residues in contact with ALA 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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208C ASP* 2.9 10.6 + - - +
209C MET* 1.3 76.3 - - - +
211C GLU* 1.3 65.6 + - + +
213C MET* 3.4 9.0 + - - +
214C HIS* 3.0 38.3 + - + +
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Residues in contact with GLU 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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206C GLY 4.4 2.8 - - - +
207C LEU* 3.7 24.5 - - + -
208C ASP* 2.8 47.1 + - - +
210C ALA* 1.3 73.2 - - + +
212C ALA* 1.3 63.0 + - - +
213C MET 3.3 0.2 + - - -
214C HIS* 3.4 6.0 + - - +
215C ARG* 3.0 37.8 + - - +
136D LYS* 5.9 0.3 + - - -
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Residues in contact with ALA 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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207C LEU* 3.8 13.2 - - + +
208C ASP 2.9 17.9 + - - +
209C MET* 3.6 5.2 - - - +
210C ALA 3.3 0.2 - - - -
211C GLU* 1.3 76.0 - - - +
213C MET* 1.3 57.8 + - - +
216C THR* 2.8 37.9 + - - +
230C PRO* 4.2 9.0 - - + -
231C VAL* 3.4 23.8 - - + -
242C LEU* 4.1 17.3 - - + -
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Residues in contact with MET 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 MET* 3.0 43.9 + - + +
210C ALA* 3.8 7.2 - - - +
211C GLU 3.3 0.2 - - - -
212C ALA* 1.3 76.9 - - - +
214C HIS* 1.3 66.2 + - + +
216C THR* 3.9 1.5 + - - -
217C ARG* 3.2 26.4 + - - +
241C GLN* 6.3 1.8 - - + -
242C LEU* 4.2 11.4 - - + -
245C ASP* 4.4 17.7 - - - +
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Residues in contact with HIS 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 ALA* 3.0 30.7 + - + +
211C GLU* 3.9 5.6 - - - +
213C MET* 1.3 81.6 - - + +
215C ARG* 1.3 59.6 + - + +
217C ARG* 3.5 11.4 + - - +
218C GLN* 3.2 39.2 + - - +
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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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175C GLY* 3.9 11.2 + - - -
176C ARG 2.6 30.3 + - - -
177C ASP* 3.4 16.2 + - - +
179C PRO* 3.7 34.2 - - + +
182C ASP* 3.5 21.2 + - - -
203C PHE* 4.4 8.6 - - + -
207C LEU* 3.7 37.8 - - + +
211C GLU* 3.0 22.8 + - - +
214C HIS* 1.3 77.6 - - + +
216C THR* 1.3 66.5 + - - +
217C ARG 3.1 1.8 - - - -
218C GLN* 3.1 21.7 + - - +
219C ILE* 3.3 19.1 + - - +
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Residues in contact with THR 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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203C PHE* 4.4 7.9 - - + -
207C LEU* 5.3 0.4 - - + -
212C ALA* 2.8 28.2 + - + +
213C MET* 3.9 2.9 + - - -
215C ARG* 1.3 76.8 - - + +
217C ARG* 1.3 64.5 + - - +
219C ILE* 3.3 12.3 + - - +
220C ASP 3.2 17.0 + - - -
227C ILE* 4.2 17.0 - - + -
230C PRO* 4.1 24.9 - - + -
242C LEU* 4.0 8.8 - - + +
246C LEU* 3.3 38.9 - - + +
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Residues in contact with ARG 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 MET 3.2 17.6 + - - +
214C HIS* 3.5 10.6 + - - +
215C ARG 3.1 0.4 - - - -
216C THR* 1.3 82.4 + - - +
218C GLN* 1.3 62.0 + - + +
219C ILE 3.2 0.7 + - - -
220C ASP* 3.3 19.5 + - + +
221C ASP* 4.8 2.9 + - - +
246C LEU* 4.4 4.0 - - + -
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Residues in contact with GLN 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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179C PRO* 3.3 33.1 - - - +
180C ALA* 5.0 0.5 + - - -
183C ILE* 4.1 26.7 - - + +
214C HIS* 3.2 27.1 + - - +
215C ARG* 3.1 13.6 + - - +
217C ARG* 1.3 77.4 - - + +
219C ILE* 1.3 60.9 + - + +
220C ASP 3.4 0.6 + - - -
221C ASP* 4.8 1.9 + - - +
222C LEU* 4.7 6.1 - - - +
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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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174C MET* 4.3 17.9 - - - -
182C ASP* 5.7 0.9 - - + -
183C ILE* 4.0 23.8 - - + -
201C VAL* 4.4 1.1 - - + -
203C PHE* 3.9 29.2 - - + -
215C ARG 3.5 10.3 - - - +
216C THR* 3.3 14.1 - - - +
217C ARG 3.2 0.2 - - - -
218C GLN* 1.3 80.3 - - + +
220C ASP* 1.3 62.5 + - - +
221C ASP 3.2 3.4 + - - -
222C LEU* 3.3 27.4 + - + +
223C GLY 4.8 0.2 + - - -
224C LEU* 3.7 32.0 - - + +
227C ILE* 3.7 20.8 - - + +
248C THR* 4.6 2.1 + - - -
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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