Contacts of the helix formed by residues 222 - 241 (chain A) in PDB entry 2VR2
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 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A GLU* 3.5 10.7 - - - +
219A LEU* 3.4 16.4 - - - +
220A CYS 3.5 4.9 - - - +
221A ARG* 1.4 93.8 - - - +
223A GLU* 1.3 58.5 + - - +
224A ALA* 3.1 11.9 - - + +
225A VAL* 2.8 36.6 + - + +
226A GLU 3.8 1.4 + - - -
302A ARG* 3.8 3.6 - - - +
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Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A GLU* 5.0 0.2 + - - -
222A PRO* 1.3 71.7 - - + +
224A ALA* 1.3 57.6 + - - +
225A VAL 3.2 0.2 - - - -
226A GLU* 3.3 3.1 + - - +
227A ALA* 2.8 31.5 + - - +
251A SER* 3.5 26.8 + - - +
252A LYS* 3.7 8.9 + - - +
253A SER* 2.7 39.6 + - - +
302A ARG* 3.4 35.5 - - - +
303A PRO* 5.6 1.7 - - - +
304A ASP* 5.0 10.9 - - - +
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Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A PRO* 2.9 10.7 + - + +
223A GLU* 1.3 80.8 - - - +
225A VAL* 1.3 54.3 + - + +
227A ALA* 3.8 5.9 - - - +
228A GLU* 2.8 37.0 + - - +
253A SER* 5.7 0.9 - - - -
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Residues in contact with VAL 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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194A GLU* 4.3 6.5 - - + +
195A ASN* 3.4 43.4 + - + +
198A LEU* 3.8 29.2 - - + -
199A ILE* 3.9 14.8 - - + -
220A CYS 4.9 2.7 - - - +
221A ARG* 4.5 6.7 - - - -
222A PRO* 2.8 31.1 + - + +
224A ALA* 1.3 75.6 - - + +
226A GLU* 1.3 64.3 + - - +
228A GLU* 3.6 5.6 + - - +
229A ALA 3.3 16.1 + - - -
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Residues in contact with GLU 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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193A ALA* 3.4 24.7 - - + +
194A GLU* 4.2 5.8 - - + +
222A PRO 3.8 0.8 + - - -
223A GLU 3.3 8.3 + - - +
225A VAL* 1.3 81.0 - - - +
227A ALA* 1.3 52.8 + - - +
230A THR* 2.7 36.6 + - - +
248A HIS 4.3 0.2 - - - +
249A VAL* 3.9 4.5 - - - -
250A MET* 3.0 24.4 + - - +
251A SER* 3.2 25.4 + - - -
254A ALA* 3.4 15.4 - - + +
299A PRO* 3.7 21.2 - - + +
302A ARG* 3.0 30.2 + - - +
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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 GLU 2.8 20.6 + - - +
224A ALA* 3.8 5.4 - - - +
226A GLU* 1.3 72.0 - - - +
228A GLU* 1.3 64.4 + - - +
230A THR* 3.3 7.8 + - - -
231A LEU* 3.1 23.9 + - - +
253A SER* 3.8 26.2 - - - +
254A ALA* 4.0 10.7 - - - +
257A VAL* 4.3 10.6 - - + +
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Residues in contact with GLU 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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195A ASN* 3.0 19.7 + - + +
198A LEU* 5.7 5.2 - - + -
224A ALA 2.8 22.1 + - - +
225A VAL* 3.8 6.1 - - - +
226A GLU 3.4 0.2 - - - -
227A ALA* 1.3 73.6 - - - +
229A ALA* 1.3 64.7 + - - +
231A LEU* 3.4 6.2 + - - +
232A ARG* 2.8 64.6 + - - +
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Residues in contact with ALA 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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162A MET* 3.3 26.7 - - + +
193A ALA* 3.5 6.1 - - - -
194A GLU* 3.3 44.4 - - - +
195A ASN 3.8 3.1 - - - +
225A VAL 3.3 3.7 + - - +
228A GLU* 1.3 84.7 + - - +
230A THR* 1.3 55.9 + - - +
232A ARG* 3.2 1.7 + - - +
233A ALA* 2.8 31.5 + - - +
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Residues in contact with THR 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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193A ALA* 3.3 18.3 + - - +
226A GLU* 2.7 25.1 + - - +
227A ALA* 3.5 9.0 - - - -
228A GLU 3.3 0.2 - - - -
229A ALA* 1.3 76.9 - - - +
231A LEU* 1.3 57.3 + - - +
233A ALA* 3.4 3.4 + - - +
234A ILE* 3.0 41.0 + - + +
246A ILE* 4.5 11.3 - - + +
254A ALA* 3.8 18.5 - - - +
257A VAL* 4.0 4.7 - - + -
258A ILE* 3.7 33.9 - - + -
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Residues in contact with LEU 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 3.1 16.0 + - - +
228A GLU* 3.8 6.1 - - - +
230A THR* 1.3 76.5 - - - +
232A ARG* 1.3 54.0 + - - +
234A ILE* 3.4 10.1 + - + +
235A THR* 2.6 48.0 + - - +
257A VAL* 3.9 25.5 - - + +
261A ALA* 6.3 0.9 - - + -
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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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162A MET* 3.4 30.2 + - + +
169A MET* 6.0 5.3 - - - +
170A VAL 5.8 1.8 + - - -
172A ASP* 2.6 48.3 + - - +
175A LEU* 4.9 1.0 - - - +
195A ASN* 3.2 27.8 - - - +
228A GLU* 2.8 51.3 + - - +
229A ALA* 3.4 9.3 - - - +
231A LEU* 1.3 73.2 - - - +
233A ALA* 1.3 66.7 + - - +
235A THR* 3.0 8.2 + - - -
236A ILE* 2.8 38.5 + - + +
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Residues in contact with ALA 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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162A MET* 4.0 18.1 - - - +
175A LEU* 5.3 0.9 - - - -
179A PHE* 3.7 8.1 - - - -
191A VAL* 4.3 14.1 - - + -
193A ALA* 5.2 0.2 - - + -
229A ALA 2.8 20.1 + - - +
230A THR* 3.6 5.2 - - - +
232A ARG* 1.3 73.1 - - - +
234A ILE* 1.3 56.5 + - - +
236A ILE* 3.3 5.1 + - - -
237A ALA* 2.9 31.9 + - - +
244A LEU* 3.5 16.0 - - + +
246A ILE* 4.2 11.2 - - + -
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Residues in contact with ILE 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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230A THR* 3.0 30.9 + - + +
231A LEU* 3.6 11.9 - - + +
233A ALA* 1.3 73.5 - - - +
235A THR* 1.3 57.7 + - - +
237A ALA* 3.8 1.3 - - - +
238A SER* 2.9 32.6 + - - -
244A LEU* 3.6 19.5 - - + -
246A ILE* 4.9 0.7 - - + -
257A VAL* 3.9 23.8 - - + -
258A ILE* 4.2 5.8 - - - -
261A ALA* 3.9 30.5 - - + -
266A LYS* 4.0 23.1 - - + +
268A VAL* 3.8 19.5 - - + -
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Residues in contact with THR 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 LEU* 2.6 39.1 + - - +
232A ARG* 3.0 7.5 + - - -
234A ILE* 1.3 71.3 - - - +
236A ILE* 1.3 66.3 + - + +
238A SER* 3.6 6.0 + - - -
239A ALA* 3.1 25.1 + - + +
266A LYS* 6.2 0.7 - - - +
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Residues in contact with ILE 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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172A ASP* 4.3 24.5 - - + +
175A LEU* 4.0 8.5 - - + -
176A TYR* 3.6 45.5 - - + +
179A PHE* 3.7 18.4 - - + -
232A ARG* 2.8 38.7 + - + +
233A ALA* 4.5 2.5 - - - -
235A THR* 1.3 74.8 - - + +
237A ALA* 1.3 61.8 + - - +
239A ALA* 3.3 6.7 + - - +
240A VAL* 3.3 23.6 + - + +
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Residues in contact with ALA 237 (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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179A PHE* 3.7 13.8 - - + -
233A ALA 2.9 17.3 + - - +
234A ILE 3.8 3.8 - - - +
236A ILE* 1.3 77.6 - - - +
238A SER* 1.3 57.1 + - - +
240A VAL* 3.3 1.6 + - - -
241A ASN 2.8 24.1 + - - -
242A CYS* 3.0 32.8 + - - +
244A LEU* 3.9 27.6 - - + -
267A VAL 5.7 0.2 - - - +
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Residues in contact with SER 238 (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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234A ILE 2.9 18.6 + - - -
235A THR* 3.9 5.6 - - - -
236A ILE 3.3 0.2 - - - -
237A ALA* 1.3 76.9 - - - +
239A ALA* 1.3 61.2 + - - +
240A VAL 3.4 0.3 + - - -
241A ASN* 3.4 12.1 + - - +
266A LYS* 3.7 37.5 - - - +
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Residues in contact with ALA 239 (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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176A TYR* 4.9 15.8 + - + -
235A THR* 3.1 20.2 + - + +
236A ILE* 3.7 6.5 - - - +
237A ALA 3.3 0.2 - - - -
238A SER* 1.3 77.1 + - - +
240A VAL* 1.3 59.4 + - - +
241A ASN 3.5 0.2 - - - -
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A TYR* 3.4 44.4 - - + +
179A PHE* 4.2 7.2 - - + +
180A SER* 3.3 43.1 - - - +
183A LYS* 3.8 13.7 + - + +
236A ILE 3.3 14.2 + - - +
237A ALA 4.0 2.7 - - - +
238A SER 3.2 0.4 - - - -
239A ALA* 1.3 76.1 - - - +
241A ASN* 1.3 67.3 + - - +
242A CYS* 4.4 7.6 - - + +
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Residues in contact with ASN 241 (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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183A LYS* 3.4 13.0 - - - +
237A ALA 2.8 8.2 + - - -
238A SER* 3.4 12.2 + - - +
240A VAL* 1.3 80.8 - - - +
242A CYS* 1.3 55.8 + - - +
476A ILE* 3.0 54.9 + - - +
479A ARG* 3.7 28.0 + - - +
480A ASP* 3.0 26.1 + - - +
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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
------------------------------------------------------------
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