Contacts of the helix formed by residues 216 - 236 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A VAL* 4.7 6.3 - - + -
129A ILE* 4.2 4.6 - - + +
212A SER 3.1 9.8 + - - +
214A ILE 3.5 1.0 - - - -
215A SER* 1.3 80.5 - - - +
217A TYR* 1.3 83.7 - + - +
218A ILE 3.5 1.3 - - - -
219A PRO* 3.3 4.5 - - - +
220A LEU* 2.8 63.6 + - + +
299A PHE* 4.0 21.1 - + - -
300A THR* 5.2 2.0 - - - -
303A TRP* 3.7 16.2 - - + -
304A LEU* 3.9 23.3 - - + -
307A PHE* 3.3 58.3 - + + -
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Residues in contact with TYR 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A SER* 3.1 34.2 + - - +
213A ILE* 4.2 16.2 - - + +
216A PHE* 1.3 93.6 - + - +
218A ILE* 1.3 63.1 + - + +
220A LEU* 3.3 8.7 + - + +
221A LEU* 2.8 46.2 + - + +
304A LEU* 4.1 12.8 - - + -
307A PHE* 2.9 43.9 + - + +
308A LEU* 3.4 11.3 - - + +
311A ILE* 3.1 32.7 - - + +
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Residues in contact with ILE 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ILE* 3.0 42.4 + - + +
217A TYR* 1.3 74.5 - - + +
219A PRO* 1.3 75.0 - - + +
220A LEU 3.1 0.2 + - - -
221A LEU* 3.2 11.1 + - + +
222A ILE* 3.1 39.1 + - + +
406A D10 3.7 43.5 - - + -
218B ILE* 4.2 16.8 - - + -
222B ILE* 4.2 23.1 - - + -
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Residues in contact with PRO 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ILE* 3.6 25.4 - - + +
130A GLU* 4.5 14.8 - - + +
133A CYS* 2.9 34.7 - - - -
214A ILE 3.8 17.9 - - - +
215A SER 3.6 18.4 - - - +
216A PHE 3.3 9.9 - - - +
218A ILE* 1.3 97.4 - - + +
220A LEU* 1.3 54.9 + - - +
222A ILE* 3.4 4.9 + - + -
223A MET* 3.0 14.7 + - - +
406A D10 5.3 5.4 - - + -
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Residues in contact with LEU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ILE* 4.0 15.0 - - + +
216A PHE* 2.8 52.6 + - + +
217A TYR* 3.5 12.8 - - + +
218A ILE 3.1 0.2 - - - -
219A PRO* 1.3 73.6 - - - +
221A LEU* 1.3 69.6 + - + +
223A MET* 3.2 16.9 + - + +
224A ILE* 3.0 37.5 + - + +
299A PHE* 4.8 2.2 - - + -
300A THR* 3.6 35.4 - - + +
304A LEU* 4.8 10.5 - - + -
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Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A TYR* 2.8 37.4 + - + +
218A ILE* 3.7 11.7 - - + +
220A LEU* 1.3 75.9 - - + +
222A ILE* 1.3 62.9 + - + +
224A ILE* 3.6 9.6 + - + +
225A PHE* 3.1 25.3 + - - +
222B ILE* 6.5 0.7 - - + -
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Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A CYS* 3.7 15.0 - - - +
137A ILE* 4.5 14.1 - - + -
218A ILE* 3.1 34.9 + - + +
219A PRO* 3.6 9.0 - - + +
221A LEU* 1.3 74.1 - - + +
223A MET* 1.3 68.5 + - - +
224A ILE 3.1 0.3 + - - -
225A PHE* 3.2 5.5 + - - +
226A VAL* 2.8 38.6 + - + +
218B ILE* 4.3 21.1 - - + -
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Residues in contact with MET 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ILE* 3.9 9.6 - - + -
132A LEU* 3.6 40.8 - - + +
133A CYS* 3.8 13.2 - - - +
136A ALA* 4.3 2.9 - - + +
219A PRO 3.0 14.9 + - - +
220A LEU* 3.6 15.9 - - + +
222A ILE* 1.3 80.4 - - - +
224A ILE* 1.3 66.7 + - + +
226A VAL* 3.8 4.9 - - - +
227A ALA* 2.8 32.0 + - + +
296A MET* 3.8 50.7 - - + +
299A PHE* 5.5 0.7 - - + -
300A THR* 4.0 10.5 - - - +
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Residues in contact with ILE 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A LEU* 3.0 46.5 + - + +
221A LEU* 4.0 8.7 - - + +
223A MET* 1.3 84.8 - - + +
225A PHE* 1.3 70.0 + - - +
226A VAL 3.1 0.2 + - - -
227A ALA* 3.2 3.7 + - + +
228A LEU* 2.8 45.4 + - + +
300A THR* 4.9 9.9 - - + +
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Residues in contact with PHE 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A LEU 3.1 17.2 + - - +
222A ILE* 3.8 4.3 - - - +
224A ILE* 1.3 80.9 - - - +
226A VAL* 1.3 72.1 + - + +
228A LEU* 3.6 7.9 + - + +
229A ARG* 3.2 46.5 + - + +
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Residues in contact with VAL 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ALA* 3.5 40.8 - - + +
137A ILE* 3.7 18.6 - - + +
140A TYR* 4.2 12.3 - - + -
222A ILE* 2.8 34.4 + - + +
223A MET* 3.9 3.1 - - - +
225A PHE* 1.3 83.8 - - + +
227A ALA* 1.3 64.5 + - - +
229A ARG* 3.1 10.8 + - + +
230A VAL* 3.0 20.3 + - + +
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Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A MET* 2.8 25.0 + - + +
224A ILE* 3.8 4.7 - - - +
226A VAL* 1.3 74.0 - - - +
228A LEU* 1.3 59.9 + - + +
230A VAL* 3.3 0.8 + - - -
231A TYR* 3.0 25.3 + - - +
296A MET* 4.2 10.3 - - + -
405A SOG 3.4 45.1 - - + +
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ILE* 2.8 37.1 + - + +
225A PHE* 3.8 7.9 - - + +
227A ALA* 1.3 81.2 - - + +
229A ARG* 1.3 57.7 + - - +
231A TYR* 3.4 15.2 + - + +
232A ARG* 3.0 28.1 + - - +
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Residues in contact with ARG 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A TYR* 4.1 25.2 + - + -
225A PHE* 3.2 41.2 + - + +
226A VAL* 3.1 12.3 + - + +
228A LEU* 1.3 79.5 - - - +
230A VAL* 1.3 56.3 + - - +
232A ARG* 3.4 35.1 + - - +
233A GLU* 3.1 41.5 + - - +
236A GLU* 5.5 1.2 + - - -
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Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ALA 3.9 7.4 - - - +
139A ARG* 4.7 8.3 - - + -
140A TYR* 3.2 43.5 - - + +
143A ILE* 4.8 7.3 - - + +
226A VAL* 3.0 16.0 + - + +
227A ALA* 3.6 8.7 - - - +
228A LEU 3.3 0.4 - - - -
229A ARG* 1.3 72.6 - - - +
231A TYR* 1.3 61.7 + - - +
233A GLU* 3.3 6.2 + - - +
234A ALA* 2.8 28.8 + - - +
289A LEU* 4.3 17.7 - - + -
405A SOG 3.9 27.1 - - + -
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Residues in contact with TYR 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ALA 3.0 14.5 + - - +
228A LEU* 3.5 20.4 - - + +
230A VAL* 1.3 76.0 - - - +
232A ARG* 1.3 61.6 + - + +
234A ALA* 3.3 5.4 + - - +
235A LYS* 2.9 53.0 + - + +
405A SOG 3.4 64.0 + - + +
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Residues in contact with ARG 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LEU 3.0 13.1 + - - +
229A ARG* 3.5 40.8 - - - +
231A TYR* 1.3 80.8 - - + +
233A GLU* 1.3 58.5 + - + +
235A LYS* 4.0 18.1 - - - +
236A GLU* 2.8 66.7 + - - +
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Residues in contact with GLU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A TYR* 4.6 7.8 + - + -
143A ILE* 4.0 20.8 - - + +
144A THR* 3.4 30.5 - - + +
229A ARG* 3.1 29.3 + - - +
230A VAL* 3.6 6.1 - - - +
231A TYR 3.1 0.2 - - - -
232A ARG* 1.3 76.3 - - - +
234A ALA* 1.3 60.4 + - - +
235A LYS 3.1 1.7 + - - -
236A GLU* 3.6 19.2 - - - +
237A GLN* 2.8 33.7 + - - +
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Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ILE* 4.5 3.5 - - + +
230A VAL 2.8 20.5 + - - +
231A TYR 4.0 1.8 - - - +
233A GLU* 1.3 72.7 - - - +
235A LYS* 1.3 61.8 + - - +
237A GLN* 3.6 8.5 - - - +
238A ILE* 3.4 6.6 + - - +
286A HIS* 2.6 37.9 - - + +
289A LEU* 3.9 22.9 - - + -
405A SOG 3.2 21.8 - - - +
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Residues in contact with LYS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A TYR* 2.9 39.4 + - + +
232A ARG* 4.0 19.7 - - - +
234A ALA* 1.3 74.0 - - - +
236A GLU* 1.3 56.8 + - - +
237A GLN 2.5 16.3 + - - -
238A ILE* 2.8 38.9 + - + +
405A SOG 3.2 12.3 + - - +
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Residues in contact with GLU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ARG* 5.5 1.4 + - - -
232A ARG* 2.8 55.4 + - - +
233A GLU* 3.6 24.7 - - - +
235A LYS* 1.3 79.7 - - - +
237A GLN* 1.3 57.0 + - - +
238A ILE 4.7 2.5 - - - -
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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