Contacts of the helix formed by residues 221 - 241 (chain A) in PDB entry 3HB8
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 LEU 221 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LYS* 4.1 15.7 - - - +
218A ASP* 2.9 42.8 + - + +
220A GLY* 1.3 87.6 - - - +
222A GLY* 1.3 64.0 + - - +
224A PRO* 4.0 5.6 - - - +
225A PHE* 4.3 6.1 + - - +
258A TYR* 4.8 4.0 - - + -
261A HIS* 4.2 26.7 - - + +
314A UMP 6.1 0.7 - - + -
315A EDO 4.0 14.8 + - - -
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Residues in contact with GLY 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ASP* 2.9 15.9 + - - +
221A LEU* 1.3 72.3 - - - +
223A VAL* 1.3 67.1 + - - -
224A PRO 3.2 2.2 - - - -
225A PHE* 2.7 20.1 + - - +
226A ASN* 3.1 17.4 + - - -
314A UMP 4.2 14.1 - - - +
315A EDO 3.7 15.9 - - - -
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Residues in contact with VAL 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TYR* 4.2 12.6 - - + -
36A GLN* 5.4 1.1 - - - +
65A TYR* 5.7 0.2 - - - +
214A GLN* 4.4 5.3 - - - +
217A GLY* 3.9 14.4 - - - -
218A ASP 3.2 17.0 + - - +
219A MET* 3.6 31.2 - - + +
222A GLY* 1.3 70.2 - - - +
224A PRO* 1.3 59.3 - - + +
226A ASN* 3.0 12.1 + - - +
227A ILE* 2.7 54.2 + - + +
250A HIS* 3.8 22.2 - - + +
252A LEU* 4.5 4.5 - - + -
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Residues in contact with PRO 224 (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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33A TYR* 3.3 23.6 - - + +
72A PRO 5.2 0.9 - - - +
73A LEU* 5.4 0.3 - - - +
74A LEU* 3.5 32.5 + - + +
77A LYS* 6.5 0.4 - - + -
79A VAL* 4.1 20.1 - - + +
219A MET 3.6 9.0 - - - +
220A GLY 4.1 7.9 - - - +
221A LEU 4.0 9.6 - - - +
222A GLY 3.3 5.8 - - - -
223A VAL* 1.3 93.2 - - + +
225A PHE* 1.3 61.0 + - - +
227A ILE* 3.5 5.4 + - + +
228A ALA* 3.3 20.8 + - - +
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Residues in contact with PHE 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 3.9 13.1 - - + +
80A PHE* 3.3 32.1 - + + -
83A GLY* 3.4 11.7 - - - -
84A VAL* 3.2 40.2 - - + +
87A GLU* 3.7 24.7 - - - -
108A ILE* 4.0 14.4 - - + -
221A LEU 4.3 5.6 + - - +
222A GLY 2.7 14.0 + - - +
224A PRO* 1.3 76.3 - - - +
226A ASN* 1.3 65.8 + - - +
228A ALA* 3.4 5.4 + - - +
229A SER* 3.1 31.9 + - - -
314A UMP 4.6 2.9 - - - -
315A EDO 3.7 28.3 - - - +
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Residues in contact with ASN 226 (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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196A HIS* 3.4 20.4 + - + -
212A LEU* 4.9 2.7 - - + -
214A GLN* 2.9 39.1 + - - +
222A GLY 3.4 16.6 + - - -
223A VAL* 3.0 7.0 + - - +
225A PHE* 1.3 83.6 - - - +
227A ILE* 1.3 68.1 + - - +
229A SER* 3.2 16.4 + - - -
230A TYR* 3.2 17.7 + - - +
248A PHE* 4.7 0.3 - - - -
250A HIS* 4.6 3.6 - - + -
314A UMP 2.6 34.9 + - - -
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Residues in contact with ILE 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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33A TYR* 4.4 8.5 - - + -
65A TYR* 3.6 37.2 - - + +
72A PRO* 3.4 38.1 - - + +
74A LEU* 4.5 9.6 - - + -
223A VAL* 2.7 43.9 + - + +
224A PRO* 3.7 9.2 - - + +
226A ASN* 1.3 71.9 - - - +
228A ALA* 1.3 65.2 + - - +
230A TYR 3.7 0.2 + - - -
231A ALA* 3.1 21.8 + - - +
248A PHE* 3.8 25.7 - - + -
250A HIS* 4.7 6.3 - - + +
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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
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71A PHE* 3.5 18.3 - - + -
72A PRO 4.6 2.7 + - - +
73A LEU* 4.0 25.4 - - + -
79A VAL* 4.7 0.2 - - + -
81A TRP* 4.6 0.2 - - + -
84A VAL* 3.8 21.1 - - + -
224A PRO 3.3 10.0 + - - +
225A PHE* 3.5 9.4 - - - +
226A ASN 3.1 0.2 - - - -
227A ILE* 1.3 80.5 - - - +
229A SER* 1.3 65.0 + - - +
231A ALA* 2.8 4.6 + - - +
232A LEU* 2.7 22.2 + - - +
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Residues in contact with SER 229 (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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84A VAL* 3.6 21.1 + - - +
87A GLU* 3.8 18.0 + - - -
88A LEU* 4.0 14.1 - - - +
91A PHE* 5.7 2.0 - - - -
196A HIS* 6.1 0.7 - - - -
225A PHE* 3.1 18.1 + - - -
226A ASN* 3.2 11.0 + - - -
228A ALA* 1.3 77.9 - - - +
230A TYR* 1.3 68.9 + - - +
232A LEU* 3.1 4.1 + - - +
233A LEU* 2.9 27.6 + - - +
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Residues in contact with TYR 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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88A LEU* 6.3 0.4 - - + -
91A PHE* 5.8 3.0 - + - -
135A TYR* 4.9 3.8 - - - -
139A TRP* 3.6 24.7 + + - -
196A HIS* 3.4 42.5 + + - +
199A CYS* 4.1 29.4 - - + -
210A CYS* 4.4 7.6 - - - -
212A LEU* 3.4 27.1 - - + -
226A ASN 3.2 9.7 + - - +
229A SER* 1.3 83.7 - - - +
231A ALA* 1.3 59.6 + - - +
233A LEU* 3.9 28.9 - - + +
234A THR* 2.8 27.2 + - - -
248A PHE* 3.4 31.1 - - + -
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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
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67A LEU* 4.0 14.8 - - + -
71A PHE* 3.6 18.2 - - + -
72A PRO* 3.8 22.0 - - + -
227A ILE 3.1 18.5 + - - +
228A ALA 2.8 5.2 + - - +
230A TYR* 1.3 74.7 - - - +
232A LEU* 1.3 66.0 + - - +
234A THR* 3.3 5.7 + - - -
235A TYR* 3.1 27.5 + - - -
248A PHE* 4.8 5.6 - - + -
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Residues in contact with LEU 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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71A PHE* 3.2 14.7 - - + -
81A TRP* 4.0 14.4 - - + -
84A VAL* 4.3 7.4 - - + -
85A LEU* 3.6 38.1 - - + -
88A LEU* 3.4 22.9 - - + -
228A ALA 2.7 11.3 + - - +
229A SER 3.3 7.4 - - - +
231A ALA* 1.3 79.1 - - - +
233A LEU* 1.3 60.9 + - - +
235A TYR* 3.1 6.5 + - - +
236A MET* 3.0 25.6 + - + +
279A LEU* 3.9 13.2 - - + -
296A PHE* 3.7 35.9 - - + -
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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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88A LEU* 3.6 24.2 - - + +
92A ILE* 5.1 3.4 - - + -
139A TRP* 4.0 26.2 - - + -
161A LEU* 4.4 11.0 - - + -
179A MET* 4.1 14.4 - - + -
201A PHE* 4.2 12.8 - - + -
229A SER 2.9 14.7 + - - +
230A TYR* 4.0 26.5 - - + +
232A LEU* 1.3 75.2 - - - +
234A THR* 1.3 65.0 + - - +
236A MET* 3.3 4.8 + - + +
237A ILE* 3.0 42.5 + - + +
288A ILE* 4.8 9.6 - - + -
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Residues in contact with THR 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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67A LEU* 3.6 27.5 - - + +
201A PHE* 4.1 8.4 - - + -
208A LEU* 3.9 32.3 - - + +
210A CYS* 3.2 27.5 - - + +
230A TYR 2.8 17.9 + - - -
231A ALA 3.3 8.4 + - - -
232A LEU 3.2 0.4 - - - -
233A LEU* 1.3 75.4 - - - +
235A TYR* 1.3 66.8 + - - +
236A MET 3.1 0.3 + - - -
237A ILE* 3.1 3.6 + - - +
238A ALA* 2.7 25.6 + - + +
245A PRO* 4.9 3.8 - - + -
248A PHE* 5.0 0.5 - - - -
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Residues in contact with TYR 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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67A LEU* 2.8 42.1 + - + -
69A ASP* 4.5 1.6 + - - -
70A GLU 2.9 24.2 + - - -
71A PHE* 3.3 26.6 - + - +
231A ALA 3.1 24.3 + - - -
232A LEU* 3.1 9.2 + - + +
234A THR* 1.3 75.3 - - - +
236A MET* 1.3 57.4 + - - +
238A ALA* 3.2 7.4 + - - +
239A HIS* 2.8 31.9 + - - +
245A PRO* 3.9 20.1 - - + +
279A LEU* 3.4 41.6 + - + +
281A ILE* 4.5 12.0 - - + +
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Residues in contact with MET 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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88A LEU* 3.7 28.9 - - - -
89A LEU* 4.5 5.4 - - + -
92A ILE* 3.4 28.5 - - + -
232A LEU* 3.0 15.5 + - - +
233A LEU* 3.4 9.4 - - - +
235A TYR* 1.3 76.0 - - - +
237A ILE* 1.3 58.8 + - - +
239A HIS* 3.0 6.4 + - - +
240A ILE* 2.9 31.5 + - - +
281A ILE* 4.9 0.9 - - - -
288A ILE* 3.6 9.2 - - + -
291A PHE* 3.1 50.9 - - + -
296A PHE* 3.5 31.6 - - + -
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Residues in contact with ILE 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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161A LEU* 4.3 12.8 - - + -
164A VAL* 4.5 4.0 - - + -
165A ILE* 4.0 32.3 - - + -
168A ILE* 4.4 12.1 - - + -
201A PHE* 3.7 29.8 - - + -
208A LEU* 3.9 14.8 - - + -
233A LEU* 3.0 35.4 + - + +
234A THR 3.9 2.7 - - - +
236A MET* 1.3 73.7 - - - +
238A ALA* 1.3 52.0 - - - +
240A ILE* 3.9 7.4 - - - -
241A THR* 2.2 44.5 + - + +
288A ILE* 4.4 4.7 - - + -
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Residues in contact with ALA 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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208A LEU* 3.7 17.2 - - + +
234A THR 2.7 16.8 + - - +
235A TYR 3.4 5.8 - - - +
237A ILE* 1.3 76.5 - - - +
239A HIS* 1.3 58.4 + - - +
241A THR* 3.1 5.9 + - - -
242A GLY 3.0 9.9 + - - -
243A LEU* 2.7 49.6 + - - +
245A PRO* 4.2 20.0 - - + -
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Residues in contact with HIS 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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235A TYR 2.8 12.5 + - - +
236A MET 3.2 8.1 - - - +
238A ALA* 1.3 78.9 - - - +
240A ILE* 1.3 59.2 + - - +
241A THR 3.5 0.3 + - - -
242A GLY* 3.6 8.4 + - - +
243A LEU 4.4 2.0 + - - -
281A ILE* 3.7 30.0 - - + +
283A ARG 3.8 4.8 + - - -
284A LYS* 3.6 33.8 + - + -
285A VAL 3.2 30.4 + - - +
291A PHE* 3.5 26.7 - + - -
120D SER* 4.5 15.7 - - - -
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Residues in contact with ILE 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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165A ILE* 4.1 14.1 - - + -
169A LYS* 5.2 0.2 - - - +
236A MET 2.9 14.7 + - - +
237A ILE* 4.0 4.7 - - - +
239A HIS* 1.3 76.6 - - - +
241A THR* 1.3 58.3 + - - +
242A GLY 3.5 0.6 + - - -
284A LYS* 5.7 1.0 + - - -
285A VAL 4.5 9.0 - - - +
286A GLU* 3.3 24.1 - - - +
287A LYS* 3.4 5.2 - - - +
288A ILE* 3.1 52.0 - - + +
291A PHE* 3.5 22.9 - - + -
51D THR* 3.4 32.7 + - + -
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Residues in contact with THR 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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165A ILE* 3.9 26.0 - - + -
168A ILE* 4.0 29.5 - - + +
169A LYS* 4.1 21.6 - - + +
208A LEU* 4.6 0.2 - - - +
237A ILE* 2.2 34.0 + - + +
238A ALA* 3.1 8.5 + - - -
240A ILE* 1.3 81.0 - - + +
242A GLY* 1.3 61.2 + - - +
243A LEU* 3.4 16.9 + - - +
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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