Contacts of the helix formed by residues 216 - 236 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D VAL* 4.7 6.7 - - + -
129D ILE* 4.2 4.8 - - + +
212D SER 3.1 10.2 + - - +
214D ILE 3.5 1.0 - - - -
215D SER* 1.3 80.0 - - - +
217D TYR* 1.3 78.7 + + - +
218D ILE 3.5 1.3 - - - -
219D PRO* 3.3 4.2 - - - +
220D LEU* 2.8 67.6 + - + +
299D PHE* 4.0 20.6 - + - -
300D THR* 5.2 2.2 - - - -
303D TRP* 3.7 16.2 - - + -
304D LEU* 3.9 23.1 - - + -
307D PHE* 3.3 57.4 - + + -
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Residues in contact with TYR 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D SER* 3.1 33.6 + - - +
213D ILE* 4.2 16.4 - - + +
216D PHE* 1.3 94.0 - + - +
218D ILE* 1.3 62.1 + - + +
220D LEU* 3.4 9.3 + - + +
221D LEU* 2.8 45.9 + - + +
304D LEU* 4.1 13.0 - - + -
307D PHE* 2.9 44.2 + - + +
308D LEU* 3.4 12.1 - - + +
311D ILE* 3.1 32.4 - - + +
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Residues in contact with ILE 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C ILE* 4.5 10.1 - - + -
222C ILE* 4.3 24.9 - - + -
406C D10 4.0 43.1 - - + -
213D ILE* 3.0 40.6 + - + +
214D ILE* 4.9 0.2 - - - -
217D TYR* 1.3 73.5 - - + +
219D PRO* 1.3 77.3 - - + +
220D LEU 3.1 0.2 + - - -
221D LEU* 3.2 12.1 + - + +
222D ILE* 3.1 39.2 + - + +
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Residues in contact with PRO 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406C D10 4.6 9.4 - - + -
129D ILE* 3.5 26.2 - - + +
130D GLU* 4.5 14.1 - - + -
133D CYS* 2.9 34.8 - - - -
214D ILE 3.8 17.7 - - - +
215D SER 3.5 18.4 - - - +
216D PHE 3.3 10.1 - - - +
218D ILE* 1.3 97.7 - - + +
220D LEU* 1.3 55.3 + - - +
222D ILE* 3.5 4.9 + - + -
223D MET* 3.0 14.2 + - - +
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Residues in contact with LEU 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ILE* 4.0 15.8 - - + +
216D PHE* 2.8 53.2 + - + +
217D TYR* 3.4 11.9 - - + +
219D PRO* 1.3 72.5 - - - +
221D LEU* 1.3 70.5 + - + +
223D MET* 3.1 16.2 + - + +
224D ILE* 3.0 37.5 + - + +
299D PHE* 4.8 2.2 - - + -
300D THR* 3.7 36.1 - - + +
304D LEU* 4.8 10.3 - - + -
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Residues in contact with LEU 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D TYR* 2.8 36.7 + - + +
218D ILE* 3.7 10.5 - - + +
220D LEU* 1.3 75.9 - - + +
222D ILE* 1.3 63.3 + - + +
224D ILE* 3.6 9.6 + - + +
225D PHE* 3.1 25.1 + - - +
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Residues in contact with ILE 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C ILE* 4.6 12.8 - - + -
406C D10 4.5 20.2 - - + -
133D CYS* 3.7 13.9 - - - -
137D ILE* 4.5 14.8 - - + -
218D ILE* 3.1 34.9 + - + +
219D PRO* 3.6 6.1 - - + +
221D LEU* 1.3 74.8 - - + +
223D MET* 1.3 69.1 + - - +
224D ILE 3.1 0.3 + - - -
225D PHE* 3.2 5.9 + - - +
226D VAL* 2.8 38.6 + - + +
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Residues in contact with MET 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ILE* 4.0 9.0 - - + -
132D LEU* 3.6 40.6 - - - +
133D CYS* 3.8 13.7 - - - +
136D ALA* 4.3 2.7 - - + +
219D PRO 3.0 15.3 + - - +
220D LEU* 3.6 15.0 - - + +
222D ILE* 1.3 80.3 - - - +
224D ILE* 1.3 68.3 + - + +
226D VAL* 3.8 4.6 - - - +
227D ALA* 2.8 32.9 + - + +
296D MET* 3.7 50.9 - - + +
299D PHE* 5.6 0.7 - - + -
300D THR* 4.0 10.8 - - - +
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Residues in contact with ILE 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D LEU* 3.0 46.1 + - + +
221D LEU* 4.0 8.7 - - + +
223D MET* 1.3 84.3 - - + +
225D PHE* 1.3 69.9 + - - +
226D VAL 3.1 0.2 + - - -
227D ALA* 3.2 4.3 + - - +
228D LEU* 2.8 45.0 + - + +
300D THR* 4.9 9.4 - - + +
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Residues in contact with PHE 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D LEU 3.1 16.5 + - - +
222D ILE* 3.8 4.7 - - - +
224D ILE* 1.3 82.9 - - - +
226D VAL* 1.3 72.4 + - + +
228D LEU* 3.6 7.9 + - + +
229D ARG* 3.3 67.1 + - + +
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Residues in contact with VAL 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ALA* 3.4 42.0 - - + +
137D ILE* 3.7 17.3 - - + +
140D TYR* 4.2 12.1 - - + -
222D ILE* 2.8 34.6 + - + +
223D MET* 3.9 2.5 - - - +
225D PHE* 1.3 84.7 - - + +
227D ALA* 1.3 65.2 + - - +
229D ARG* 3.1 9.3 + - - +
230D VAL* 3.0 20.8 + - - +
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Residues in contact with ALA 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ALA* 4.7 1.1 - - + -
223D MET* 2.8 25.2 + - + +
224D ILE* 3.8 4.9 - - - +
226D VAL* 1.3 74.3 - - - +
228D LEU* 1.3 60.0 + - + +
230D VAL* 3.4 4.5 + - - +
231D TYR* 3.0 27.9 + - - +
296D MET* 4.2 10.5 - - + -
405D SOG 3.9 35.2 - - + +
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Residues in contact with LEU 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D ILE* 2.8 36.7 + - + +
225D PHE* 3.8 8.1 - - + +
227D ALA* 1.3 78.5 - - + +
229D ARG* 1.3 67.4 + - - +
231D TYR* 3.4 14.0 + - + +
232D ARG* 3.1 32.0 + - + +
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Residues in contact with ARG 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D TYR* 4.1 22.9 - - + -
225D PHE* 3.3 53.1 + - + +
226D VAL* 3.1 10.2 + - - +
228D LEU* 1.3 77.3 - - - +
230D VAL* 1.3 57.9 + - - +
232D ARG* 3.0 18.5 + - - +
233D GLU* 2.8 33.5 + - + +
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Residues in contact with VAL 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ALA 3.9 7.4 - - - +
139D ARG* 4.7 9.9 - - + -
140D TYR* 3.2 43.7 - - + +
143D ILE* 4.8 7.1 - - + +
226D VAL* 3.0 17.0 + - + +
227D ALA* 3.6 8.7 - - - +
228D LEU 3.3 0.2 - - - -
229D ARG* 1.3 74.3 - - - +
231D TYR* 1.3 57.6 + - - +
233D GLU* 3.3 7.7 + - - +
234D ALA* 2.8 28.4 + - - +
289D LEU* 4.3 16.4 - - + -
405D SOG 3.8 27.4 - - + -
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Residues in contact with TYR 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D ALA 3.0 14.5 + - - +
228D LEU* 3.5 18.8 - - + +
230D VAL* 1.3 73.6 - - - +
232D ARG* 1.3 96.2 + - - +
234D ALA* 3.3 2.6 + - - +
235D LYS* 2.9 31.4 + - + +
405D SOG 3.5 80.3 + - + +
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Residues in contact with ARG 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D LEU* 3.1 18.6 + - - +
229D ARG* 3.0 22.0 + - - +
231D TYR* 1.3 97.8 - - - +
233D GLU* 1.3 58.9 + - + +
235D LYS* 2.9 21.1 + - - +
236D GLU* 2.9 47.0 + - + +
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Residues in contact with GLU 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D TYR* 4.6 8.9 + - + -
143D ILE* 4.0 20.9 - - + +
144D THR* 3.4 30.0 - - + +
229D ARG* 2.8 19.7 + - + +
230D VAL* 3.6 6.3 - - - +
232D ARG* 1.3 78.6 - - + +
234D ALA* 1.3 57.9 + - - +
235D LYS 3.4 0.2 + - - -
236D GLU* 5.6 2.8 - - - +
237D GLN* 2.8 33.3 + - - +
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Residues in contact with ALA 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ILE* 4.5 3.5 - - + +
230D VAL 2.8 20.4 + - - +
231D TYR* 3.9 5.6 - - - +
233D GLU* 1.3 72.7 - - - +
235D LYS* 1.3 62.8 + - - +
237D GLN* 4.0 7.6 - - - -
238D ILE* 3.3 6.1 + - - +
286D HIS* 2.6 45.3 + - + +
289D LEU* 3.9 22.7 - - + -
405D SOG 5.1 10.5 - - + -
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Residues in contact with LYS 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D TYR* 2.9 20.0 + - + +
232D ARG* 2.9 28.6 + - - +
234D ALA* 1.3 73.5 - - - +
236D GLU* 1.3 84.8 + - - +
237D GLN 2.5 16.2 + - - -
238D ILE* 3.0 22.2 + - + +
405D SOG 3.2 31.6 + - - +
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Residues in contact with GLU 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D ARG* 2.9 26.3 + - + +
233D GLU* 4.4 3.8 - - - +
235D LYS* 1.3 111.7 + - - +
237D GLN* 1.3 57.8 + - - +
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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