Contacts of the helix formed by residues 216 - 236 (chain C) in PDB entry 2VT4
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 PHE 216 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125C VAL* 5.1 2.0 - - + -
129C ILE* 4.4 7.9 - - + +
212C SER 2.9 11.3 + - - +
214C ILE 3.5 0.8 - - - -
215C SER* 1.3 80.6 - - - +
217C TYR* 1.3 71.8 + + - +
219C PRO* 3.2 6.1 - - - +
220C LEU* 2.8 53.0 + - + +
299C PHE* 3.8 30.1 - + - -
300C THR* 5.1 2.5 - - - -
303C TRP* 3.9 5.2 - - + -
304C LEU* 3.6 43.1 - - + -
307C PHE* 3.4 60.6 - + + -
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Residues in contact with TYR 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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212C SER* 3.0 44.5 + - - -
213C ILE* 3.2 21.0 + - + -
216C PHE* 1.3 80.6 - + - +
218C ILE* 1.3 58.6 + - - +
220C LEU* 2.9 10.5 + - + +
221C LEU* 2.8 47.6 + - + +
304C LEU* 4.3 13.4 - - + +
307C PHE* 2.9 38.8 + - + +
308C LEU* 3.5 15.5 + - + +
311C ILE* 3.1 30.3 - - + +
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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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213C ILE* 2.9 37.4 + - + +
214C ILE* 4.5 5.6 - - + -
217C TYR* 1.3 71.7 - - + +
219C PRO* 1.3 73.2 - - + +
220C LEU 3.0 1.2 + - - -
221C LEU* 3.8 9.0 - - + +
222C ILE* 3.0 40.3 + - + +
406C D10 3.5 54.3 - - + -
218D ILE* 4.5 14.6 - - + -
222D ILE* 4.6 12.3 - - + -
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Residues in contact with PRO 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C THR* 6.2 0.2 - - + -
129C ILE* 3.7 30.6 - - + +
130C GLU* 4.7 12.6 - - + +
133C CYS* 3.3 19.9 - - - -
214C ILE 3.8 16.8 - - - +
215C SER 3.8 16.6 - - - +
216C PHE 3.2 12.8 - - - +
218C ILE* 1.3 99.9 - - + +
220C LEU* 1.3 55.4 + - - +
222C ILE* 4.1 3.4 - - + -
223C MET* 3.1 23.0 + - - +
406C D10 4.7 7.4 - - + -
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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
----------------------------------------------------------
129C ILE* 4.1 13.9 - - + -
216C PHE* 2.8 44.8 + - + +
217C TYR* 2.9 10.3 + - + +
219C PRO* 1.3 76.4 - - - +
221C LEU* 1.3 80.8 + - + +
223C MET* 3.2 25.4 + - + +
224C ILE* 2.9 38.9 + - + +
299C PHE* 5.3 0.4 - - + -
300C THR* 3.9 24.7 - - + +
304C LEU* 4.7 9.6 - - + -
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Residues in contact with LEU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C TYR* 2.8 31.8 + - + +
218C ILE* 3.8 7.2 - - + +
220C LEU* 1.3 82.3 - - + +
222C ILE* 1.3 65.9 + - + +
224C ILE* 2.8 23.9 + - + +
225C PHE* 3.0 15.4 + - - +
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Residues in contact with ILE 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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133C CYS* 3.5 20.6 - - - -
137C ILE* 4.4 13.5 - - + -
218C ILE* 3.0 34.2 + - + +
219C PRO* 4.8 2.7 - - + -
221C LEU* 1.3 78.3 - - + +
223C MET* 1.3 63.9 + - - +
225C PHE* 3.4 4.7 + - - +
226C VAL* 3.0 38.2 + - + +
218D ILE* 4.3 22.7 - - + -
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Residues in contact with MET 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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129C ILE* 3.9 10.3 - - + -
132C LEU* 3.7 37.0 - - + +
133C CYS* 4.0 15.0 - - - +
136C ALA* 4.4 3.9 - - + +
219C PRO 3.1 17.4 + - - +
220C LEU* 3.2 20.2 + - + +
222C ILE* 1.3 81.6 - - - +
224C ILE* 1.3 66.0 + - + +
226C VAL* 4.4 3.3 - - - +
227C ALA* 2.9 31.9 + - + +
296C MET* 3.7 37.5 - - + +
299C PHE* 5.4 0.4 - - + -
300C THR* 3.8 22.4 - - - +
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Residues in contact with ILE 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 LEU* 2.9 45.3 + - + +
221C LEU* 2.8 22.1 + - + +
223C MET* 1.3 82.8 - - + +
225C PHE* 1.3 63.0 + - + +
227C ALA* 3.6 4.2 - - - +
228C LEU* 3.0 44.6 + - + +
300C THR* 4.7 10.1 - - + +
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Residues in contact with PHE 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 LEU 3.0 10.7 + - - +
222C ILE* 3.7 9.4 - - - +
224C ILE* 1.3 75.0 - - + +
226C VAL* 1.3 94.8 + - + +
228C LEU* 2.7 24.4 + - - +
229C ARG* 3.1 48.4 + - + +
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Residues in contact with VAL 226 (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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136C ALA* 3.8 9.6 - - + +
137C ILE* 3.7 49.6 - - + +
140C TYR* 3.8 15.7 - - + -
222C ILE* 3.0 26.8 + - + +
223C MET* 4.4 2.2 - - - +
225C PHE* 1.3 93.3 - - + +
227C ALA* 1.3 61.1 + - - +
229C ARG* 3.3 8.3 + - - +
230C VAL* 3.1 21.7 + - - +
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Residues in contact with ALA 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ALA* 4.5 2.2 - - + +
223C MET* 2.9 22.8 + - + +
224C ILE* 3.6 5.6 - - - +
225C PHE 2.8 0.6 + - - -
226C VAL* 1.3 75.5 - - - +
228C LEU* 1.3 66.3 + - + +
230C VAL* 3.2 13.9 + - - +
231C TYR* 3.2 11.3 + - - +
296C MET* 4.3 10.8 - - - -
405C SOG 3.8 34.2 - - + +
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Residues in contact with LEU 228 (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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224C ILE* 3.0 35.6 + - + +
225C PHE* 2.7 16.6 + - - +
227C ALA* 1.3 71.3 - - + +
229C ARG* 1.3 63.6 + - + +
231C TYR* 2.9 22.2 + - + +
232C ARG* 3.2 33.5 + - - +
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Residues in contact with ARG 229 (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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140C TYR* 3.9 26.2 - - + -
225C PHE* 3.1 52.1 + - + +
226C VAL* 3.4 9.6 - - - +
228C LEU* 1.3 77.6 - - + +
230C VAL* 1.3 63.4 + - - +
232C ARG* 3.0 35.6 + - - +
233C GLU* 2.9 25.4 + - + +
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Residues in contact with VAL 230 (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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136C ALA 4.0 7.0 - - - +
139C ARG* 4.5 9.4 - - + -
140C TYR* 3.4 37.9 - - + +
143C ILE* 4.2 9.8 - - + +
226C VAL 3.1 15.9 + - - +
227C ALA* 3.2 8.0 + - - +
229C ARG* 1.3 75.3 - - - +
231C TYR* 1.3 57.5 + - - +
233C GLU* 3.5 7.2 + - - +
234C ALA* 2.9 26.7 + - - +
289C LEU* 4.1 23.1 - - + -
405C SOG 3.8 23.1 - - + -
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Residues in contact with TYR 231 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227C ALA 3.2 9.6 + - - +
228C LEU* 2.9 19.6 + - + +
230C VAL* 1.3 76.2 - - - +
232C ARG* 1.3 72.4 + - + +
234C ALA* 3.2 6.5 + - + +
235C LYS* 3.0 65.6 + - + +
405C SOG 3.3 67.6 - - + +
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Residues in contact with ARG 232 (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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228C LEU* 3.2 27.3 + - - +
229C ARG* 3.0 39.5 + - - +
231C TYR* 1.3 81.9 - - + +
233C GLU* 1.3 58.8 + - + +
235C LYS* 3.0 11.5 + - + +
236C GLU* 2.8 45.2 + - + +
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Residues in contact with GLU 233 (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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140C TYR* 4.6 8.6 + - + -
143C ILE* 3.8 29.9 - - + +
144C THR* 4.1 18.5 - - + +
229C ARG* 2.9 14.3 + - + +
230C VAL* 3.7 8.1 - - - +
232C ARG* 1.3 78.0 - - + +
234C ALA* 1.3 61.4 + - - +
236C GLU* 3.2 27.3 + - - +
237C GLN* 3.2 32.1 + - + +
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Residues in contact with ALA 234 (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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143C ILE* 4.3 14.1 - - + +
230C VAL 2.9 18.0 + - - +
231C TYR* 3.2 10.3 + - + +
233C GLU* 1.3 76.7 - - - +
235C LYS* 1.3 59.1 + - - +
237C GLN* 3.3 14.9 + - - +
238C ILE* 3.4 4.0 + - - +
286C HIS* 3.2 40.8 - - + +
289C LEU* 4.5 10.5 - - + -
405C SOG 4.4 10.1 - - + +
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Residues in contact with LYS 235 (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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231C TYR* 3.0 56.7 + - + +
232C ARG* 3.3 11.7 - - + +
234C ALA* 1.3 73.5 - - - +
236C GLU* 1.3 58.6 + - + +
237C GLN 2.8 10.8 + - - -
238C ILE* 2.9 33.1 + - + +
405C SOG 5.0 12.6 - - - +
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Residues in contact with GLU 236 (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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232C ARG* 2.8 35.1 + - + +
233C GLU* 3.2 31.5 + - - +
235C LYS* 1.3 70.7 - - + +
237C GLN* 1.3 59.0 + - - +
238C ILE 5.2 0.4 - - - -
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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