Contacts of the helix formed by residues 252 - 272 (chain B) in PDB entry 2G5W
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 ASP 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B ASP* 2.8 14.5 + - - +
251B SER* 1.3 85.2 + - - +
253B PRO* 1.3 64.7 - - - +
254B LEU* 3.6 8.7 + - - +
255B SER* 3.2 34.7 + - - +
256B LEU* 3.1 17.2 + - - +
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Residues in contact with PRO 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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241B PRO* 3.6 35.6 - - - +
242B ALA* 4.3 14.6 - - + -
249B THR* 6.3 0.4 - - + -
250B ASP* 3.4 17.4 - - + +
251B SER 3.6 4.3 - - - +
252B ASP* 1.3 87.2 - - - +
254B LEU* 1.3 63.5 + - - +
256B LEU* 3.2 7.3 + - + +
257B GLY* 3.0 20.8 + - - -
305B LEU* 4.5 8.0 - - + +
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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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252B ASP* 3.3 8.6 + - - +
253B PRO* 1.3 79.8 - - - +
255B SER* 1.3 63.3 + - - +
257B GLY* 3.5 1.2 + - - -
258B LEU* 3.1 51.2 + - + +
305B LEU* 3.7 32.4 - - + +
308B SER* 4.3 20.2 - - - +
309B LEU* 4.3 1.6 - - + +
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Residues in contact with SER 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ILE* 3.6 24.9 - - - +
252B ASP* 3.2 36.2 + - - +
254B LEU* 1.3 77.8 - - - +
256B LEU* 1.3 61.3 + - - +
258B LEU* 3.3 9.6 + - - +
259B ALA* 2.8 30.8 + - - +
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Residues in contact with LEU 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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194B ASP* 5.3 0.7 - - - +
197B LEU* 3.7 45.8 - - + +
198B LYS* 4.0 24.9 - - + -
212B ILE* 4.2 21.1 - - + -
215B ARG* 4.4 1.1 - - + +
216B CYS* 4.8 2.2 - - - -
241B PRO* 4.1 18.4 - - + +
250B ASP* 3.9 22.9 - - + +
252B ASP 3.1 9.0 + - - +
253B PRO 3.5 7.2 - - - +
255B SER* 1.3 82.2 + - - +
257B GLY* 1.3 63.1 + - - +
259B ALA* 3.1 7.5 + - - +
260B VAL* 3.0 28.2 + - + +
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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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239B VAL* 6.0 2.5 - - - -
241B PRO* 4.1 11.4 - - - +
253B PRO 3.0 13.2 + - - -
254B LEU 3.9 0.9 - - - -
256B LEU* 1.3 76.3 - - - +
258B LEU* 1.3 57.6 + - - +
260B VAL* 3.4 9.1 + - - +
261B VAL* 3.0 31.7 + - - +
309B LEU* 3.5 26.1 - - - +
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Residues in contact with LEU 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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254B LEU* 3.1 45.1 + - + +
255B SER* 3.7 8.1 - - - +
256B LEU 3.2 0.2 - - - -
257B GLY* 1.3 73.2 - - - +
259B ALA* 1.3 56.9 + - - +
261B VAL* 3.6 3.8 - - + +
262B GLY* 2.8 32.2 + - - -
308B SER* 4.4 8.5 - - - +
309B LEU* 3.6 15.7 - - + +
312B ALA* 4.0 25.6 - - + -
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Residues in contact with ALA 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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212B ILE* 3.6 29.2 - - + +
213B ALA* 5.6 1.1 - - - +
216B CYS* 4.1 11.7 - - - -
255B SER 2.8 18.2 + - - +
256B LEU 3.1 5.8 + - - +
258B LEU* 1.3 75.4 - - - +
260B VAL* 1.3 58.4 + - - +
262B GLY* 3.9 1.3 - - - -
263B MET* 3.0 28.8 + - - +
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU* 4.1 14.4 - - + -
216B CYS* 3.9 20.0 - - - -
219B LEU* 4.0 26.7 - - + -
239B VAL* 4.3 24.0 - - + -
256B LEU* 3.0 21.6 + - + +
257B GLY* 3.5 10.5 - - - +
259B ALA* 1.3 74.9 - - - +
261B VAL* 1.3 61.5 + - + +
263B MET* 3.4 4.9 + - - +
264B LEU* 2.9 45.4 + - + +
278B LEU* 4.9 3.1 - - + -
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B GLY 3.0 21.6 + - - +
258B LEU* 3.6 7.4 - - - +
260B VAL* 1.3 76.2 - - + +
262B GLY* 1.3 54.1 + - - +
264B LEU* 3.2 7.2 + - - +
265B ASN* 2.8 38.6 + - - +
278B LEU* 3.8 27.1 - - + -
309B LEU* 3.9 23.3 - - + +
312B ALA* 3.6 17.5 - - + +
313B TYR* 3.5 32.1 - - + +
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Residues in contact with GLY 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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258B LEU 2.8 19.9 + - - -
259B ALA* 3.9 2.0 - - - -
261B VAL* 1.3 74.6 - - - +
263B MET* 1.3 60.4 - - - +
265B ASN* 4.0 5.9 - - - +
266B LYS* 3.2 29.4 + - - +
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Residues in contact with MET 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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216B CYS* 4.8 13.9 - - + +
219B LEU* 3.6 37.7 - - + -
220B LYS* 3.9 39.9 - - + +
223B VAL* 5.1 0.2 - - + -
259B ALA 3.0 19.3 + - - +
260B VAL* 3.6 14.6 - - - +
262B GLY* 1.3 76.4 - - - +
264B LEU* 1.3 76.9 + - + +
266B LYS* 3.5 7.5 + - - +
267B LEU* 3.0 43.1 + - - +
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Residues in contact with LEU 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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223B VAL* 3.9 25.8 - - + -
237B VAL* 4.1 15.0 - - + -
260B VAL* 2.9 26.6 + - + +
261B VAL* 3.7 4.0 - - - +
263B MET* 1.3 94.0 - - + +
265B ASN* 1.3 61.6 + - - +
267B LEU* 3.2 6.3 + - + +
268B GLN* 2.9 32.8 + - - +
275B LEU* 3.7 30.3 - - + -
278B LEU* 3.9 34.5 - - + -
313B TYR* 4.7 8.7 - - + -
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Residues in contact with ASN 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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261B VAL* 2.8 25.2 + - - +
262B GLY* 4.0 6.2 - - - +
264B LEU* 1.3 69.8 - - - +
266B LYS* 1.3 61.0 + - - +
268B GLN* 3.4 15.4 + - - +
269B GLY* 3.1 22.0 + - - -
312B ALA 2.8 28.9 + - - -
313B TYR* 3.5 9.8 - - - +
314B ASN* 3.1 33.9 + - - +
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Residues in contact with LYS 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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220B LYS* 6.2 4.7 - - - -
262B GLY 3.2 18.5 + - - +
263B MET* 3.7 7.2 - - - +
265B ASN* 1.3 77.7 - - - +
267B LEU* 1.3 58.0 + - - +
269B GLY* 3.1 2.7 + - - +
270B VAL* 2.8 40.9 + - + +
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Residues in contact with LEU 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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220B LYS* 4.1 11.4 - - + +
223B VAL* 3.8 32.3 - - + -
224B GLU* 3.8 34.8 - - + +
227B VAL* 4.4 20.2 - - + -
232B ALA* 6.1 0.7 - - + -
263B MET* 3.0 33.0 + - - +
264B LEU* 3.4 10.3 - - + +
265B ASN 3.2 0.2 - - - -
266B LYS* 1.3 77.8 - - - +
268B GLN* 1.3 58.2 + - + +
270B VAL* 3.7 7.9 + - + +
271B ASN* 3.0 33.3 + - + +
275B LEU* 5.1 6.5 - - + -
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Residues in contact with GLN 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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232B ALA* 5.8 0.2 - - + -
264B LEU 2.9 18.1 + - - +
265B ASN* 3.4 16.6 - - - +
266B LYS 3.3 0.2 - - - -
267B LEU* 1.3 75.7 - - + +
269B GLY* 1.3 57.1 + - - +
271B ASN* 4.3 1.3 - - - -
272B GLY* 2.8 28.3 + - - -
273B SER 3.1 28.6 + - - +
274B LYS* 3.7 10.6 - - + +
275B LEU* 2.9 40.2 - - + +
313B TYR* 3.0 29.5 + - - -
314B ASN* 3.0 25.3 + - - +
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Residues in contact with GLY 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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265B ASN 3.1 13.7 + - - -
266B LYS* 3.1 5.1 + - - -
268B GLN* 1.3 74.9 - - - +
270B VAL* 1.3 64.2 + - - +
272B GLY* 3.2 13.4 + - - -
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Residues in contact with VAL 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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224B GLU* 6.0 2.5 - - - +
266B LYS* 2.8 31.2 + - + +
267B LEU* 4.0 7.9 - - + +
269B GLY* 1.3 70.7 - - - +
271B ASN* 1.3 62.6 + - + +
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Residues in contact with ASN 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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227B VAL* 3.6 32.8 - - + +
228B SER* 5.5 1.0 + - - -
231B GLY* 5.7 0.4 - - - -
232B ALA* 3.9 7.6 - - + +
267B LEU* 3.0 23.0 + - + +
268B GLN* 3.9 4.7 - - - +
270B VAL* 1.3 80.8 - - + +
272B GLY* 1.3 59.8 + - - +
273B SER* 3.8 21.5 - - - +
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Residues in contact with GLY 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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268B GLN 2.8 15.4 + - - -
269B GLY* 3.2 9.8 + - - -
271B ASN* 1.3 73.4 - - - +
273B SER* 1.3 61.9 + - - +
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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