Contacts of the helix formed by residues 230 - 245 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A LEU* 3.8 25.5 + - + +
228A GLY 3.2 0.6 - - - -
229A PRO* 1.3 96.8 - - + +
231A ALA* 1.3 55.7 + - - +
232A GLY 3.1 6.5 - - - +
233A PHE* 3.0 51.0 + + + +
234A ALA 4.0 0.5 + - - -
278A VAL* 4.3 18.2 - - + +
335A GLU* 4.6 8.3 - - + -
336A ILE* 3.7 31.2 - - + -
431A PHE* 3.3 35.2 - - + -
433A LYS* 3.8 30.1 - - + -
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU 3.5 20.9 + - - +
226A ASN* 4.3 2.5 - - - +
227A GLY 3.6 2.5 - - - +
228A GLY 3.2 18.8 + - - +
229A PRO 3.5 1.0 - - - -
230A PHE* 1.3 72.8 - - - +
232A GLY* 1.3 63.2 + - - +
233A PHE 3.1 0.2 - - - -
234A ALA* 3.0 15.4 + - - +
235A LEU* 3.1 12.8 + - - +
281A TYR* 3.8 11.6 + - - +
284A LEU* 3.1 30.8 - - + +
286A VAL* 4.5 2.1 - - + +
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Residues in contact with GLY 232 (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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229A PRO 5.2 0.2 + - - -
230A PHE* 3.1 3.2 - - - +
231A ALA* 1.3 77.0 - - - +
233A PHE* 1.3 51.2 + - - +
235A LEU* 3.4 4.4 + - - +
236A ALA* 2.8 28.9 + - - +
267A ILE* 3.9 2.3 - - - +
277A VAL* 3.3 29.0 + - - +
278A VAL* 5.8 0.6 - - - +
281A TYR* 3.5 33.3 + - - +
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Residues in contact with PHE 233 (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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95A ASP* 3.6 35.7 - - + -
149A PHE* 4.0 2.0 - + - -
225A LEU* 3.8 13.9 - - + -
230A PHE* 3.0 41.1 + + + +
232A GLY* 1.3 73.2 - - - +
234A ALA* 1.4 58.5 + - - +
236A ALA* 3.4 5.8 + - + +
237A GLY 3.0 23.2 + - - -
274A LEU* 4.1 9.4 - - + -
277A VAL* 3.7 19.2 - - + +
278A VAL* 3.7 17.7 - - + -
336A ILE* 4.5 9.4 - - + -
431A PHE* 3.5 40.2 - + - -
442A 1PE 3.4 26.0 - - - +
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Residues in contact with ALA 234 (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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222A PHE* 3.8 26.9 - - + +
225A LEU* 4.1 20.7 - - + +
226A ASN* 4.1 10.5 - - - +
230A PHE 4.0 1.0 + - - -
231A ALA 3.0 12.0 + - - +
233A PHE* 1.4 73.1 - - - +
235A LEU* 1.3 66.9 + - - +
237A GLY* 3.2 3.1 + - - -
238A VAL* 3.0 25.5 + - - +
286A VAL* 4.2 8.7 - - + -
442A 1PE 4.0 11.6 - - - +
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Residues in contact with LEU 235 (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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231A ALA 3.1 9.4 + - - +
232A GLY* 3.7 6.7 - - - +
234A ALA* 1.3 78.8 - - - +
236A ALA* 1.3 63.9 + - - +
238A VAL* 3.3 10.1 + - + +
239A SER* 3.0 22.9 + - - -
263A THR* 3.4 29.4 - - + -
264A LEU* 5.1 10.8 - - + -
267A ILE* 4.0 16.2 - - + -
281A TYR* 3.7 24.7 - - + +
284A LEU* 3.8 12.3 - - + -
286A VAL* 3.9 21.0 - - + +
289A LEU* 3.5 26.5 - - + -
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Residues in contact with ALA 236 (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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95A ASP 4.7 6.5 - - - +
96A ALA* 5.0 1.1 - - - -
97A THR* 3.5 11.0 - - + +
149A PHE* 3.7 19.2 - - + -
232A GLY 2.8 21.1 + - - +
233A PHE* 3.6 9.2 - - + +
234A ALA 3.2 0.2 - - - -
235A LEU* 1.3 73.2 - - - +
237A GLY* 1.3 51.9 + - - +
239A SER* 3.3 4.6 + - - -
240A GLY* 2.7 32.9 + - - -
267A ILE* 3.6 17.7 - - + +
277A VAL* 4.5 11.0 - - + -
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Residues in contact with GLY 237 (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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149A PHE* 3.7 4.8 - - - -
150A ILE* 3.6 21.5 - - - -
233A PHE 3.0 11.7 + - - -
234A ALA 3.2 3.3 + - - -
236A ALA* 1.3 73.0 - - - +
238A VAL* 1.3 58.2 + - - +
241A LEU* 2.8 36.2 + - - +
442A 1PE 3.8 20.6 - - - -
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Residues in contact with VAL 238 (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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222A PHE* 4.1 14.4 - - + -
234A ALA 3.0 20.1 + - - +
235A LEU* 3.6 12.1 - - + +
237A GLY* 1.3 74.2 - - - +
239A SER* 1.4 59.9 + - - +
241A LEU* 3.8 1.2 - - - +
242A SER* 2.9 35.6 + - - +
248A MET* 4.0 3.2 - - + +
252A ILE* 4.0 30.5 - - + -
264A LEU* 5.3 5.6 - - + -
286A VAL* 4.1 17.5 - - + -
442A 1PE 3.8 31.8 - - - +
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Residues in contact with SER 239 (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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97A THR* 2.8 26.9 + - - -
235A LEU 3.0 14.9 + - - -
236A ALA 3.4 7.9 - - - -
238A VAL* 1.4 76.5 - - - +
240A GLY* 1.3 56.3 + - - +
242A SER* 3.3 1.3 + - - -
243A LEU* 3.0 26.8 + - - +
264A LEU* 3.8 17.9 - - - +
267A ILE* 4.0 7.0 - - - -
268A ARG* 2.8 39.8 + - - +
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Residues in contact with GLY 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A THR* 3.5 7.1 - - - +
148A ALA* 3.3 24.6 - - - +
149A PHE 3.2 35.2 - - - -
236A ALA 2.7 15.7 + - - -
239A SER* 1.3 69.2 + - - +
241A LEU* 1.3 64.2 + - - +
243A LEU* 3.1 10.8 + - - -
244A ALA* 3.3 2.3 + - - +
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Residues in contact with LEU 241 (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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149A PHE 3.6 1.2 + - - -
150A ILE* 3.4 34.5 - - + +
151A ALA* 3.8 9.4 - - + -
218A ALA* 4.1 11.4 - - + -
237A GLY 2.8 21.5 + - - +
238A VAL 3.9 2.9 - - - +
240A GLY* 1.3 72.7 - - - +
242A SER* 1.3 60.5 + - - +
244A ALA* 3.1 4.1 + - - -
245A HIS* 3.0 29.6 + - + +
248A MET* 3.9 17.3 - - + -
304A ILE* 4.9 3.1 - - + -
305A LEU* 3.9 20.6 - - + -
308A GLU* 3.8 23.6 - - + +
442A 1PE 3.5 26.2 - - - +
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Residues in contact with SER 242 (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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238A VAL* 2.9 26.0 + - - +
241A LEU* 1.3 71.8 - - - +
243A LEU* 1.3 60.6 + - - +
244A ALA 3.2 0.2 - - - -
245A HIS 3.3 15.1 + - - +
246A PRO* 4.4 0.9 - - - +
248A MET* 3.6 7.4 - - - +
249A GLU* 2.8 50.6 - - - +
252A ILE* 3.4 28.2 - - - +
264A LEU* 5.9 0.6 - - - +
268A ARG* 3.6 7.6 - - - -
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Residues in contact with LEU 243 (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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97A THR* 3.9 9.0 - - - +
146A LYS* 3.2 57.9 - - + +
147A ALA 3.7 13.0 - - - +
148A ALA* 4.1 6.7 - - + +
154A GLU* 5.4 1.0 - - - +
239A SER* 3.0 26.4 + - - +
240A GLY 3.1 7.3 + - - +
242A SER* 1.3 76.5 - - - +
244A ALA* 1.3 58.2 + - - +
245A HIS 5.3 0.2 - - - -
246A PRO* 6.0 0.4 - - - +
249A GLU* 4.8 1.8 - - - +
268A ARG* 3.7 34.1 - - + +
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Residues in contact with ALA 244 (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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64A THR* 3.6 22.2 - - - +
65A GLN* 2.8 29.6 + - - +
148A ALA* 3.9 5.6 - - + -
151A ALA* 3.4 33.4 - - + -
154A GLU* 3.8 9.9 - - - +
240A GLY 3.3 1.6 + - - +
241A LEU 3.1 7.2 + - - +
243A LEU* 1.3 80.7 - - - +
245A HIS* 1.3 56.8 + - + +
246A PRO* 3.7 4.6 - - - +
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Residues in contact with HIS 245 (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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64A THR* 3.6 19.8 - - + +
65A GLN* 4.1 1.0 + - - -
153A TYR* 5.5 2.0 - + - -
241A LEU* 3.0 28.8 + - - +
242A SER 3.3 6.7 + - - +
244A ALA* 1.3 84.1 - - + +
246A PRO* 1.4 69.3 - - - +
247A ASP 3.4 1.8 - - - -
248A MET* 3.2 5.0 + - + +
249A GLU 3.0 17.7 + - - -
304A ILE* 3.7 34.6 - - + +
307A GLN* 4.3 10.8 - - + -
308A GLU* 2.6 31.7 + - + -
443A GOL 2.2 38.7 + - - +
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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