Contacts of the helix formed by residues 215 - 223 (chain C) in PDB entry 3R2W
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 ILE 215 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100C VAL* 4.8 10.1 - - + -
102C LEU* 5.0 11.7 - - + -
151C MET* 3.3 34.3 - - + -
177C PHE* 4.7 13.0 - - + -
179C GLN* 5.7 1.3 - - - +
212C HIS 3.8 12.3 - - - +
213C GLY 2.8 12.9 + - - +
214C ASP* 1.3 75.6 - - - +
216C TYR* 1.3 85.5 + - + +
217C ALA 3.2 2.3 - - - +
218C SER* 3.9 5.4 - - - -
219C PHE* 2.8 40.7 + - + +
238C VAL* 5.2 13.0 - - + -
323C ILE* 6.0 1.8 - - + -
361C VAL* 4.7 9.6 - - + -
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Residues in contact with TYR 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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213C GLY 3.9 8.0 + - - -
215C ILE* 1.3 85.9 - - + +
217C ALA* 1.3 60.3 + - - +
218C SER 3.5 0.2 - - - -
219C PHE* 4.3 4.4 - - - +
220C TYR* 3.8 19.9 + - - +
225C LEU* 4.6 2.4 - - - +
267C PHE* 4.4 7.4 - - - -
323C ILE* 4.1 30.5 - - + +
328C VAL* 4.8 21.5 - - + +
332C GLN* 3.9 13.5 - - + +
337C ILE* 4.0 24.5 - - + -
339C MET* 3.6 37.2 - - + -
361C VAL* 2.8 39.2 + - + +
364C ALA* 3.7 16.8 - - + +
368C PHE* 5.1 7.9 - + - -
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Residues in contact with ALA 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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214C ASP* 3.6 18.6 - - - +
215C ILE 3.2 1.9 - - - +
216C TYR* 1.3 81.3 - - - +
218C SER* 1.3 56.8 + - - +
219C PHE 3.6 0.2 - - - -
220C TYR* 4.2 6.1 - - - +
221C ASN* 3.5 22.7 + - - +
332C GLN* 5.6 1.1 - - - -
337C ILE* 5.4 8.3 - - + -
339C MET* 6.0 2.9 - - + +
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Residues in contact with SER 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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177C PHE* 3.7 21.4 - - - -
178C ASN 4.4 3.2 - - - +
179C GLN* 4.1 19.9 - - - +
180C SER* 4.5 2.2 - - - -
214C ASP* 3.0 37.8 + - - -
215C ILE* 3.6 4.1 + - - +
217C ALA* 1.3 77.0 - - - +
219C PHE* 1.3 61.4 + - - +
220C TYR 3.4 0.2 - - - -
221C ASN* 3.2 30.2 - - - +
222C SER* 3.7 6.2 + - - -
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Residues in contact with PHE 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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100C VAL* 4.5 21.3 - - + -
149C VAL* 4.9 5.6 - - + -
177C PHE* 3.7 33.2 - + - -
215C ILE* 2.8 26.4 + - + +
216C TYR* 4.3 5.4 - - - +
218C SER* 1.3 76.5 - - - +
220C TYR* 1.3 62.9 + - - +
222C SER* 3.4 17.1 + - - -
223C GLY 3.5 4.2 + - - -
224C LEU* 4.5 8.7 - - + +
225C LEU* 3.6 57.3 + - + -
228C PHE* 5.4 5.4 - - + -
236C ILE* 4.6 25.1 - - + -
325C LEU* 5.0 4.7 - - + -
328C VAL* 5.6 3.1 - - + -
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Residues in contact with TYR 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 TYR 3.8 15.5 + - - +
217C ALA* 4.3 4.9 - - - +
219C PHE* 1.3 79.7 - - - +
221C ASN* 1.3 63.1 + - - +
223C GLY* 3.2 14.5 + - - +
225C LEU* 3.8 28.0 - - + +
226C ASP* 4.0 17.7 - - - -
329C LYS* 6.6 0.2 - - - -
332C GLN* 4.5 14.6 - - + -
333C GLU* 3.9 37.7 + - + +
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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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38C GLU 5.7 0.2 - - - +
39C HIS* 5.2 12.4 + - - +
42C LYS* 3.9 25.2 - - - +
43C ASP* 5.4 2.2 - - - +
180C SER* 4.2 20.2 + - - +
217C ALA 3.5 10.8 + - - +
218C SER* 3.2 32.1 - - - +
219C PHE 3.2 0.2 - - - -
220C TYR* 1.3 80.1 - - - +
222C SER* 1.3 60.7 + - - +
223C GLY 3.4 0.3 + - - -
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Residues in contact with SER 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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177C PHE* 4.2 23.8 - - - +
218C SER 3.7 7.6 + - - -
219C PHE* 3.4 8.8 + - - -
221C ASN* 1.3 80.6 - - - +
223C GLY* 1.3 58.3 + - - +
224C LEU* 3.2 37.8 + - - +
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Residues in contact with GLY 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 PHE 3.5 2.4 + - - -
220C TYR* 3.2 17.2 + - - -
221C ASN 3.2 4.0 - - - -
222C SER* 1.3 78.1 + - - +
224C LEU* 1.3 56.6 + - - +
225C LEU* 2.9 13.3 + - - -
226C ASP* 3.2 17.1 + - - +
227C THR* 3.5 9.9 + - - -
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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