Contacts of the helix formed by residues 249 - 273 (chain B) in PDB entry 2GRA
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 GLY 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245B LEU 3.3 1.4 + - - -
246B GLU* 3.8 9.4 + - - -
247B SER 3.5 2.8 - - - -
248B GLY* 1.3 76.4 - - - +
250B PHE* 1.3 64.8 + - - +
251B ARG* 2.7 7.6 + - - -
252B SER* 2.7 32.7 + - - -
253B LEU* 3.3 6.2 + - - +
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Residues in contact with PHE 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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184B ALA* 6.5 1.8 - - + -
245B LEU* 3.5 60.1 + - + +
246B GLU* 4.4 2.8 - - + +
248B GLY 2.9 6.3 + - - -
249B GLY* 1.3 75.7 - - - +
251B ARG* 1.3 73.5 + - + +
253B LEU* 3.6 20.7 - - + +
254B LEU* 3.7 33.7 + - + +
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Residues in contact with ARG 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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228B LYS* 5.2 14.3 - - - +
246B GLU* 3.1 41.7 + - - +
249B GLY 2.7 5.5 + - - -
250B PHE* 1.3 79.8 - - + +
252B SER* 1.3 56.6 + - - +
254B LEU* 2.4 46.0 + - - +
255B ILE* 3.4 10.0 + - + -
186E ASP* 4.6 13.9 + - - -
190E ASP* 5.5 0.4 + - - -
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Residues in contact with SER 252 (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 GLY* 2.7 22.7 + - - -
251B ARG* 1.3 76.5 - - - +
253B LEU* 1.3 70.8 + - - -
255B ILE* 3.0 11.6 + - - +
256B ASN* 2.8 34.4 + - - +
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Residues in contact with LEU 253 (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 GLY 4.6 10.3 - - - +
249B GLY* 3.7 16.2 - - - +
250B PHE* 3.6 14.4 - - + +
251B ARG 2.6 3.8 + - - -
252B SER* 1.3 79.8 - - - +
254B LEU* 1.3 57.6 + - + +
256B ASN* 3.2 16.0 - - - +
257B ALA* 2.9 27.4 + - - +
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Residues in contact with LEU 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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180B TYR* 4.8 28.0 - - + -
250B PHE* 3.9 42.0 - - + +
251B ARG* 2.4 26.5 + - + +
253B LEU* 1.3 66.5 - - + +
255B ILE* 1.3 68.7 + - + +
257B ALA* 3.0 6.9 + - + +
258B VAL* 2.8 23.6 + - - +
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Residues in contact with ILE 255 (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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251B ARG* 4.2 11.7 - - + +
252B SER* 3.0 14.1 + - - +
254B LEU* 1.3 78.2 - - + +
256B ASN* 1.3 69.5 + - - +
258B VAL* 2.9 16.0 - - + +
259B GLU* 2.9 34.3 + - + +
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Residues in contact with ASN 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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252B SER* 2.8 22.9 + - - +
253B LEU* 3.2 20.0 - - - +
255B ILE* 1.3 80.5 - - - +
257B ALA* 1.3 56.3 + - - +
259B GLU* 3.7 12.5 - - - +
260B ALA* 2.8 32.8 + - - +
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Residues in contact with ALA 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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180B TYR* 3.6 27.2 + - + -
253B LEU 2.9 16.1 + - - +
254B LEU* 3.0 7.8 + - + +
256B ASN* 1.3 76.5 - - - +
258B VAL* 1.3 67.7 + - - +
260B ALA* 4.0 4.4 - - - +
261B SER* 2.8 26.7 + - - -
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Residues in contact with VAL 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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169B ALA* 4.9 2.7 - - - +
172B GLY* 3.7 1.5 - - - -
173B LEU* 3.7 42.2 - - + +
180B TYR* 4.1 12.7 + - + -
254B LEU 2.8 14.5 + - - +
255B ILE* 2.9 32.5 - - + +
257B ALA* 1.3 73.2 - - - +
259B GLU* 1.3 71.8 + - - +
261B SER* 3.4 1.9 - - - -
262B CYS* 2.8 31.9 + - + +
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Residues in contact with GLU 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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255B ILE* 3.2 19.9 - - + +
256B ASN* 3.7 12.6 - - - +
258B VAL* 1.3 82.6 - - + +
260B ALA* 1.3 68.5 + - - +
261B SER 2.7 2.4 + - - -
262B CYS* 2.7 18.2 + - - -
263B ILE* 2.8 36.0 + - + +
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Residues in contact with ALA 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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256B ASN 2.8 24.1 + - - +
257B ALA* 4.0 5.4 - - - +
259B GLU* 1.3 74.9 + - - +
261B SER* 1.3 59.2 + - - +
263B ILE* 4.0 11.3 - - - +
264B ARG* 3.3 21.5 + - - +
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Residues in contact with SER 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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171B THR* 4.3 1.7 - - - +
172B GLY* 3.0 21.0 + - - -
176B SER* 3.0 17.2 + - - -
180B TYR* 3.7 10.3 - - - -
257B ALA 2.8 20.1 + - - -
258B VAL 3.4 3.6 - - - -
259B GLU 2.7 3.6 + - - -
260B ALA* 1.3 71.8 - - - +
262B CYS* 1.3 66.5 + - - -
264B ARG* 3.1 9.1 + - - +
265B THR* 3.0 23.0 + - - -
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Residues in contact with CYS 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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168B ASP 3.8 31.6 - - - +
169B ALA* 4.0 10.5 - - - +
172B GLY* 3.6 6.2 - - - -
258B VAL* 2.8 15.0 + - + +
259B GLU* 2.7 15.7 + - - +
261B SER* 1.3 71.5 + - - +
263B ILE* 1.3 65.2 + - + +
265B THR* 2.8 21.7 + - - -
266B ARG* 3.0 42.3 + - - +
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Residues in contact with ILE 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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259B GLU* 2.8 50.4 + - + +
260B ALA* 4.0 8.3 - - - +
262B CYS* 1.3 73.1 - - + +
264B ARG* 1.3 66.0 + - - +
266B ARG* 2.7 38.7 + - + +
267B GLU* 2.9 27.4 + - + -
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Residues in contact with ARG 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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260B ALA 3.3 12.5 + - - +
261B SER* 3.1 12.3 + - - +
263B ILE* 1.3 78.8 - - - +
265B THR* 1.3 65.1 + - - +
267B GLU* 3.1 29.7 + - - +
268B LEU* 2.9 59.2 + - + +
271B MET* 5.4 5.5 - - - -
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Residues in contact with THR 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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97B ALA 5.8 0.2 - - - -
98B GLY* 4.6 16.0 - - - +
119B ARG* 5.0 2.5 - - - +
168B ASP* 3.3 33.2 - - - +
171B THR* 3.7 28.1 - - + +
261B SER* 3.0 13.7 + - - -
262B CYS* 2.8 17.6 + - - -
264B ARG* 1.3 76.0 - - - +
266B ARG* 1.3 61.4 + - - +
268B LEU* 2.9 29.6 + - + +
269B GLN* 3.2 6.1 + - - +
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Residues in contact with ARG 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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168B ASP* 4.0 23.5 + - - +
169B ALA* 5.7 3.0 - - - +
262B CYS* 3.0 33.4 + - - +
263B ILE* 2.7 31.7 + - + +
265B THR* 1.3 75.7 - - - +
267B GLU* 1.3 63.9 + - + +
269B GLN* 2.9 34.6 + - + +
270B SER* 3.1 8.0 + - - +
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Residues in contact with GLU 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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263B ILE* 2.9 29.9 + - + +
264B ARG* 3.3 36.1 + - - +
266B ARG* 1.3 75.7 - - + +
268B LEU* 1.3 62.4 + - - +
270B SER* 3.3 20.4 + - - -
271B MET* 3.5 14.4 - - - +
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Residues in contact with LEU 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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97B ALA* 6.1 3.6 - - + -
98B GLY* 5.0 12.1 - - - +
264B ARG* 3.0 56.5 - - + +
265B THR* 2.9 20.8 + - + +
267B GLU* 1.3 74.1 - - - +
269B GLN* 1.3 63.6 + - - +
270B SER 3.0 1.6 - - - -
271B MET* 2.9 34.1 + - - +
272B ALA* 3.2 7.5 + - - +
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Residues in contact with GLN 269 (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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98B GLY* 3.1 28.6 + - - +
100B THR* 4.2 9.8 + - - +
119B ARG* 4.9 4.9 + - - -
168B ASP* 3.2 28.4 + - - +
265B THR 3.2 4.0 + - - +
266B ARG* 2.9 27.6 + - + +
268B LEU* 1.3 73.5 - - - +
270B SER* 1.3 57.5 + - - +
271B MET 2.9 5.6 - - - -
272B ALA* 4.2 3.1 - - - +
273B ASP* 2.5 59.5 + - - +
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Residues in contact with SER 270 (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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266B ARG* 3.1 13.2 + - - +
267B GLU* 3.4 16.6 - - - -
268B LEU 3.0 1.0 - - - -
269B GLN* 1.3 82.4 + - - +
271B MET* 1.3 58.8 + - - +
273B ASP* 4.1 9.2 - - - -
274B GLN* 3.6 23.9 - - - +
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Residues in contact with MET 271 (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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264B ARG* 5.4 6.3 - - - -
267B GLU 3.5 11.7 - - - +
268B LEU* 2.9 31.2 + - - +
269B GLN 2.9 0.4 - - - -
270B SER* 1.3 78.2 - - - +
272B ALA* 1.3 59.9 + - - +
273B ASP 3.1 4.5 - - - -
274B GLN* 4.8 2.0 - - - -
275B GLU* 3.2 38.2 + - - +
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Residues in contact with ALA 272 (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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75B ILE* 3.6 37.3 - - + +
98B GLY 4.7 6.7 - - - +
99B VAL* 5.0 4.0 - - + -
103B SER* 4.1 12.2 + - - +
268B LEU 3.2 8.1 + - - +
269B GLN* 3.0 10.0 + - - +
271B MET* 1.3 80.0 - - - +
273B ASP* 1.3 63.0 + - - +
274B GLN 3.6 0.4 - - - -
275B GLU 4.8 6.8 - - - -
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Residues in contact with ASP 273 (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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98B GLY 4.4 0.7 - - - +
100B THR* 3.5 20.8 + - - +
103B SER* 3.3 18.1 + - - -
269B GLN* 2.5 46.2 + - - +
270B SER* 4.2 6.1 - - - -
271B MET 3.1 0.2 - - - -
272B ALA* 1.3 81.3 - - - +
274B GLN* 1.3 58.3 + - - +
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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