Contacts of the helix formed by residues 212 - 222 (chain C) in PDB entry 2VF7
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 212 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210C GLU 4.2 3.1 - - - +
211C LEU* 1.4 96.4 - - + +
213C GLU* 1.3 65.7 + - - +
214C GLU* 4.2 9.9 - - + +
215C THR* 3.2 21.3 + - - +
216C ARG* 3.2 18.9 + - - +
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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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165C GLU* 4.1 12.5 - - - +
211C LEU 3.6 1.2 + - - -
212C PRO* 1.3 72.3 - - - +
214C GLU* 1.3 57.5 + - - +
216C ARG* 2.8 39.3 + - - +
217C HIS* 3.0 36.1 + - + +
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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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212C PRO* 4.2 8.5 - - + +
213C GLU* 1.3 78.3 - - - +
215C THR* 1.3 63.8 + - - +
217C HIS* 4.0 8.0 + - - +
218C TRP* 3.2 29.0 + - + +
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Residues in contact with THR 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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202C ILE* 4.0 29.2 - - + -
211C LEU* 4.6 15.5 - - + -
212C PRO* 3.2 32.0 + - - +
214C GLU* 1.3 79.3 - - - +
216C ARG* 1.3 62.0 + - - +
218C TRP* 3.5 6.4 + - + +
219C ILE* 3.2 41.1 + - + +
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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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165C GLU* 3.3 24.2 + - - +
172C PRO* 5.8 1.0 - - - +
208C TRP* 3.2 57.0 - - + +
209C ARG* 4.0 23.6 + - - +
211C LEU* 3.2 31.2 + - + -
212C PRO 3.2 11.3 + - - +
213C GLU* 2.8 42.6 + - - +
215C THR* 1.3 73.9 - - - +
217C HIS* 1.3 65.1 + - - +
219C ILE 3.7 0.5 + - - -
220C LEU* 3.2 32.0 + - + +
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Residues in contact with HIS 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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165C GLU* 6.1 0.2 - - - -
213C GLU* 3.0 20.4 + - + +
214C GLU* 4.0 9.3 + - - +
216C ARG* 1.3 76.0 - - - +
218C TRP* 1.3 59.1 + - - +
220C LEU* 5.1 0.2 - - - -
221C PHE* 2.9 68.0 + + + +
222C THR* 4.0 9.0 + - + +
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Residues in contact with TRP 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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197C LEU* 4.3 5.6 - - + -
200C LEU* 3.8 26.9 - - + -
202C ILE* 4.7 8.7 - - + -
214C GLU* 3.2 20.7 + - + +
215C THR* 3.5 7.4 - - + +
216C ARG 3.3 0.2 - - - -
217C HIS* 1.3 76.8 + - - +
219C ILE* 1.3 84.8 + - + +
220C LEU 3.3 0.7 + - - -
222C THR* 2.8 61.5 + - + +
224C GLU* 3.5 35.1 + - + -
226C PRO* 4.5 11.0 - - + -
255C PHE* 3.6 35.9 - + - -
257C SER* 4.3 1.2 - - - -
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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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176C ILE* 4.4 2.5 - - + -
181C VAL* 4.6 5.2 - - + -
184C TRP* 3.8 27.8 - - + -
197C LEU* 3.9 35.2 - - + -
202C ILE* 4.3 8.5 - - + -
208C TRP* 4.0 34.3 - - + -
215C THR* 3.2 36.4 + - + +
217C HIS 3.6 0.2 - - - -
218C TRP* 1.3 90.1 - - + +
220C LEU* 1.3 61.8 + - + +
255C PHE* 4.2 4.4 - - + -
257C SER* 3.3 8.3 - - - -
258C ALA 3.1 20.4 + - - -
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Residues in contact with LEU 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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165C GLU* 3.7 44.2 - - + +
168C MET* 3.8 16.2 - - + +
169C VAL* 4.1 14.1 - - + -
181C VAL* 4.6 3.4 - - + -
208C TRP* 3.7 26.9 - - + -
216C ARG 3.2 18.6 + - - +
217C HIS 5.0 0.2 - - - +
218C TRP 3.2 0.8 - - - -
219C ILE* 1.3 83.1 - - + +
221C PHE* 1.3 82.2 + - + +
222C THR 3.9 0.2 - - - -
257C SER* 3.8 1.5 - - - -
258C ALA* 3.6 16.2 + - + -
259C ARG* 2.9 32.6 + - - +
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Residues in contact with PHE 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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163C VAL* 3.6 22.0 - - + -
164C THR* 4.1 22.4 - - - -
165C GLU* 4.2 7.0 - - + -
168C MET* 3.7 11.9 - - + -
217C HIS* 2.9 50.1 + + + +
220C LEU* 1.3 100.1 - - + +
222C THR* 1.3 67.3 + - - +
223C ASP* 3.6 1.9 + - - +
257C SER* 4.0 2.5 - - - -
259C ARG* 3.3 36.0 + - + +
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Residues in contact with THR 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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217C HIS* 4.3 11.4 - - + +
218C TRP* 2.8 68.4 + - + +
220C LEU 3.9 0.4 - - - -
221C PHE* 1.3 75.7 - - - +
223C ASP* 1.3 59.4 + - - +
224C GLU* 3.2 19.5 + - - +
255C PHE* 4.5 1.9 - - - -
257C SER* 2.9 28.1 + - - -
260C ARG* 4.6 1.4 + - - -
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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