Contacts of the helix formed by residues 54 - 80 (chain A) 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 ILE 54 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A HIS 3.9 13.9 - - - +
50A ILE* 3.0 21.8 + - + +
53A ASN* 1.3 89.8 - - + +
55A ARG* 1.3 71.4 + - + +
57A PRO* 3.4 6.7 - - - +
58A ARG* 3.1 31.1 + - + +
187A GLY 6.2 0.2 - - - +
189A ALA* 4.5 14.0 - - + +
190A GLN* 6.2 2.0 - - + -
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A SER 4.7 1.8 - - - -
26A ALA* 3.7 20.6 + - + +
27A ASN 3.6 12.1 + - - -
28A MET 3.4 29.3 + - - -
50A ILE* 2.9 35.5 + - + +
51A TRP* 4.2 14.7 - - + +
54A ILE* 1.3 75.9 - - + +
56A LEU* 1.3 65.9 + - - +
58A ARG* 3.2 8.3 + - - +
59A VAL* 2.9 32.6 + - + +
299A ARG* 3.7 27.9 - - - +
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 5.9 5.8 - - + -
51A TRP* 3.0 49.0 + - + +
52A LEU* 3.9 17.0 - - + +
55A ARG* 1.3 75.0 - - - +
57A PRO* 1.3 63.0 - - + +
59A VAL* 3.5 7.1 + - + +
60A LEU* 2.9 47.0 + - + +
191A TRP* 3.7 27.4 - - + -
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Residues in contact with PRO 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU 3.6 12.8 - - - +
53A ASN 3.6 12.1 - - - +
54A ILE* 3.4 16.8 - - - +
56A LEU* 1.3 94.8 - - + +
58A ARG* 1.3 54.9 + - - -
60A LEU* 4.2 0.4 - - + -
61A LEU* 2.9 27.8 + - - +
189A ALA* 4.0 10.2 - - - +
190A GLN* 4.2 12.6 - - - +
191A TRP* 3.6 32.5 - - + +
194A LEU* 3.8 24.4 - - + +
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Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 3.1 24.5 + - + +
55A ARG* 3.8 8.5 - - - +
56A LEU 3.2 0.2 - - - -
57A PRO* 1.3 73.3 - - - +
59A VAL* 1.3 64.0 + - + +
61A LEU* 3.2 1.8 + - - +
62A ALA* 2.9 27.7 + - - +
186A LEU* 3.0 38.7 + - + +
187A GLY* 3.2 19.4 + - - +
189A ALA* 3.6 16.6 - - + +
295A ASP* 2.7 29.3 + - - +
298A ALA* 5.3 1.8 - - - +
299A ARG* 3.3 50.4 - - - +
306A GLU* 4.9 12.1 + - - +
307A MET 5.6 2.0 + - - -
309A VAL* 5.7 0.4 - - - +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 3.8 37.9 - - + +
25A SER* 4.1 26.5 - - - +
26A ALA* 4.6 5.2 - - + +
55A ARG* 2.9 20.4 + - + +
56A LEU* 3.8 8.5 - - + +
58A ARG* 1.3 79.1 - - + +
60A LEU* 1.3 70.3 + - + +
62A ALA* 3.1 5.7 + - - +
63A VAL* 3.0 23.1 + - + +
292A LEU* 3.7 22.1 - - + +
296A THR* 5.0 0.9 - - - +
299A ARG* 5.1 6.1 - - - +
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 5.7 4.3 - - + -
56A LEU* 2.9 39.5 + - + +
59A VAL* 1.3 86.4 - - + +
61A LEU* 1.3 55.9 + - - +
63A VAL* 3.3 12.5 + - + +
64A VAL* 2.9 34.2 + - + +
191A TRP* 4.5 11.4 - - + -
194A LEU* 3.8 26.2 - - + -
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO 2.9 21.1 + - - +
58A ARG* 3.2 6.5 + - - +
59A VAL 3.2 0.4 - - - -
60A LEU* 1.3 71.7 - - - +
62A ALA* 1.3 60.9 + - - +
64A VAL* 4.4 2.2 - - + +
65A VAL* 2.9 40.8 + - + +
186A LEU* 3.5 33.2 - - + -
188A GLN 5.4 1.1 - - - +
189A ALA* 4.1 21.8 - - + -
193A THR* 5.1 1.6 - - - +
194A LEU* 3.6 32.3 - - + +
197A ALA* 4.8 5.8 - - + -
253A VAL* 3.6 33.4 - - + +
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG 2.9 13.2 + - - +
59A VAL 3.4 8.7 - - - +
61A LEU* 1.3 75.0 - - - +
63A VAL* 1.3 58.3 + - - +
66A GLY* 2.9 28.1 + - - -
186A LEU* 3.5 15.6 - - + +
288A ALA* 4.3 2.2 - - - -
291A LEU* 3.6 11.7 - - + +
292A LEU* 3.6 35.0 - - + +
295A ASP* 4.4 9.9 - - + -
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Residues in contact with VAL 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.6 35.9 - - + -
22A ALA* 5.3 3.1 - - + -
59A VAL* 3.0 20.9 + - + +
60A LEU* 3.5 18.6 - - + +
61A LEU 3.2 0.2 - - - -
62A ALA* 1.3 77.8 - - - +
64A VAL* 1.3 63.2 + - + +
67A CYS* 2.9 28.6 + - + +
288A ALA* 3.3 22.2 - - + +
292A LEU* 3.9 14.8 - - + -
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 2.9 26.0 + - + +
61A LEU* 4.2 3.1 - - + +
63A VAL* 1.3 78.1 - - + +
65A VAL* 1.3 59.8 + - + +
67A CYS* 3.6 6.8 - - - +
68A ALA* 2.9 24.9 + - - +
194A LEU* 4.2 17.0 - - + -
197A ALA* 4.7 2.5 - - + -
198A SER* 4.1 27.8 - - - +
201A ILE* 3.6 32.1 - - + +
202A LEU* 4.3 12.3 - - + -
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 2.9 40.1 + - + +
64A VAL* 1.3 74.3 - - + +
66A GLY* 1.3 60.9 + - - +
68A ALA* 3.0 6.4 + - - +
69A LEU* 2.9 37.0 + - + +
186A LEU* 4.9 1.8 - - + -
197A ALA* 6.0 0.9 - - + -
201A ILE* 4.9 4.7 - - + -
250A ALA* 4.2 21.1 - - + +
253A VAL* 5.0 4.7 - - + -
254A SER* 3.7 34.1 - - - +
257A ILE* 4.7 1.1 - - + -
291A LEU* 3.5 19.1 - - + -
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Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA 2.9 14.8 + - - -
65A VAL* 1.3 75.7 - - - +
67A CYS* 1.3 57.5 + - - +
69A LEU 3.5 0.2 + - - -
70A ALA* 2.9 31.9 + - - +
260A ILE* 3.6 6.8 - - - +
287A GLY* 3.5 27.2 - - - -
291A LEU* 3.3 16.2 - - - +
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Residues in contact with CYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL* 2.9 20.7 + - + +
64A VAL* 3.6 8.1 - - - +
66A GLY* 1.3 72.5 - - - +
68A ALA* 1.3 64.4 + - - +
71A VAL* 3.0 25.1 + - - +
201A ILE* 4.9 3.4 - - - -
202A LEU* 6.3 3.1 - - - -
205A CYS* 3.4 26.2 - - - -
284A ALA* 3.5 40.2 - - - +
288A ALA* 3.8 3.0 - - + +
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL 2.9 15.3 + - - +
65A VAL 3.0 8.0 + - - +
67A CYS* 1.3 76.4 - - - +
69A LEU* 1.3 57.9 + - - +
72A SER* 2.9 32.6 + - - -
201A ILE* 3.6 24.7 - - + -
246A LEU* 3.5 25.3 - - + +
250A ALA* 3.7 17.9 - - + -
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 2.9 26.9 + - + +
68A ALA* 1.3 70.9 - - - +
70A ALA* 1.3 61.6 + - - +
72A SER* 4.0 2.4 - - - -
73A GLY 2.8 24.8 + - - -
86A ASP* 6.1 0.2 - - - +
87A PRO* 4.1 20.6 - - + +
93A SER* 5.3 3.6 - - - +
247A ILE* 5.2 8.1 - - + -
250A ALA* 3.8 20.6 - - + -
251A VAL* 5.6 2.5 - - + -
254A SER* 5.5 0.9 - - - +
257A ILE* 3.7 48.9 - - + +
260A ILE* 3.5 32.1 - - + -
261A GLY* 3.3 12.6 - - - +
291A LEU* 5.1 0.7 - - + -
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLY 2.9 19.8 + - - +
67A CYS 3.8 3.1 - - - +
69A LEU* 1.3 78.2 - - - +
71A VAL* 1.3 58.2 + - - +
73A GLY* 3.7 0.9 - - - -
74A THR* 3.0 31.4 + - - -
260A ILE 3.2 11.3 + - - -
264A VAL* 3.4 15.7 - - + -
265A PRO* 4.1 3.1 - - - +
283A ALA* 3.3 33.0 - - - +
284A ALA* 4.1 1.1 - - - +
287A GLY* 3.7 2.9 - - - -
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A CYS 3.0 17.3 + - - +
68A ALA 4.1 1.3 - - - +
70A ALA* 1.3 78.0 - - - +
72A SER* 1.3 58.4 + - - +
74A THR* 3.2 7.1 + - - -
75A ILE* 2.9 39.4 + - + +
205A CYS* 3.7 29.8 - - + +
208A GLY* 5.3 0.9 - - - -
246A LEU* 3.6 17.9 - - + -
280A LEU* 4.2 21.1 - - + +
283A ALA* 5.2 1.3 - - - -
284A ALA* 3.5 31.0 - - + +
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Residues in contact with SER 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA 2.9 22.2 + - - -
69A LEU* 4.0 3.1 - - - -
71A VAL* 1.3 78.0 - - - +
73A GLY* 1.3 51.5 + - - +
75A ILE* 3.5 2.2 + - - +
76A MET* 2.8 46.9 + - - +
87A PRO* 3.9 3.2 - - - +
243A SER* 3.5 6.7 - - - -
246A LEU* 3.6 24.4 - - - +
247A ILE* 3.0 29.2 - - - +
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Residues in contact with GLY 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU 2.8 21.6 + - - -
70A ALA 3.7 0.2 - - - -
72A SER* 1.3 72.8 + - - +
74A THR* 1.3 56.9 + - - +
77A GLN* 2.9 36.1 + - - +
85A ALA 3.4 1.9 - - - +
87A PRO* 3.5 21.0 - - - +
261A GLY 3.6 19.1 - - - -
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Residues in contact with THR 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA 3.0 13.6 + - - -
71A VAL* 3.2 6.0 + - - -
73A GLY* 1.3 74.3 - - - +
75A ILE* 1.3 66.9 + - - +
77A GLN* 3.5 4.0 + - - +
78A GLY* 3.0 20.1 + - - -
265A PRO* 3.0 32.0 - - - +
269A ARG* 5.2 1.9 + - - +
276A HIS* 4.1 14.2 + - + -
279A LEU* 3.9 29.1 - - + +
280A LEU* 4.2 22.2 - - + -
283A ALA* 3.8 10.8 - - - +
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Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 2.9 41.8 + - + +
72A SER* 3.8 3.8 - - - +
74A THR* 1.3 72.7 - - - +
76A MET* 1.3 59.1 + - - +
78A GLY* 3.1 2.4 + - - -
79A LEU* 2.8 28.0 + - + +
208A GLY* 4.5 5.2 - - - -
215A LEU* 4.2 15.1 - - + +
239A LEU* 3.7 45.8 - - + +
242A LEU* 3.7 29.8 - - + -
243A SER* 4.2 6.5 - - - +
246A LEU* 3.8 9.6 - - + -
280A LEU* 4.0 15.3 - - + -
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Residues in contact with MET 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A SER* 2.8 41.2 + - - +
73A GLY 3.6 1.8 - - - +
75A ILE* 1.3 76.7 - - - +
77A GLN* 1.3 63.5 + - - +
79A LEU* 3.0 17.6 + - - +
80A PHE* 3.0 44.6 + - + -
85A ALA* 3.2 21.8 - - + +
87A PRO* 3.7 8.7 - - + -
90A LEU* 3.9 4.9 - - + -
92A ILE* 3.5 27.8 - - - -
131A SER* 4.3 2.2 - - - -
243A SER* 3.5 18.4 - - - -
247A ILE* 3.3 17.0 - - + -
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Residues in contact with GLN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLY 2.9 19.0 + - - +
74A THR 3.8 3.6 - - - +
76A MET* 1.3 72.5 - - - +
78A GLY* 1.3 60.8 + - - +
81A ARG 3.2 1.6 + - - -
82A ASN 3.0 44.5 + - - +
83A PRO 3.6 4.2 + - - -
85A ALA* 3.5 20.5 + - - +
261A GLY 2.9 28.1 + - - -
262A LEU* 3.7 14.5 + - - +
265A PRO* 3.7 11.9 - - - +
266A HIS* 3.1 21.9 + - - -
269A ARG* 2.8 26.8 + - - +
98D PHE* 3.2 13.2 - - + -
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Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR 3.0 12.0 + - - -
75A ILE 3.5 4.0 - - - -
76A MET 3.1 0.2 - - - -
77A GLN* 1.3 75.2 - - - +
79A LEU* 1.3 63.7 + - - +
81A ARG* 3.1 12.0 + - - +
215A LEU* 3.5 18.4 - - - -
218A LEU* 5.4 3.7 - - - +
219A GLN* 2.8 30.2 + - - -
269A ARG* 5.7 0.2 - - - +
276A HIS* 4.3 4.5 + - - -
98D PHE* 4.4 2.2 - - - -
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE* 2.8 20.3 + - + +
76A MET* 3.0 5.6 + - - +
78A GLY* 1.3 72.8 - - - +
80A PHE* 1.3 80.8 + - + +
81A ARG* 3.4 3.3 + - - -
135A PHE* 4.3 4.5 - - + -
139A ARG* 2.3 50.0 + - - +
215A LEU* 4.5 1.4 - - - +
218A LEU* 4.8 7.2 - - + -
236A LYS* 3.7 30.1 - - + +
239A LEU* 3.8 22.0 - - + -
240A LEU* 3.6 39.9 - - + +
243A SER* 5.5 2.0 - - - +
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Residues in contact with PHE 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A MET* 3.0 38.6 + - + +
79A LEU* 1.3 92.4 - - + +
81A ARG* 1.3 71.7 + - - +
82A ASN* 3.2 16.7 + - + +
85A ALA* 3.5 20.9 - - + -
90A LEU* 3.5 16.8 - - + -
92A ILE* 5.3 0.4 - - + -
131A SER* 4.4 6.7 - - - -
134A ILE* 4.1 4.7 - - + -
135A PHE* 3.5 47.6 - + + -
138A SER* 3.6 25.2 + - - +
139A ARG* 5.0 1.6 - - - -
148A LEU* 4.2 14.9 - - + +
240A LEU* 4.9 3.8 - - + -
----------------------------------------------------------
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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