Contacts of the helix formed by residues 231 - 255 (chain B) in PDB entry 4G1U
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 ASN 231 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B GLN* 5.8 0.2 + - - -
226B HIS* 6.0 0.9 - - - -
229B GLY 3.2 5.7 + - - +
230B VAL* 1.3 70.7 - - - +
232B VAL* 1.3 62.8 + - - +
233B ARG* 3.6 8.7 + - - +
234B GLN* 3.5 46.2 + - + +
235B ALA* 3.1 22.0 + - - +
80C PRO* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LEU* 3.6 14.4 - - + -
222B ASP* 3.3 34.1 - - + +
225B ALA* 4.0 9.6 - - + -
226B HIS* 3.5 19.5 - - + +
230B VAL* 2.9 19.8 + - + +
231B ASN* 1.3 70.8 + - - +
233B ARG* 1.3 60.7 + - + +
235B ALA* 3.5 2.8 + - - +
236B LYS* 2.9 55.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ASN* 3.3 8.1 + - - +
232B VAL* 1.3 78.1 - - + +
234B GLN* 1.3 63.5 + - - +
236B LYS* 3.2 10.2 + - + +
237B LEU* 2.9 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ASN* 3.5 37.0 + - - +
232B VAL 3.4 0.2 - - - -
233B ARG* 1.3 80.7 - - - +
235B ALA* 1.3 57.5 + - - +
237B LEU* 3.3 6.1 + - - +
238B ARG* 2.9 81.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B GLN* 4.7 5.8 - - - -
214B GLN* 3.8 23.6 - - + -
218B LEU* 3.6 24.0 - - + -
230B VAL* 4.6 2.9 - - + -
231B ASN 3.1 15.1 + - - +
232B VAL* 3.8 3.8 - - - +
234B GLN* 1.3 78.8 - - - +
236B LYS* 1.3 57.6 + - - +
238B ARG* 4.1 3.7 - - - +
239B LEU* 2.9 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 3.8 13.3 - - + +
135B PHE* 3.5 28.0 - - + -
139B ARG* 3.3 36.5 - - - +
140B TRP* 5.2 9.7 - - - -
218B LEU* 4.9 3.8 - - + -
222B ASP* 2.8 45.1 + - - +
232B VAL* 2.9 33.3 + - + +
233B ARG* 3.5 8.5 - - + +
235B ALA* 1.3 77.0 - - - +
237B LEU* 1.3 65.0 + - + +
239B LEU* 3.8 1.2 - - - +
240B LEU* 2.9 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PHE* 5.7 6.7 - - + -
233B ARG* 2.9 22.4 + - + +
234B GLN* 3.7 6.1 - - - +
236B LYS* 1.3 75.9 - - + +
238B ARG* 1.3 66.4 + - + +
240B LEU* 3.0 18.0 + - + +
241B LEU* 2.9 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B GLN* 4.0 39.5 + - + +
234B GLN* 2.9 66.8 + - + +
235B ALA* 4.1 2.5 - - - +
237B LEU* 1.3 74.9 - - + +
239B LEU* 1.3 59.5 + - - +
241B LEU* 3.7 6.0 - - - +
242B LEU* 2.9 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ILE* 3.7 22.0 - - + +
79B LEU* 3.8 20.2 - - + -
208B GLY* 5.6 0.7 - - - +
211B GLN* 3.9 26.5 - - + +
214B GLN* 5.2 0.7 - - + -
215B LEU* 3.6 43.3 - - + +
218B LEU* 4.1 16.6 - - + -
235B ALA* 2.9 30.9 + - + +
236B LYS 3.8 2.7 - - - +
238B ARG* 1.3 76.4 - - - +
240B LEU* 1.3 65.9 + - - +
242B LEU* 3.2 9.6 - - + +
243B SER* 3.0 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 3.6 14.8 - - + +
80B PHE* 4.8 3.4 - - + -
128B LEU* 5.3 7.4 - - + +
131B SER* 3.4 41.3 - - - +
132B THR* 3.6 30.5 - - - +
135B PHE* 4.1 26.0 - - + -
236B LYS 2.9 12.9 + - - +
237B LEU* 3.3 19.5 - - + +
239B LEU* 1.3 75.5 - - - +
241B LEU* 1.3 67.9 + - + +
243B SER* 3.1 6.7 + - - +
244B ALA* 2.9 24.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PHE* 4.4 21.8 - - + -
128B LEU* 3.9 17.9 - - + -
237B LEU* 2.9 30.0 + - + +
238B ARG* 3.7 7.4 - - - +
240B LEU* 1.3 75.7 - - + +
242B LEU* 1.3 68.0 + - + +
244B ALA* 2.8 17.2 + - - +
245B ILE* 2.9 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ILE* 3.7 17.9 - - + -
204B THR* 3.1 43.7 + - - +
207B LEU* 4.1 23.3 - - + +
208B GLY* 3.5 21.1 - - - +
211B GLN* 5.4 2.5 - - + -
238B ARG* 2.9 27.4 + - + +
239B LEU* 3.2 14.8 - - + +
241B LEU* 1.3 77.7 - - + +
243B SER* 1.3 63.6 + - - +
245B ILE* 3.3 8.8 + - + +
246B LEU* 3.0 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B SER* 3.5 24.9 - - - -
75B ILE* 4.2 11.9 - - - +
76B MET* 3.5 24.6 + - - +
79B LEU* 5.5 1.6 - - - +
131B SER* 4.3 4.7 + - - -
239B LEU 3.0 10.7 + - - -
240B LEU* 3.1 14.0 + - - +
242B LEU* 1.3 78.8 - - - +
244B ALA* 1.3 57.2 + - - +
246B LEU* 3.6 7.6 - - - +
247B ILE* 2.9 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PHE* 4.0 10.7 - - + -
127B SER* 3.2 15.3 + - - +
128B LEU* 3.9 36.6 - - + +
131B SER* 4.9 6.1 - - - -
240B LEU 2.9 13.3 + - - +
241B LEU* 2.8 14.3 + - - +
243B SER* 1.3 75.3 + - - +
245B ILE* 1.3 59.8 + - - +
247B ILE* 5.2 0.2 - - - -
248B GLY* 2.9 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PHE* 3.7 25.5 - - + +
200B LEU* 4.2 37.4 - - + +
204B THR* 4.3 14.8 - - + +
241B LEU* 2.9 30.7 + - + +
242B LEU* 3.6 8.7 - - + +
244B ALA* 1.3 75.7 - - - +
246B LEU* 1.3 65.2 + - - +
248B GLY* 3.3 1.0 + - - -
249B ALA* 3.0 23.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA* 3.5 35.6 - - + +
71B VAL* 3.6 26.7 - - + -
72B SER* 3.6 24.0 - - - +
75B ILE* 3.8 12.6 - - + -
201B ILE* 4.1 4.9 - - + -
204B THR* 3.6 27.8 - - + -
205B CYS* 3.8 13.0 - - - -
242B LEU* 3.0 16.6 + - + +
243B SER* 3.6 7.9 - - - +
245B ILE* 1.3 79.4 - - - +
247B ILE* 1.3 57.2 + - - +
249B ALA* 3.4 3.9 + - - +
250B ALA* 3.0 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 5.2 3.8 - - + -
72B SER* 3.1 27.6 - - - +
76B MET* 3.4 19.7 - - + -
87B PRO* 3.5 23.1 - - + -
92B ILE* 3.8 25.1 - - + -
93B SER* 3.8 14.1 - - - +
96B ALA* 5.0 0.7 - - + -
127B SER* 3.5 14.4 - - - +
131B SER* 5.3 0.2 - - - +
243B SER 2.9 17.1 + - - +
244B ALA* 5.2 0.4 - - - -
246B LEU* 1.3 68.6 - - - +
248B GLY* 1.3 67.2 + - - +
250B ALA* 4.4 5.4 - - - -
251B VAL* 2.8 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B MET* 5.0 3.8 - - - -
123B ALA* 3.5 31.0 - - - +
124B PHE* 4.1 6.3 - - - -
127B SER* 3.8 1.0 + - - -
244B ALA 2.9 18.3 + - - -
245B ILE 3.6 0.7 - - - -
247B ILE* 1.3 76.6 - - - +
249B ALA* 1.3 56.5 + - - +
251B VAL* 4.9 0.4 - - - -
252B ALA* 3.0 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B MET* 4.0 23.7 - - - -
197B ALA* 4.5 8.5 - - - +
200B LEU* 4.5 11.6 - - + +
201B ILE* 3.8 28.0 - - + -
245B ILE 3.0 15.0 + - - +
246B LEU 3.8 0.4 - - - +
248B GLY* 1.3 74.5 - - - +
250B ALA* 1.3 64.0 + - - +
251B VAL 3.2 0.3 + - - -
252B ALA* 3.2 1.7 + - - +
253B VAL* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 4.2 18.8 - - + +
68B ALA* 3.7 22.4 - - + -
69B LEU* 3.8 24.2 - - + -
201B ILE* 4.4 2.8 - - - +
246B LEU 3.0 17.5 + - - +
247B ILE* 4.0 2.2 - - - +
249B ALA* 1.3 76.2 - - - +
251B VAL* 1.3 53.9 + - - +
253B VAL* 3.5 0.7 + - - -
254B SER* 2.4 40.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 5.6 3.4 - - + -
93B SER* 3.5 30.7 - - - +
96B ALA* 3.6 22.7 - - + -
97B ALA* 3.7 19.5 - - + +
100B VAL* 5.1 0.2 - - + -
123B ALA* 4.7 0.9 - - + -
181B TRP* 3.4 5.4 - - + -
247B ILE* 2.8 33.4 + - + +
248B GLY 4.0 1.6 - - - +
250B ALA* 1.3 68.9 - - + +
252B ALA* 1.3 60.8 + - - +
253B VAL 3.0 7.8 + - - -
254B SER* 4.1 0.9 - - - -
255B GLY* 2.6 51.1 + - - +
256B VAL* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B VAL* 4.3 2.0 - - + -
119B HIS* 3.5 34.7 - - + +
120B MET* 3.5 21.6 - - + +
123B ALA* 3.6 6.3 - - + -
181B TRP* 3.4 21.4 - - - -
248B GLY 3.0 19.3 + - - +
251B VAL* 1.3 78.3 - - - +
253B VAL* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.6 37.6 - - + +
65B VAL* 5.0 3.8 - - + -
120B MET* 3.6 17.3 - - + -
181B TRP* 3.9 13.0 + - - +
185B SER 4.2 2.3 - - - +
186B LEU* 4.1 6.8 - - - +
188B GLN 5.6 3.6 - - - +
193B THR* 4.3 24.5 - - + +
197B ALA* 3.8 19.7 - - + -
249B ALA 3.0 15.7 + - - +
250B ALA 4.3 1.8 - - - +
251B VAL 3.0 0.6 - - - -
252B ALA* 1.3 84.6 - - - +
254B SER* 1.3 57.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 3.7 21.2 - - - +
69B LEU* 5.5 1.4 - - - +
181B TRP* 3.7 5.4 - - - +
184B GLY* 3.2 3.3 - - - -
185B SER 2.8 31.9 + - - +
186B LEU* 3.4 25.1 - - - -
250B ALA* 2.4 26.8 + - - +
251B VAL* 4.1 1.0 - - - +
253B VAL* 1.3 78.3 - - - +
255B GLY* 1.3 63.0 + - - +
257B ILE* 4.0 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA* 5.6 0.4 - - - -
181B TRP* 3.6 25.7 - - - -
182B SER* 4.4 3.6 - - - -
251B VAL* 2.6 53.6 + - - +
253B VAL 3.9 0.2 - - - -
254B SER* 1.3 74.9 + - - +
256B VAL* 1.3 64.1 + - - +
257B ILE 4.2 1.1 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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