Contacts of the helix formed by residues 249 - 267 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A GLY 3.4 7.8 + - - +
248A ILE* 1.3 76.8 - - - +
250A PRO* 1.3 75.7 - - + +
251A GLU* 3.1 23.9 + - - +
252A LEU* 3.1 29.1 + - + +
253A ARG* 3.0 21.7 + - - +
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Residues in contact with PRO 250 (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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248A ILE 4.5 2.0 - - - +
249A THR* 1.3 85.5 - - - +
251A GLU* 1.3 70.5 + - - +
253A ARG* 3.6 22.7 - - + +
254A ARG* 3.0 47.9 + - - +
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Residues in contact with GLU 251 (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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249A THR* 3.0 21.7 + - - +
250A PRO* 1.3 93.8 - - - +
252A LEU* 1.3 65.1 + - + +
254A ARG* 3.5 17.9 + - - +
255A TYR* 3.1 22.5 + - - +
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Residues in contact with LEU 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLY 4.6 3.8 - - - +
248A ILE* 3.9 26.0 - - + -
249A THR* 3.1 32.8 + - + +
251A GLU* 1.3 73.0 - - - +
253A ARG* 1.3 66.3 + - - +
255A TYR* 3.1 12.4 + - + +
256A ILE* 3.0 29.7 + - - +
279A PHE* 4.3 12.8 - - + -
282A GLY* 4.2 18.8 - - - +
284A PHE* 4.5 14.4 - - + -
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Residues in contact with ARG 253 (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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212A ILE* 5.7 1.5 - - + +
224A TYR* 4.0 14.4 - - + -
226A ALA* 4.0 10.9 - - - +
227A GLU* 2.8 42.7 + - - +
244A PRO* 3.2 21.3 - - - +
245A ALA 4.8 0.2 + - - -
248A ILE* 3.8 22.8 + - + +
249A THR 3.0 10.3 + - - +
250A PRO* 3.6 32.3 - - - +
252A LEU* 1.3 77.1 - - - +
254A ARG* 1.3 56.5 + - - +
256A ILE* 3.6 7.0 - - - +
257A GLY* 2.9 30.7 + - - -
330A VAL* 3.9 31.4 - - - +
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Residues in contact with ARG 254 (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 TYR* 3.6 16.1 + - - +
250A PRO* 3.0 41.9 + - - +
251A GLU* 3.8 17.8 + - - +
253A ARG* 1.3 77.5 - - - +
255A TYR* 1.3 62.4 + - - +
258A GLU* 3.1 52.8 + - - +
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Residues in contact with TYR 255 (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 PRO* 5.3 10.6 - - + +
251A GLU 3.1 13.8 + - - +
252A LEU* 3.1 19.9 + - + +
254A ARG* 1.3 77.3 - - - +
256A ILE* 1.3 73.5 + - + +
258A GLU* 4.1 2.7 - - - +
259A ARG* 3.1 81.3 + - - +
284A PHE* 5.7 4.7 - + + -
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Residues in contact with ILE 256 (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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128A VAL* 5.2 0.7 - - + -
129A PRO* 4.2 16.8 - - + -
212A ILE* 3.8 22.2 - - + -
227A GLU* 6.0 0.2 - - + -
248A ILE* 6.0 0.4 - - + -
252A LEU 3.0 18.4 + - - +
253A ARG* 3.6 8.5 - - - +
255A TYR* 1.3 81.6 - - + +
257A GLY* 1.3 68.0 + - - +
259A ARG* 3.6 5.0 + - + -
260A CYS* 3.2 22.9 + - - -
277A PHE* 3.5 42.4 - - + -
284A PHE* 3.9 45.8 - - + -
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Residues in contact with GLY 257 (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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212A ILE* 4.5 5.2 - - - -
224A TYR* 3.2 38.0 - - - -
253A ARG 2.9 18.8 + - - -
256A ILE* 1.3 79.7 - - - +
258A GLU* 1.3 60.7 + - - +
260A CYS* 3.2 7.0 + - - +
261A ALA 3.0 18.5 + - - -
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Residues in contact with GLU 258 (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 TYR* 3.7 16.4 + - + -
254A ARG* 3.1 47.5 + - - +
255A TYR* 4.1 4.4 - - - +
256A ILE 3.4 0.2 - - - -
257A GLY* 1.3 75.7 - - - +
259A ARG* 1.3 64.0 + - - +
261A ALA* 3.4 5.9 + - + +
262A LYS* 3.0 27.6 + - - +
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Residues in contact with ARG 259 (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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126A ALA 4.9 3.3 - - - +
127A GLY* 3.5 27.4 + - - +
128A VAL* 3.5 14.0 - - + +
129A PRO* 4.4 10.3 - - + +
255A TYR* 3.1 75.2 + - - +
256A ILE* 3.6 7.1 + - + +
257A GLY 3.3 0.8 - - - -
258A GLU* 1.3 80.7 + - + +
260A CYS* 1.3 60.1 + - - +
262A LYS* 3.8 7.1 - - + +
263A ALA* 3.0 27.9 + - - +
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Residues in contact with CYS 260 (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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128A VAL* 4.7 2.7 - - - -
212A ILE* 3.8 15.3 - - + -
214A VAL* 4.2 9.0 - - + -
256A ILE* 3.2 23.3 + - - +
257A GLY 3.2 8.5 + - - +
259A ARG* 1.3 75.2 - - - +
261A ALA* 1.3 64.2 + - - +
263A ALA* 3.4 6.5 + - - +
264A CYS* 3.1 25.9 + - - -
275A PHE* 3.5 30.8 - - + -
277A PHE* 3.6 36.3 - - - -
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Residues in contact with ALA 261 (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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214A VAL* 4.9 3.5 - - - +
222A ALA* 3.8 26.4 - - + +
223A ILE* 4.7 3.1 - - - +
224A TYR* 4.5 11.4 - - + -
257A GLY 3.0 13.8 + - - +
258A GLU* 3.7 8.7 - - - +
260A CYS* 1.3 73.4 - - - +
262A LYS* 1.3 65.2 + - - +
264A CYS* 3.2 19.1 + - - +
265A VAL* 3.2 18.4 + - - +
325A GLN* 5.3 0.2 - - - +
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Residues in contact with LYS 262 (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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125A LYS 4.8 2.8 + - - -
126A ALA* 3.4 29.0 + - - +
258A GLU 3.0 17.3 + - - +
259A ARG* 3.8 8.3 - - + +
260A CYS 3.3 0.2 - - - -
261A ALA* 1.3 74.9 - - - +
263A ALA* 1.3 65.1 + - - +
265A VAL* 3.1 10.0 + - + +
266A ASP* 3.0 57.2 + - - +
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Residues in contact with ALA 263 (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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123A MET* 4.1 11.9 - - + -
126A ALA* 4.1 13.9 - - + +
128A VAL* 3.8 18.2 - - + -
259A ARG 3.0 14.7 + - - +
260A CYS 3.4 9.6 - - - +
262A LYS* 1.3 77.8 - - - +
264A CYS* 1.3 61.4 + - - +
266A ASP* 3.4 0.5 + - - +
267A ILE* 3.1 32.0 + - - +
275A PHE* 3.8 16.8 - - + -
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Residues in contact with CYS 264 (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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214A VAL* 3.7 33.7 - - - -
216A ALA* 4.5 5.2 - - + -
222A ALA* 3.9 17.3 - - + -
260A CYS 3.1 19.2 + - - -
261A ALA* 3.2 10.5 + - - +
263A ALA* 1.3 75.8 - - - +
265A VAL* 1.3 63.2 + - - +
267A ILE* 4.0 1.8 - - - -
268A GLY* 3.1 3.3 + - - -
269A TYR* 2.8 54.2 + - + +
275A PHE* 3.8 9.2 - - - -
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Residues in contact with VAL 265 (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 GLY 4.2 14.6 - - - +
222A ALA* 4.0 16.2 - - + -
261A ALA 3.2 14.1 + - - +
262A LYS* 3.1 11.3 + - + +
264A CYS* 1.3 74.2 - - - +
266A ASP* 1.3 72.6 + - - +
268A GLY* 3.2 11.7 + - - -
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Residues in contact with ASP 266 (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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125A LYS 5.0 0.2 - - - +
126A ALA* 3.4 22.2 - - + +
262A LYS* 3.0 52.9 + - - +
263A ALA 3.7 4.3 - - - +
265A VAL* 1.3 82.5 - - - +
267A ILE* 1.3 62.1 + - + +
268A GLY 3.6 0.5 + - - -
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Residues in contact with ILE 267 (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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109A THR* 4.2 15.5 + - + +
112A LEU* 4.8 9.4 - - + +
113A MET* 3.5 28.3 - - + -
122A ALA* 4.7 11.9 - - + +
123A MET* 4.3 18.4 - - + -
126A ALA* 5.7 0.4 - - + -
263A ALA* 3.1 21.6 + - - +
264A CYS* 3.7 7.9 - - - +
266A ASP* 1.3 81.1 - - + +
268A GLY* 1.3 62.3 - - - +
269A TYR* 3.7 29.6 - - + +
275A PHE* 5.6 1.3 - - + -
289A MET* 4.5 7.9 - - - -
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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