Contacts of the helix formed by residues 225 - 249 (chain A) in PDB entry 3MB8
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 GLY 225 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ASP* 3.1 32.8 + - - -
223A ALA 3.4 2.2 - - - -
224A THR* 1.3 77.8 - - - +
226A VAL* 1.3 60.6 + - - -
227A LYS 3.3 2.9 + - - -
228A ALA 3.4 3.5 + - - -
229A THR* 2.8 30.1 + - - -
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Residues in contact with VAL 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLY* 1.3 69.8 - - - -
227A LYS* 1.3 75.4 + - + +
229A THR* 3.9 6.7 - - - -
230A THR* 2.8 40.8 + - - +
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Residues in contact with LYS 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LYS* 6.0 3.6 - - - -
107A GLN* 3.7 49.1 - - + +
108A GLY* 3.1 12.0 - - - -
225A GLY 3.3 1.2 - - - -
226A VAL* 1.3 89.6 - - + +
228A ALA* 1.3 57.9 + - - +
230A THR* 3.7 4.5 - - - -
231A GLY 3.0 23.4 + - - -
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A THR* 6.4 0.9 - - + -
107A GLN* 4.9 1.9 - - + +
108A GLY* 4.2 1.7 - - - +
208A ALA* 4.8 1.5 - - - +
209A VAL 4.2 20.6 - - - +
210A ASP* 4.4 7.0 - - + -
222A ASP 3.3 24.6 + - - +
223A ALA* 3.5 19.5 - - - +
225A GLY 3.4 3.8 + - - +
226A VAL 3.4 0.2 - - - -
227A LYS* 1.3 77.7 - - - +
229A THR* 1.3 58.1 + - - +
231A GLY* 3.7 0.5 - - - -
232A LYS* 3.0 37.6 + - + +
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Residues in contact with THR 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ALA 4.7 1.0 + - - -
224A THR* 3.3 15.8 + - - -
225A GLY 2.8 21.8 + - - -
226A VAL* 3.9 7.9 - - - -
227A LYS 3.3 0.2 - - - -
228A ALA* 1.3 76.9 - - - +
230A THR* 1.3 58.4 + - - +
232A LYS* 3.5 15.5 + - - +
233A GLU* 3.1 43.6 + - + +
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Residues in contact with THR 230 (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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226A VAL* 2.8 32.3 + - - +
227A LYS* 3.7 4.7 - - - -
229A THR* 1.3 74.9 - - - +
231A GLY* 1.3 59.3 + - - +
233A GLU* 3.2 18.0 + - - +
234A ASN* 2.9 45.8 + - - +
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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
----------------------------------------------------------
108A GLY* 3.2 28.4 + - - -
110A VAL* 3.4 13.1 - - - +
208A ALA* 3.8 9.4 - - - -
227A LYS 3.0 13.3 + - - -
228A ALA 3.7 2.9 - - - -
230A THR* 1.3 75.7 - - - +
232A LYS* 1.3 56.8 + - - +
234A ASN* 3.2 4.8 + - - +
235A MET* 2.9 24.8 + - - +
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Residues in contact with LYS 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG* 4.0 22.7 - - - +
35A GLU* 4.7 17.3 + - - +
96A THR* 3.7 24.2 - - + +
208A ALA* 3.8 19.2 - - + +
223A ALA 4.2 15.2 + - - -
224A THR* 5.9 0.2 - - - +
228A ALA* 3.0 25.0 + - + +
229A THR* 3.8 18.5 + - - +
231A GLY* 1.3 71.3 - - - +
233A GLU* 1.3 66.1 + - + +
235A MET* 3.3 11.8 + - + +
236A VAL* 2.9 32.6 + - + +
283B GOL 5.7 2.8 + - - -
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Residues in contact with GLU 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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39A MET* 3.9 24.1 - - + +
229A THR* 3.1 35.3 + - + +
230A THR* 3.5 20.9 + - - +
232A LYS* 1.3 76.0 - - - +
234A ASN* 1.3 64.9 - - - +
236A VAL* 3.3 4.1 + - - +
237A LYS* 3.0 36.8 + - - +
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Residues in contact with ASN 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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108A GLY 5.0 3.8 + - - -
110A VAL* 4.3 6.2 - - + +
152A ILE* 3.8 39.9 - - + +
230A THR* 2.9 33.5 + - - +
231A GLY* 3.2 10.8 + - - +
233A GLU* 1.3 77.5 - - - +
235A MET* 1.3 62.6 + - - +
237A LYS* 3.2 17.5 + - - +
238A ILE* 3.0 28.9 + - - +
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Residues in contact with MET 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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32A ARG* 4.4 11.9 - - - -
94A ALA* 3.7 20.4 - - + +
95A GLY* 3.2 33.0 - - - +
110A VAL* 4.0 14.7 - - + +
206A ILE* 3.5 45.0 - - + +
208A ALA* 3.8 11.2 - - + -
231A GLY 2.9 13.8 + - - +
232A LYS* 3.5 29.8 - - + +
234A ASN* 1.3 75.1 - - - +
236A VAL* 1.3 55.5 + - + +
238A ILE* 3.4 4.0 + - - +
239A THR* 2.7 38.4 + - - +
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Residues in contact with VAL 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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25A ILE* 6.4 0.2 - - + -
32A ARG* 4.8 10.1 - - + -
35A GLU* 5.5 2.2 - - + -
36A VAL* 3.9 33.4 - - + +
39A MET* 3.7 24.0 - - + -
94A ALA* 5.5 4.0 - - + -
232A LYS* 2.9 23.8 + - + +
233A GLU* 3.7 5.6 - - - +
234A ASN 3.2 0.2 - - - -
235A MET* 1.3 84.8 - - + +
237A LYS* 1.3 60.6 + - - +
239A THR* 3.7 5.8 - - - -
240A LEU* 2.8 48.1 + - + +
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Residues in contact with LYS 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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39A MET* 4.4 22.2 - - - -
59A TYR* 4.7 7.7 + - - +
150A LEU* 3.7 19.7 - - + +
152A ILE* 4.3 14.1 - - + -
233A GLU* 3.0 28.5 + - - +
234A ASN* 3.2 19.0 + - - +
236A VAL* 1.3 75.8 - - - +
238A ILE* 1.3 61.3 + - - +
240A LEU* 4.1 4.7 - - - +
241A LYS* 3.2 25.1 + - - +
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Residues in contact with ILE 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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110A VAL* 4.4 9.9 - - + -
112A VAL* 5.6 0.7 - - + -
143A LEU* 3.4 33.7 - - + +
146A ALA* 3.6 5.7 - - + +
147A ALA* 3.9 26.2 - - + -
150A LEU* 3.9 13.5 - - + -
152A ILE* 3.8 25.6 - - + -
154A ALA* 4.6 4.3 - - + -
206A ILE* 3.7 27.6 - - + -
234A ASN 3.0 21.3 + - - +
235A MET 3.6 5.2 - - - +
237A LYS* 1.3 75.7 - - - +
239A THR* 1.3 58.4 + - - +
241A LYS 3.4 0.2 + - - -
242A ALA* 3.0 28.4 + - - +
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Residues in contact with THR 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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25A ILE* 3.8 35.0 - - + -
92A ILE* 4.1 20.0 - - + -
94A ALA* 3.9 6.9 - - + +
143A LEU* 3.9 7.9 - - + -
206A ILE* 3.3 21.8 - - - +
235A MET 2.7 22.2 + - - -
236A VAL* 3.7 7.2 - - - -
238A ILE* 1.3 77.0 - - - +
240A LEU* 1.3 58.8 + - - +
242A ALA* 3.3 1.2 + - - +
243A CYS* 2.8 40.7 + - - +
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Residues in contact with LEU 240 (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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25A ILE* 3.8 21.5 - - + -
36A VAL* 3.9 9.9 - - + +
39A MET* 3.8 25.8 - - + -
40A CYS* 3.8 22.7 - - - -
57A VAL* 4.5 6.5 - - + -
59A TYR* 3.6 45.8 - - + -
64A ILE* 4.5 4.5 - - + +
236A VAL* 2.8 41.6 + - + +
237A LYS* 4.1 2.7 - - - +
239A THR* 1.3 72.6 - - - +
241A LYS* 1.3 62.9 + - - +
243A CYS* 3.4 3.7 + - - +
244A ALA* 3.0 19.8 + - - +
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Residues in contact with LYS 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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59A TYR* 3.9 20.1 - - + +
60A ASP* 5.9 0.8 + - - -
146A ALA* 3.8 23.3 - - + +
149A GLU* 3.0 30.8 + - - +
150A LEU* 3.4 38.8 - - + -
237A LYS 3.2 16.8 + - - +
238A ILE 3.8 3.1 - - - +
240A LEU* 1.3 79.4 - - - +
242A ALA* 1.3 61.0 + - - +
244A ALA* 3.5 3.4 + - - +
245A ASN* 3.3 32.7 + - - +
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Residues in contact with ALA 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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92A ILE* 5.1 1.3 - - + -
142A ALA* 3.4 39.1 - - + +
143A LEU* 3.7 20.2 - - + +
146A ALA* 3.9 2.0 - - + +
238A ILE 3.0 17.6 + - - +
239A THR 3.8 0.7 - - - +
241A LYS* 1.3 76.9 - - - +
243A CYS* 1.3 57.6 + - - +
245A ASN* 3.2 8.5 + - - +
246A LEU* 2.9 35.4 + - + +
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Residues in contact with CYS 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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23A VAL* 3.8 24.0 - - + +
24A VAL 5.1 0.7 - - - -
25A ILE* 3.5 31.6 - - + -
64A ILE* 3.9 14.6 - - + -
92A ILE* 3.8 26.2 - - - -
239A THR* 2.8 23.7 + - - +
240A LEU 3.8 3.1 - - - +
242A ALA* 1.3 74.8 - - - +
244A ALA* 1.3 59.1 + - - +
246A LEU* 3.7 4.0 - - - +
247A ARG* 2.8 32.2 + - - +
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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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59A TYR* 3.5 27.6 - - + +
60A ASP* 4.0 17.3 - - + +
62A GLN* 3.4 24.9 - - + +
64A ILE* 3.9 3.9 - - + +
240A LEU 3.0 17.2 + - - +
241A LYS* 3.9 4.9 - - - +
243A CYS* 1.3 75.8 - - - +
245A ASN* 1.3 63.7 + - - +
247A ARG 3.2 0.9 + - - -
248A ARG* 3.2 24.0 + - - +
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Residues in contact with ASN 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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60A ASP* 5.2 1.9 - - - +
142A ALA* 5.6 6.0 + - + +
146A ALA* 5.6 2.8 - - - +
149A GLU* 5.7 2.0 + - - -
241A LYS* 3.3 25.8 + - - +
242A ALA* 3.2 10.6 + - - +
244A ALA* 1.3 80.5 - - - +
246A LEU* 1.3 64.4 + - + +
248A ARG* 3.0 36.7 + - - +
249A GLN* 3.8 9.7 - - - +
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Residues in contact with LEU 246 (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 VAL* 4.0 11.7 - - + -
90A VAL* 4.1 19.1 - - + -
92A ILE* 4.0 26.5 - - + -
138A HIS* 3.9 30.5 - - + +
139A VAL* 4.2 8.7 - - + -
142A ALA* 4.1 24.2 - - + -
242A ALA* 2.9 23.0 + - + +
243A CYS* 3.8 6.1 - - - +
244A ALA 3.3 0.2 - - - -
245A ASN* 1.3 75.7 - - - +
247A ARG* 1.3 62.9 + - - +
249A GLN* 3.2 26.9 + - - +
250A TYR* 3.3 16.9 - - + -
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Residues in contact with ARG 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 2.8 23.6 + - - -
22A PRO* 3.6 25.7 - - - +
23A VAL* 3.6 19.3 - - + +
62A GLN* 3.5 24.3 + - + +
63A PRO* 3.0 42.3 + - + +
64A ILE* 4.5 2.2 - - + -
243A CYS 2.8 22.8 + - - +
244A ALA 3.2 5.4 + - - +
246A LEU* 1.3 71.8 - - - +
248A ARG* 1.3 62.2 + - - +
250A TYR* 3.1 33.8 + - - +
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Residues in contact with ARG 248 (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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60A ASP* 3.1 41.4 + - - +
62A GLN* 3.3 30.0 + - - +
244A ALA* 3.2 10.9 + - - +
245A ASN* 3.0 47.8 + - - +
246A LEU 3.2 0.4 - - - -
247A ARG* 1.3 77.3 - - - +
249A GLN* 1.3 60.0 + - + +
250A TYR 3.2 6.5 + - - +
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Residues in contact with GLN 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A HIS* 4.8 7.6 + - - -
245A ASN 3.8 11.4 - - - +
246A LEU* 3.2 31.8 + - - +
248A ARG* 1.3 73.8 - - + +
250A TYR* 1.3 69.4 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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