Contacts of the helix formed by residues 230 - 245 (chain B) in PDB entry 3GUU
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 PHE 230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B LEU* 3.7 28.2 + - + +
228B GLY 3.2 0.8 - - - -
229B PRO* 1.3 98.4 - - + +
231B ALA* 1.3 59.1 + - - +
232B GLY 3.1 3.8 - - - +
233B PHE* 3.0 50.2 + + + +
234B ALA 3.9 1.0 + - - -
278B VAL* 4.3 15.5 - - + +
335B GLU* 4.6 13.2 - - + -
336B ILE* 4.0 25.8 - - + -
431B PHE* 3.5 38.1 - + + -
433B LYS* 4.1 26.5 - - + -
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Residues in contact with ALA 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU 3.5 12.0 + - - +
226B ASN* 4.5 1.6 - - - +
227B GLY 3.7 9.9 - - - +
228B GLY 3.0 18.3 + - - +
229B PRO 3.4 1.2 + - - -
230B PHE* 1.3 75.7 - - - +
232B GLY* 1.3 65.8 + - - +
233B PHE 3.1 0.2 - - - -
234B ALA* 3.1 14.5 + - - +
235B LEU* 3.1 11.8 + - - +
281B TYR* 3.6 13.0 + - - +
284B LEU* 3.1 31.0 - - + +
286B VAL* 4.6 2.1 - - - +
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Residues in contact with GLY 232 (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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229B PRO 5.1 0.2 + - - -
230B PHE* 3.1 3.4 - - - +
231B ALA* 1.3 77.7 - - - +
233B PHE* 1.3 55.3 + - - +
235B LEU* 3.2 5.2 + - - +
236B ALA* 2.8 24.9 + - - +
267B ILE* 4.0 1.4 - - - +
277B VAL* 3.3 29.5 + - - +
281B TYR* 3.4 34.0 + - - +
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Residues in contact with PHE 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ASP* 3.5 44.6 - - + -
149B PHE* 4.0 4.1 - + - -
225B LEU* 4.0 13.5 - - + -
230B PHE* 3.0 32.1 + + + +
232B GLY* 1.3 74.7 - - - +
234B ALA* 1.3 63.0 + - - +
236B ALA* 3.7 5.8 - - + +
237B GLY* 3.1 18.2 + - - -
274B LEU* 3.7 17.0 - - + -
277B VAL* 3.6 17.3 - - + -
278B VAL* 3.6 34.3 - - + -
336B ILE* 5.3 3.4 - - + -
431B PHE* 3.7 22.2 - + - -
442B 1PE 3.5 27.0 - - - +
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B PHE* 3.8 24.0 - - + +
225B LEU* 4.1 10.9 - - + +
226B ASN* 4.1 24.5 - - - +
230B PHE 3.9 1.6 + - - -
231B ALA 3.1 11.4 + - - +
233B PHE* 1.3 74.9 - - - +
235B LEU* 1.3 62.5 + - - +
237B GLY* 3.4 2.1 + - - -
238B VAL* 3.2 26.2 + - - +
286B VAL* 4.3 7.2 - - + -
442B 1PE 3.9 12.9 - - - +
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Residues in contact with LEU 235 (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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231B ALA 3.1 11.3 + - - +
232B GLY* 3.5 8.1 - - - +
234B ALA* 1.3 76.2 - - - +
236B ALA* 1.3 52.0 + - - +
238B VAL* 3.2 11.2 + - + +
239B SER* 2.8 31.9 + - - -
263B THR* 3.5 27.8 - - + -
264B LEU* 4.9 16.4 - - + -
267B ILE* 3.6 24.7 - - + -
281B TYR* 3.7 20.6 - - + +
284B LEU* 4.1 12.8 - - + -
286B VAL* 4.0 14.6 - - + +
289B LEU* 3.9 24.7 - - + -
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Residues in contact with ALA 236 (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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95B ASP 4.6 8.5 - - - +
96B ALA* 5.0 1.6 - - - -
97B THR* 3.2 16.1 - - + +
149B PHE* 3.6 20.2 - - + -
232B GLY 2.8 18.7 + - - +
233B PHE* 3.7 9.0 - - - +
235B LEU* 1.3 72.8 - - - +
237B GLY* 1.3 52.8 + - - +
239B SER* 3.5 3.3 + - - -
240B GLY* 2.8 29.1 + - - -
267B ILE* 3.5 18.3 - - + +
277B VAL* 4.5 8.7 - - + -
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Residues in contact with GLY 237 (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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149B PHE* 3.8 4.4 - - - -
150B ILE* 3.7 20.6 - - - +
233B PHE 3.1 10.7 + - - -
235B LEU 3.2 0.2 - - - -
236B ALA* 1.3 73.2 - - - +
238B VAL* 1.3 60.7 + - - +
241B LEU* 2.8 36.0 + - - +
442B 1PE 3.7 23.6 - - - -
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Residues in contact with VAL 238 (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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222B PHE* 4.1 11.9 - - + -
234B ALA 3.2 14.6 + - - +
235B LEU* 3.2 15.8 + - + +
237B GLY* 1.3 74.1 - - - +
239B SER* 1.3 66.0 + - - +
242B SER* 2.9 31.2 + - - +
248B MET* 4.0 2.8 - - + +
252B ILE* 4.0 29.4 - - + -
264B LEU* 5.5 5.4 - - + -
286B VAL* 4.3 14.1 - - + -
442B 1PE 3.2 37.9 - - - +
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Residues in contact with SER 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B THR* 2.7 29.6 + - - -
235B LEU 2.8 16.5 + - - -
236B ALA* 3.6 4.3 - - - -
238B VAL* 1.3 78.4 - - - +
240B GLY* 1.3 61.6 + - - +
243B LEU* 3.2 12.9 + - - +
264B LEU* 3.8 18.1 - - - +
267B ILE* 4.0 7.2 - - - -
268B ARG* 3.0 44.7 + - - +
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Residues in contact with GLY 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B THR* 3.5 5.6 - - - +
148B ALA* 3.5 16.1 - - - +
149B PHE 3.2 33.9 - - - -
151B ALA* 4.3 0.6 - - - +
236B ALA 2.8 16.4 + - - -
239B SER* 1.3 69.7 - - - +
241B LEU* 1.3 65.7 + - - +
243B LEU* 3.3 3.3 + - - +
244B ALA* 3.3 17.2 + - - +
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Residues in contact with LEU 241 (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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149B PHE 3.7 1.8 + - - -
150B ILE* 3.4 31.9 - - + +
151B ALA* 3.7 14.4 - - + -
218B ALA* 4.3 6.7 - - + -
237B GLY 2.8 24.0 + - - +
240B GLY* 1.3 72.7 - - - +
242B SER* 1.3 56.0 + - - +
244B ALA* 3.2 2.7 + - - +
245B HIS* 3.0 35.9 + - + +
248B MET* 3.8 15.3 - - + -
304B ILE* 4.4 7.9 - - + -
305B LEU* 4.0 19.1 - - + -
308B GLU* 3.7 28.5 - - + +
442B 1PE 3.8 20.2 - - - +
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Residues in contact with SER 242 (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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238B VAL* 2.9 21.3 + - - +
240B GLY 3.4 0.2 - - - -
241B LEU* 1.3 76.2 - - - +
243B LEU* 1.3 59.9 + - - +
245B HIS 3.1 24.2 + - - +
246B PRO* 4.1 1.2 - - - +
248B MET* 3.5 7.6 - - - +
249B GLU* 3.0 42.3 - - - +
252B ILE* 3.4 26.9 - - - +
264B LEU* 6.0 0.9 - - - -
268B ARG* 3.5 8.1 - - - -
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Residues in contact with LEU 243 (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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65B GLN* 5.4 1.0 - - - +
97B THR* 4.0 8.3 - - - +
146B LYS* 3.4 66.7 + - + +
147B ALA 3.7 14.1 - - - +
148B ALA* 4.2 8.7 - - + -
239B SER* 3.2 33.9 + - - +
240B GLY* 3.5 8.1 - - - +
241B LEU 3.2 0.2 - - - -
242B SER* 1.3 75.1 - - - +
244B ALA* 1.3 58.3 + - - +
245B HIS 5.2 0.2 - - - -
246B PRO* 5.7 1.6 - - - +
249B GLU* 4.4 2.2 - - - +
268B ARG* 3.8 27.4 - - - +
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Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B THR* 3.5 19.9 - - - +
65B GLN* 2.7 34.9 + - - +
148B ALA* 4.0 6.7 - - + -
151B ALA* 3.4 33.0 - - + -
154B GLU* 4.1 8.5 - - - +
240B GLY 3.3 4.3 + - - +
241B LEU 3.2 6.5 + - - +
242B SER 3.2 0.2 - - - -
243B LEU* 1.3 78.7 - - - +
245B HIS* 1.3 57.2 + - + +
246B PRO* 3.9 2.7 - - - -
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Residues in contact with HIS 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B THR* 3.7 20.4 - - + +
153B TYR* 5.4 1.8 - + - -
241B LEU* 3.0 29.8 + - + +
242B SER 3.1 7.7 + - - +
244B ALA* 1.3 86.0 + - + +
246B PRO* 1.3 62.4 - - - +
247B ASP 3.3 2.7 - - - -
248B MET* 3.1 12.0 + - + +
249B GLU 2.9 23.7 + - - -
304B ILE* 3.4 33.8 - - + +
307B GLN* 4.0 13.0 - - - -
308B GLU* 2.8 31.4 + - + -
443B SO4 2.7 27.5 + - - +
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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