Contacts of the helix formed by residues 216 - 236 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B VAL* 5.1 2.2 - - + -
129B ILE* 4.4 7.6 - - + +
212B SER 2.9 11.3 + - - +
214B ILE 3.5 0.8 - - - -
215B SER* 1.3 81.0 - - - +
217B TYR* 1.3 71.9 + + - +
219B PRO* 3.3 5.4 - - - +
220B LEU* 2.9 51.9 + - + +
299B PHE* 3.8 29.8 - + - -
300B THR* 5.1 2.7 - - + -
303B TRP* 3.9 5.4 - - + -
304B LEU* 3.6 43.5 - - + -
307B PHE* 3.3 61.5 - + + -
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Residues in contact with TYR 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B SER* 3.0 43.9 + - - -
213B ILE* 3.2 21.0 + - + -
216B PHE* 1.3 79.9 - + - +
218B ILE* 1.3 58.5 + - - +
220B LEU* 2.9 11.0 + - + +
221B LEU* 2.8 47.2 + - + +
304B LEU* 4.3 13.4 - - + +
307B PHE* 2.9 39.2 + - + +
308B LEU* 3.5 15.3 + - + +
311B ILE* 3.1 30.8 - - + +
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Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ILE* 4.2 12.6 - - + -
222A ILE* 4.3 24.7 - - + -
406A D10 4.0 41.3 - - + -
213B ILE* 2.9 37.4 + - + +
214B ILE* 4.5 5.2 - - + -
217B TYR* 1.3 72.5 - - + +
219B PRO* 1.3 74.2 - - + +
220B LEU 3.0 1.2 + - - -
221B LEU* 3.3 9.6 + - + +
222B ILE* 3.0 40.5 + - + +
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Residues in contact with PRO 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A D10 4.7 14.6 - - + -
129B ILE* 3.8 30.6 - - + +
130B GLU* 4.7 9.0 - - + +
133B CYS* 3.3 19.6 - - - -
214B ILE 3.8 16.8 - - - +
215B SER 3.8 16.2 - - - +
216B PHE 3.3 12.8 - - - +
218B ILE* 1.3 100.1 - - + +
220B LEU* 1.3 55.5 + - - +
222B ILE* 4.1 2.7 - - + -
223B MET* 3.2 22.7 + - - +
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Residues in contact with LEU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ILE* 4.1 13.7 - - + -
216B PHE* 2.9 45.0 + - + +
217B TYR* 2.9 10.5 + - + +
219B PRO* 1.3 76.3 - - - +
221B LEU* 1.3 80.3 + - + +
223B MET* 3.2 24.8 + - + +
224B ILE* 2.9 38.4 + - + +
299B PHE* 5.3 0.4 - - + -
300B THR* 3.9 25.6 - - + +
304B LEU* 4.7 9.9 - - + -
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B TYR* 2.8 31.8 + - + +
218B ILE* 3.8 7.2 - - + +
220B LEU* 1.3 83.2 - - + +
222B ILE* 1.3 65.9 + - + +
224B ILE* 2.8 23.8 + - + +
225B PHE* 3.0 14.8 + - - +
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Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ILE* 4.2 24.0 - - + -
221A LEU* 6.5 0.7 - - + -
406A D10 4.8 11.7 - - + -
133B CYS* 3.5 19.7 - - - -
137B ILE* 4.4 13.2 - - + -
218B ILE* 3.0 34.4 + - + +
219B PRO* 4.8 0.4 - - + -
221B LEU* 1.3 78.3 - - + +
223B MET* 1.3 64.5 + - - +
225B PHE* 3.4 5.0 + - - +
226B VAL* 3.0 37.4 + - + +
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Residues in contact with MET 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ILE* 3.9 10.3 - - + -
132B LEU* 3.7 36.1 - - + +
133B CYS* 4.0 14.6 - - - +
136B ALA* 4.4 4.3 - - + +
219B PRO 3.2 16.9 + - - +
220B LEU* 3.2 20.4 + - + +
222B ILE* 1.3 81.2 - - - +
224B ILE* 1.3 65.9 + - + +
226B VAL* 4.4 3.3 - - - +
227B ALA* 2.9 32.0 + - + +
296B MET* 3.7 38.1 - - + +
299B PHE* 5.4 0.4 - - + -
300B THR* 3.8 22.0 - - - +
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Residues in contact with ILE 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B LEU* 2.9 45.3 + - + +
221B LEU* 2.8 21.8 + - + +
223B MET* 1.3 83.0 - - + +
225B PHE* 1.3 62.7 + - + +
227B ALA* 3.6 4.0 - - - +
228B LEU* 3.0 44.6 + - + +
300B THR* 4.7 10.3 - - + +
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Residues in contact with PHE 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B LEU 3.0 10.5 + - - +
222B ILE* 3.7 9.2 - - - +
224B ILE* 1.3 76.0 - - + +
226B VAL* 1.3 95.1 + - + +
228B LEU* 2.8 24.0 + - - +
229B ARG* 3.1 48.3 + - + +
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Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ALA* 3.8 9.9 - - + +
137B ILE* 3.7 50.3 - - + +
140B TYR* 3.8 15.2 - - + -
222B ILE* 3.0 26.4 + - + +
223B MET* 4.4 1.8 - - - +
225B PHE* 1.3 92.6 - - + +
227B ALA* 1.3 61.9 + - - +
229B ARG* 3.3 8.1 + - - +
230B VAL* 3.1 21.7 + - - +
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Residues in contact with ALA 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ALA* 4.5 3.8 - - + +
223B MET* 2.9 21.9 + - + +
224B ILE* 3.6 5.8 - - - +
225B PHE 3.0 0.6 - - - -
226B VAL* 1.3 75.5 - - - +
228B LEU* 1.3 66.5 + - + +
230B VAL* 3.2 15.3 + - - +
231B TYR* 3.2 10.0 + - - +
296B MET* 4.3 12.6 - - - -
405B SOG 3.6 31.1 - - + +
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B ILE* 3.0 36.1 + - + +
225B PHE* 2.8 16.8 + - - +
227B ALA* 1.3 71.0 - - + +
229B ARG* 1.3 63.0 + - + +
231B TYR* 2.9 21.9 + - + +
232B ARG* 3.2 33.7 + - - +
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Residues in contact with ARG 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B TYR* 3.9 26.7 - - + -
225B PHE* 3.1 52.3 + - + +
226B VAL* 3.4 9.4 - - - +
227B ALA 3.2 0.2 - - - -
228B LEU* 1.3 77.6 - - + +
230B VAL* 1.3 63.3 + - - +
232B ARG* 3.0 34.7 + - - +
233B GLU* 2.9 25.2 + - + +
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Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ALA 4.0 7.2 - - - +
139B ARG* 4.5 11.7 - - + -
140B TYR* 3.4 37.9 - - + +
143B ILE* 4.2 9.5 - - + +
226B VAL 3.1 15.9 + - - +
227B ALA* 3.2 10.3 + - - +
229B ARG* 1.3 74.6 - - - +
231B TYR* 1.3 57.7 + - - +
233B GLU* 3.5 7.6 + - - +
234B ALA* 2.9 26.7 + - - +
289B LEU* 4.1 23.1 - - + -
405B SOG 4.0 19.3 - - + -
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Residues in contact with TYR 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B ALA 3.2 10.0 + - - +
228B LEU* 2.9 19.3 + - + +
230B VAL* 1.3 75.5 - - - +
232B ARG* 1.3 71.2 + - + +
234B ALA* 3.2 5.4 + - + +
235B LYS* 3.0 52.9 + - + +
405B SOG 2.5 86.6 + - + +
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Residues in contact with ARG 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B LEU* 3.2 28.1 + - - +
229B ARG* 3.0 39.9 + - - +
231B TYR* 1.3 83.4 - - + +
233B GLU* 1.3 57.9 + - + +
235B LYS* 3.1 12.0 + - + +
236B GLU* 2.8 45.2 + - + +
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Residues in contact with GLU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B TYR* 4.6 8.6 - - + -
143B ILE* 3.8 29.7 - - + +
144B THR* 4.1 18.9 - - + +
229B ARG* 2.9 14.4 + - + +
230B VAL 3.7 7.6 - - - +
232B ARG* 1.3 78.4 - - + +
234B ALA* 1.3 61.6 + - - +
236B GLU* 3.3 27.3 + - - +
237B GLN* 3.2 32.1 + - + +
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ILE* 4.3 14.1 - - + +
230B VAL* 2.9 18.5 + - + +
231B TYR* 3.2 8.5 + - + +
233B GLU* 1.3 76.3 - - - +
235B LYS* 1.3 59.4 + - + +
237B GLN* 3.3 14.6 + - - +
238B ILE* 3.4 4.2 + - - +
286B HIS* 3.2 40.6 - - + +
289B LEU* 4.5 10.8 - - + -
405B SOG 5.1 9.6 - - + -
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Residues in contact with LYS 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B TYR* 3.0 43.4 + - + +
232B ARG* 3.3 11.9 - - + +
234B ALA* 1.3 73.8 - - + +
236B GLU* 1.3 57.9 + - + +
237B GLN 2.8 10.4 + - - -
238B ILE* 2.9 33.0 + - + +
405B SOG 2.8 32.5 + - - +
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Residues in contact with GLU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B ARG* 2.8 35.1 + - + +
233B GLU* 3.3 31.8 + - - +
235B LYS* 1.3 70.9 - - + +
237B GLN* 1.3 59.0 + - - +
238B ILE 5.2 0.7 - - - -
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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