Contacts of the helix formed by residues 249 - 268 (chain B) in PDB entry 2VR1
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 THR 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247B GLY 3.8 9.2 + - - +
248B ILE* 1.3 77.4 - - - +
250B PRO* 1.3 69.9 - - - +
251B GLU* 3.6 7.0 + - - +
252B LEU* 3.3 24.5 + - + +
253B ARG* 2.8 28.5 + - - +
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Residues in contact with PRO 250 (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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248B ILE 4.6 1.3 - - - +
249B THR* 1.3 87.1 - - - +
251B GLU* 1.3 56.2 + - - +
253B ARG* 3.5 23.8 + - + +
254B ARG* 2.8 31.1 + - - +
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Residues in contact with GLU 251 (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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249B THR* 3.3 6.7 + - - +
250B PRO* 1.3 78.6 - - - +
252B LEU* 1.3 58.7 + - - +
254B ARG* 3.6 36.1 + - - +
255B TYR* 2.9 28.5 + - + +
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B GLY 5.4 2.0 - - - +
248B ILE* 3.9 13.7 - - + -
249B THR* 3.1 25.6 + - + +
251B GLU* 1.3 76.6 - - - +
253B ARG* 1.3 64.3 + - - +
254B ARG 3.2 0.2 - - - -
255B TYR* 4.2 15.7 - - + -
256B ILE* 3.2 24.9 + - - +
279B PHE* 3.8 29.6 - - + -
282B GLY* 4.5 15.0 - - - +
284B PHE* 3.7 22.7 - - + -
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Residues in contact with ARG 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ILE* 5.6 0.4 - - + +
224B TYR* 4.0 16.1 - - + -
226B ALA* 3.9 21.7 - - - +
227B GLU* 2.9 40.8 + - - +
244B PRO* 3.4 19.8 - - - +
245B ALA 4.8 0.2 + - - -
248B ILE* 3.8 23.7 + - + +
249B THR 2.8 9.5 + - - +
250B PRO* 3.5 41.8 - - - +
252B LEU* 1.3 76.8 - - - +
254B ARG* 1.3 52.9 + - - +
256B ILE* 3.6 8.0 - - - +
257B GLY* 2.8 33.6 + - - -
330B VAL* 4.3 19.2 - - - +
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Residues in contact with ARG 254 (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 TYR* 3.7 17.9 - - - +
250B PRO 2.8 19.3 + - - +
251B GLU* 3.6 32.2 + - - +
253B ARG* 1.3 78.3 - - - +
255B TYR* 1.3 61.9 + - - +
258B GLU* 3.1 51.3 + - - +
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Residues in contact with TYR 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PRO* 4.7 17.6 - - + +
251B GLU* 2.9 20.1 + - + +
252B LEU* 3.7 22.0 - - + +
253B ARG 3.3 0.4 - - - -
254B ARG* 1.3 79.4 - - - +
256B ILE* 1.3 80.1 + - + +
258B GLU* 4.1 0.8 - - - +
259B ARG* 3.1 77.2 + - + +
284B PHE* 5.1 5.6 - + + -
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Residues in contact with ILE 256 (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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128B VAL* 5.4 0.2 - - + -
129B PRO* 4.2 17.3 - - + -
212B ILE* 3.7 24.5 - - + -
227B GLU* 6.0 0.9 - - + -
252B LEU 3.2 15.3 + - - +
253B ARG* 3.6 9.4 - - + +
255B TYR* 1.3 84.0 - - + +
257B GLY* 1.3 66.7 + - - +
259B ARG* 3.5 6.6 + - + +
260B CYS* 3.1 23.8 + - - -
277B PHE* 3.7 37.5 - - + -
284B PHE* 3.8 44.2 - - + -
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Residues in contact with GLY 257 (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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212B ILE* 4.6 6.7 - - - -
224B TYR* 3.3 38.2 - - - -
253B ARG 2.8 18.4 + - - -
256B ILE* 1.3 80.3 - - - +
258B GLU* 1.3 60.1 + - - +
260B CYS* 3.2 4.7 + - - +
261B ALA 3.1 18.4 + - - -
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Residues in contact with GLU 258 (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 TYR* 3.8 14.7 + - + +
254B ARG* 3.1 52.9 + - - +
255B TYR* 4.1 3.1 - - - +
257B GLY* 1.3 74.9 - - - +
259B ARG* 1.3 68.7 + - - +
261B ALA* 3.3 6.2 + - - +
262B LYS* 2.9 30.4 + - - +
325B GLN* 6.3 0.4 - - + -
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Residues in contact with ARG 259 (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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126B ALA 5.1 3.4 - - - +
127B GLY* 3.2 28.8 + - - +
128B VAL* 3.5 15.6 - - + +
129B PRO* 4.9 4.0 - - + -
255B TYR* 3.1 65.9 + - + +
256B ILE* 3.7 15.7 - - + +
257B GLY 3.3 0.6 - - - -
258B GLU* 1.3 87.9 + - - +
260B CYS* 1.3 58.4 + - - +
262B LYS* 3.4 8.8 + - + +
263B ALA* 3.0 28.1 + - - +
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Residues in contact with CYS 260 (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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128B VAL* 4.4 3.8 - - - -
212B ILE* 4.0 18.6 - - + -
214B VAL* 4.1 2.9 - - + -
256B ILE* 3.1 19.9 + - - +
257B GLY 3.2 7.6 + - - +
259B ARG* 1.3 77.4 - - - +
261B ALA* 1.3 57.1 + - - +
263B ALA* 3.2 8.9 + - - +
264B CYS* 2.9 31.6 + - - -
275B PHE* 3.7 33.7 - - + -
277B PHE* 3.5 33.2 - - - -
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Residues in contact with ALA 261 (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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214B VAL* 4.7 3.5 - - - +
222B ALA* 3.8 26.4 - - - +
223B ILE* 4.6 2.9 - - - -
224B TYR* 4.5 11.4 - - + -
257B GLY 3.1 12.7 + - - +
258B GLU* 3.7 10.8 - - - +
260B CYS* 1.3 76.7 - - - +
262B LYS* 1.3 60.8 + - - +
264B CYS* 3.2 13.1 + - - +
265B VAL* 3.2 24.6 + - - +
325B GLN* 5.4 0.7 - - - +
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Residues in contact with LYS 262 (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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125B LYS 5.3 1.2 + - - -
126B ALA* 3.6 21.2 + - - +
258B GLU 2.9 17.2 + - - +
259B ARG* 3.7 8.7 - - + +
261B ALA* 1.3 76.9 - - - +
263B ALA* 1.3 58.1 + - - +
265B VAL* 3.1 10.2 + - + +
266B ASP* 2.8 64.1 + - - +
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Residues in contact with ALA 263 (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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123B MET* 4.1 13.0 - - + -
126B ALA* 4.0 16.3 - - + +
128B VAL* 3.8 19.7 - - + -
259B ARG 3.0 14.5 + - - +
260B CYS 3.3 9.4 - - - +
262B LYS* 1.3 73.4 - - - +
264B CYS* 1.3 66.0 + - - +
266B ASP* 3.2 0.7 + - - +
267B ILE* 3.0 30.8 + - - +
275B PHE* 4.0 13.2 - - + -
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Residues in contact with CYS 264 (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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214B VAL* 3.7 36.3 - - - -
216B ALA* 4.3 4.0 - - + -
222B ALA* 3.7 18.4 - - + -
260B CYS 2.9 18.7 + - - -
261B ALA* 3.2 10.9 + - - +
263B ALA* 1.3 76.4 - - - +
265B VAL* 1.3 57.3 + - - +
267B ILE* 3.7 1.7 - - - +
268B GLY* 2.9 8.8 + - - -
269B TYR* 2.9 51.8 + - + +
275B PHE* 3.7 9.6 - - - -
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Residues in contact with VAL 265 (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 GLY* 3.5 30.5 - - - +
222B ALA* 4.4 10.1 - - + +
261B ALA 3.5 13.2 - - - +
262B LYS* 3.1 12.2 + - + +
264B CYS* 1.3 76.7 - - - +
266B ASP* 1.3 71.0 + - - +
268B GLY* 3.1 14.2 + - - +
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Residues in contact with ASP 266 (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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125B LYS* 4.6 3.1 - - - +
126B ALA* 3.6 25.0 - - + +
262B LYS* 2.8 52.7 + - - +
263B ALA 3.2 5.1 + - - +
265B VAL* 1.3 82.7 - - - +
267B ILE* 1.3 61.9 + - + +
268B GLY 3.7 0.2 + - - -
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Residues in contact with ILE 267 (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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109B THR* 3.9 31.7 + - + +
112B LEU* 4.0 25.1 - - + +
113B MET* 4.4 10.3 - - + -
122B ALA* 4.4 15.9 - - + +
123B MET* 4.5 11.0 - - + -
126B ALA* 5.8 0.4 - - + -
263B ALA* 3.0 21.5 + - - +
264B CYS* 3.7 6.3 - - - +
266B ASP* 1.3 81.3 - - + +
268B GLY* 1.3 62.9 + - - +
269B TYR* 3.8 19.7 - - + +
275B PHE* 5.2 0.7 - - + -
289B MET* 4.2 17.5 - - + -
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Residues in contact with GLY 268 (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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106B LYS* 5.2 6.2 + - - +
109B THR* 4.4 6.6 + - - -
218B GLY* 4.8 6.2 - - - -
264B CYS 2.9 6.5 + - - -
265B VAL* 3.1 12.1 + - - -
266B ASP 3.4 0.2 - - - -
267B ILE* 1.3 78.9 - - - +
269B TYR* 1.3 67.4 + - - +
270B ARG* 3.7 4.5 + - - +
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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
------------------------------------------------------------
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