Contacts of the helix formed by residues 219 - 243 (chain A) in PDB entry 3LRB
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 219 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A VAL* 4.4 2.0 - - - +
218A LYS* 1.3 83.8 - - - +
220A PRO* 1.3 64.6 - - + +
221A LYS* 4.5 1.6 - - + +
222A ARG* 4.2 23.7 - - + +
223A ASN* 2.7 55.8 + - - +
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Residues in contact with PRO 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER 5.0 0.5 - - - +
68A PRO* 3.6 39.4 - - + +
214A ALA* 4.0 19.3 - - - +
215A GLY* 5.7 0.7 - - - -
217A VAL 4.1 1.8 - - - +
218A LYS 3.5 10.1 - - - +
219A ASN* 1.3 83.2 - - + +
221A LYS* 1.3 55.6 + - + +
222A ARG 2.8 12.3 + - - -
224A VAL* 3.1 40.2 + - + +
225A PRO* 3.3 2.4 - - - +
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Residues in contact with LYS 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER 4.7 2.9 - - - -
65A PHE* 3.4 47.1 - - + +
66A LEU 3.5 22.1 + - - -
68A PRO* 4.2 17.0 - - + -
219A ASN* 3.4 2.3 - - + +
220A PRO* 1.3 79.1 - - - +
222A ARG* 1.3 64.8 + - + +
225A PRO* 4.3 3.9 - - - +
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Residues in contact with ARG 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 6.1 0.2 - - + -
219A ASN* 3.5 19.1 + - + +
220A PRO 2.8 4.8 + - - -
221A LYS* 1.3 83.5 - - + +
223A ASN* 1.3 66.2 + - - +
224A VAL 3.5 0.7 - - - -
225A PRO* 3.4 7.4 - - - +
226A ILE* 2.9 33.9 - - + +
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Residues in contact with ASN 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.2 47.5 + - + +
217A VAL* 3.7 17.0 - - + -
218A LYS* 3.1 14.5 - - - +
219A ASN* 2.7 58.6 + - - +
222A ARG* 1.3 75.6 - - - +
224A VAL* 1.3 56.8 + - - +
226A ILE* 3.5 2.9 - - - +
227A ALA* 2.9 27.4 + - - +
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Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 5.8 0.2 - - - -
64A SER* 3.1 33.2 - - - +
68A PRO* 5.0 2.7 - - + -
210A ALA* 3.4 32.4 - - + +
211A SER* 4.1 1.6 - - - +
214A ALA* 4.6 8.3 - - - -
217A VAL* 4.5 17.5 - - + -
220A PRO* 3.1 35.1 + - + +
223A ASN* 1.3 74.2 - - - +
225A PRO* 1.3 72.9 - - + +
227A ALA* 3.0 9.4 + - - +
228A THR* 3.0 18.5 + - + +
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Residues in contact with PRO 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ALA* 3.1 32.3 - - + +
62A LYS* 4.1 15.7 - - - +
64A SER* 4.1 3.6 - - - +
65A PHE* 4.1 21.3 - - + +
220A PRO 3.3 9.4 - - - +
221A LYS 4.4 4.9 - - - +
222A ARG* 3.4 13.9 - - - +
224A VAL* 1.3 89.6 - - + +
226A ILE* 1.3 69.2 + - + +
227A ALA 2.8 1.6 - - - -
228A THR* 2.6 24.6 + - + -
229A ILE* 2.9 14.4 + - - +
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Residues in contact with ILE 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.5 35.2 - - + -
16A THR* 4.4 2.8 - - + +
222A ARG* 2.9 31.4 - - + +
223A ASN* 3.5 8.5 - - - +
225A PRO* 1.3 79.3 - - + +
227A ALA* 1.3 52.8 + - - +
229A ILE* 3.4 6.2 + - - +
230A GLY* 2.8 33.6 + - - -
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Residues in contact with ALA 227 (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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15A VAL* 4.0 13.7 - - + -
16A THR* 3.3 24.1 - - + -
19A VAL* 3.8 12.8 - - + +
210A ALA* 3.7 13.2 - - + -
223A ASN 2.9 15.0 + - - +
224A VAL* 3.1 13.7 - - - +
225A PRO 2.6 3.6 + - - -
226A ILE* 1.3 70.8 - - - +
228A THR* 1.3 64.5 + - - +
231A GLY* 2.8 23.9 + - - -
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Residues in contact with THR 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 3.7 11.9 - - - -
57A SER 3.2 22.5 + - - -
60A TYR* 5.0 3.1 - - + -
61A ALA* 3.4 18.4 - - - +
64A SER* 5.0 0.2 - - - +
207A VAL 3.9 18.4 - - - +
210A ALA* 3.3 15.5 - - + -
211A SER 4.4 3.1 - - - +
224A VAL* 3.0 21.9 + - + +
225A PRO* 2.6 15.1 + - + +
227A ALA* 1.3 72.0 - - - +
229A ILE* 1.3 56.3 + - - -
231A GLY* 3.8 0.3 - - - -
232A VAL* 2.7 42.5 + - - +
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Residues in contact with ILE 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A SER* 3.9 19.1 - - - +
58A MET* 4.5 12.8 - - + -
61A ALA* 3.3 28.7 - - + -
62A LYS* 3.9 17.5 - - - +
225A PRO 2.9 9.9 + - - +
226A ILE* 3.9 5.8 - - - +
228A THR* 1.3 80.4 + - - +
230A GLY* 1.3 62.6 + - - +
232A VAL* 3.8 0.3 - - - +
233A LEU* 2.8 57.0 + - + +
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Residues in contact with GLY 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 5.0 4.7 - - - -
226A ILE* 2.8 21.8 + - - -
229A ILE* 1.3 75.0 - - - +
231A GLY* 1.3 62.9 + - - +
233A LEU* 3.8 5.0 - - - +
234A ILE* 2.8 38.4 + - - +
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Residues in contact with GLY 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 3.8 7.0 + - - -
19A VAL* 4.2 3.4 - - - -
20A SER* 3.4 34.7 + - - -
227A ALA 2.8 21.9 + - - -
228A THR 3.8 0.4 - - - -
230A GLY* 1.3 72.9 - - - +
232A VAL* 1.3 55.8 + - - +
234A ILE* 3.3 3.2 + - - +
235A ALA* 2.8 28.3 + - - +
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 4.9 2.9 - - + -
23A ILE* 5.5 2.9 - - + -
53A ALA 4.5 3.4 - - - +
54A LEU* 4.4 15.3 - - + -
57A SER* 3.3 25.1 - - - +
204A PHE* 3.4 29.6 - - + -
207A VAL* 3.1 31.2 - - + -
228A THR* 2.7 33.7 + - - +
229A ILE 3.9 1.8 - - - +
231A GLY* 1.3 69.3 - - - +
233A LEU* 1.3 57.2 + - - +
235A ALA* 2.8 6.1 + - - +
236A ALA* 2.6 34.7 + - + +
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Residues in contact with LEU 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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54A LEU* 3.4 33.4 - - + -
229A ILE* 2.8 41.0 + - + +
230A GLY* 3.8 5.2 - - - +
232A VAL* 1.3 72.7 - - - +
234A ILE* 1.3 64.8 + - + +
236A ALA* 3.8 5.1 - - + +
237A VAL* 2.9 29.4 + - + +
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Residues in contact with ILE 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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16A THR* 5.1 9.6 - - - +
17A LEU* 5.7 6.5 - - + -
20A SER* 3.0 29.2 - - - +
24A MET* 5.0 2.5 - - + -
159A LEU* 5.1 12.1 - - + -
230A GLY* 2.8 31.3 + - - +
231A GLY* 3.3 4.0 - - - +
233A LEU* 1.3 76.6 - - + +
235A ALA* 1.3 63.4 + - - +
237A VAL* 3.9 4.3 - - - +
238A CYS* 2.9 45.8 + - - -
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Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER* 4.4 4.5 - - - +
23A ILE* 3.3 35.7 - - + -
24A MET* 4.2 16.9 - - - +
204A PHE* 4.8 2.0 - - + -
231A GLY 2.8 14.9 + - - +
232A VAL* 3.3 8.7 - - - +
234A ILE* 1.3 77.3 - - - +
236A ALA* 1.3 56.4 + - - +
238A CYS* 3.7 1.2 - - - +
239A TYR* 2.9 41.2 + - + -
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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
----------------------------------------------------------
50A ILE* 3.5 36.8 - - + -
54A LEU* 5.0 3.4 - - + -
204A PHE* 3.8 10.2 - - + -
232A VAL 2.6 19.0 + - - +
233A LEU* 3.8 8.3 - - + +
235A ALA* 1.3 71.8 - - - +
237A VAL* 1.3 64.5 + - - +
239A TYR* 3.0 15.2 - - - +
240A VAL* 2.9 24.1 + - - +
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Residues in contact with VAL 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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163A VAL* 6.3 2.2 - - + -
166A ALA* 5.9 1.1 - - + -
233A LEU* 2.9 17.8 + - + +
234A ILE* 3.9 5.2 - - - +
236A ALA* 1.3 75.1 - - + +
238A CYS* 1.3 73.9 + - - +
240A VAL* 3.0 15.9 + - - +
241A LEU* 3.0 37.8 + - + +
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Residues in contact with CYS 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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24A MET* 3.2 37.0 - - + -
28A VAL* 6.5 0.2 - - - -
159A LEU* 4.6 2.0 - - - -
162A ILE* 3.9 11.0 - - + +
163A VAL* 4.1 23.6 - - - -
234A ILE* 2.9 38.1 + - - +
235A ALA 3.7 2.9 - - - +
237A VAL* 1.3 84.0 - - - +
239A TYR* 1.3 53.8 + - - +
241A LEU* 4.6 1.7 - - - +
242A SER* 2.5 40.3 + - - -
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Residues in contact with TYR 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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23A ILE* 3.0 20.9 + - + -
24A MET* 3.1 20.5 + - - -
27A GLY* 5.7 1.0 - - - -
28A VAL* 3.8 13.9 + - + -
31A LEU* 3.2 33.7 - - + -
46A TRP* 3.7 19.7 - + + -
203A SER* 2.6 26.1 + - - -
204A PHE* 3.6 42.8 - + - -
235A ALA* 2.9 30.6 + - + -
236A ALA* 3.0 11.0 - - - +
238A CYS* 1.3 75.8 - - + +
240A VAL* 1.3 55.0 + - - +
242A SER* 2.7 18.6 + - - -
243A THR* 3.0 22.8 + - - +
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 5.7 6.3 - - + -
46A TRP* 4.5 20.9 - - + -
50A ILE* 3.5 31.9 - - + -
236A ALA 2.9 8.2 + - - +
237A VAL* 3.0 7.2 + - - +
239A TYR* 1.3 73.6 - - + +
241A LEU* 1.3 75.0 + - + +
242A SER 2.9 6.1 + - - -
243A THR* 3.4 3.6 + - - -
244A THR* 2.9 42.1 + - + +
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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
----------------------------------------------------------
165A ILE* 4.0 15.6 - - - +
166A ALA* 3.7 45.2 - - + +
167A VAL* 6.1 0.2 - - + -
237A VAL* 3.0 31.8 + - + +
238A CYS 4.6 0.7 - - - +
240A VAL* 1.3 87.5 - - + +
242A SER* 1.3 58.1 + - - +
244A THR* 3.3 16.4 + - - +
245A ALA 4.3 2.3 + - - -
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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
----------------------------------------------------------
28A VAL* 4.4 11.5 - - - +
32A PRO* 5.4 2.1 - - - +
162A ILE* 4.1 26.7 - - - -
165A ILE* 4.9 9.3 - - - +
238A CYS 2.5 24.2 + - - -
239A TYR* 2.7 17.2 + - - -
240A VAL 2.9 1.2 - - - -
241A LEU* 1.3 77.1 - - - +
243A THR* 1.3 63.6 + - - +
244A THR 3.1 7.4 + - - -
245A ALA* 3.4 20.3 + - - +
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Residues in contact with THR 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 5.8 2.5 - - + -
31A LEU* 4.2 12.1 - - + -
32A PRO* 3.4 42.2 - - + -
35A LEU* 4.5 10.6 - - + +
41A ILE* 6.0 0.7 - - - +
43A ILE* 6.0 1.2 - - - +
46A TRP* 3.2 32.9 + - + -
239A TYR 3.0 19.8 + - - +
240A VAL* 3.7 3.1 + - - -
242A SER* 1.3 77.6 - - - +
244A THR* 1.3 61.3 + - - +
245A ALA 3.6 1.8 - - - -
246A ILE* 3.4 19.2 - - - +
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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
------------------------------------------------------------
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