Contacts of the helix formed by residues 56 - 85 (chain A) in PDB entry 1LEG
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 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLN 3.8 2.2 + - - -
55A GLU* 1.3 80.7 + - - +
57A PRO* 1.3 75.9 - - - +
58A GLU* 3.2 17.8 + - - -
59A TYR* 3.1 11.2 + - - +
60A TRP* 3.3 11.7 - - - -
170A ARG* 5.4 1.0 - - - +
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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
----------------------------------------------------------
44A ARG* 5.1 0.5 + - - -
56A GLY* 1.3 81.7 - - - +
58A GLU* 1.3 78.8 + - + +
60A TRP* 3.2 13.7 + - + +
61A GLU* 3.0 21.8 + - - +
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLY* 3.2 13.1 + - - -
57A PRO* 1.3 102.4 - - + +
59A TYR* 1.3 71.5 + - - +
61A GLU* 3.8 7.1 - - - +
62A ARG* 3.0 40.0 + - - +
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Residues in contact with TYR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 4.5 1.4 + - - -
33A PHE* 4.3 1.4 - - - -
34A VAL* 4.2 10.1 - - + +
45A TYR* 5.3 0.5 - - - -
52A MET* 3.4 21.4 - - + +
55A GLU* 3.6 31.0 - - + +
56A GLY 3.1 14.1 + - - +
58A GLU* 1.3 83.8 + - - +
60A TRP* 1.3 88.0 + + - +
62A ARG* 3.8 11.0 - - - +
63A GLU* 2.9 57.7 + - + +
167A TRP* 3.5 24.9 - + - -
171A TYR* 2.5 32.0 + - - -
1P GLU* 3.9 16.5 + - + -
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Residues in contact with TRP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.9 8.7 - - + -
44A ARG* 3.5 9.9 - - - +
45A TYR* 3.3 33.3 - + + +
46A GLU* 3.5 20.6 - - - -
47A PRO* 3.4 36.5 - - + +
52A MET* 3.6 44.2 + - + -
53A GLU* 5.8 1.0 - - - +
55A GLU* 3.9 13.1 + - + +
56A GLY 3.3 27.1 + - - -
57A PRO* 3.2 9.5 + - + +
59A TYR* 1.3 96.1 - + + +
61A GLU* 1.3 56.7 + - - +
63A GLU* 4.1 1.0 - - - +
64A THR* 2.8 34.8 + - - -
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 3.2 26.9 + - - +
57A PRO 3.0 15.2 + - - +
58A GLU* 3.8 8.1 - - - +
60A TRP* 1.3 77.0 - - - +
62A ARG* 1.3 58.2 + - - +
64A THR* 3.3 1.2 + - - -
65A GLN* 2.6 70.9 + - + +
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Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU* 3.0 33.7 + - - +
59A TYR* 4.0 22.4 + - - +
61A GLU* 1.3 77.7 - - - +
63A GLU* 1.3 60.6 + - - +
65A GLN* 3.4 8.0 + - + +
66A LYS* 3.0 34.7 + - - +
167A TRP* 4.4 8.3 - - - -
1P GLU* 2.2 44.1 + - - -
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 4.6 0.9 + - - -
45A TYR* 3.4 36.7 - - + -
59A TYR* 2.9 47.1 + - + +
60A TRP* 4.2 0.4 - - - +
62A ARG* 1.3 75.6 + - - +
64A THR* 1.3 60.7 - - - +
66A LYS* 2.8 34.0 + - - +
67A ALA* 3.0 28.9 + - - +
1P GLU* 3.3 24.5 - - - +
2P GLN* 3.2 26.2 + - - +
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Residues in contact with THR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 4.5 2.2 - - + -
43A PRO 4.0 2.2 - - - +
44A ARG* 3.6 44.1 + - - +
45A TYR* 2.8 25.6 + - - +
60A TRP 2.8 24.2 + - - -
61A GLU 3.3 4.5 + - - -
63A GLU* 1.3 77.6 - - - +
65A GLN* 1.3 69.0 + - - +
67A ALA* 3.2 6.1 + - - +
68A LYS* 3.0 40.9 + - - +
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Residues in contact with GLN 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 4.3 3.2 - - - +
61A GLU* 2.6 48.7 + - + +
62A ARG* 3.7 7.6 - - - +
64A THR* 1.3 90.6 - - - +
66A LYS* 1.3 61.2 + - - +
68A LYS* 3.4 20.7 + - - +
69A GLY* 3.0 19.8 + - - -
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Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 3.0 23.1 + - - +
63A GLU* 2.8 30.4 + - - +
64A THR 3.2 0.2 - - - -
65A GLN* 1.3 76.7 - - - +
67A ALA* 1.3 53.2 + - - +
69A GLY* 3.1 2.7 + - - -
70A ASN* 2.7 48.5 + - - +
163A THR* 5.9 0.6 - - - +
1P GLU* 3.7 16.0 + - - +
2P GLN* 2.9 44.8 + - + +
3P TYR 3.8 2.5 - - - +
4P LYS* 3.5 39.7 - - + +
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 3.7 4.2 - - - -
24A GLU* 3.7 14.6 - - - +
36A PHE* 3.6 35.4 - - + -
45A TYR* 3.7 13.0 - - + -
63A GLU 3.0 18.8 + - - +
64A THR 3.2 5.1 + - - +
66A LYS* 1.3 78.0 - - - +
68A LYS* 1.3 52.7 + - - +
70A ASN* 3.3 2.4 + - - +
71A GLU* 2.7 35.0 + - - +
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 4.2 11.7 - - + -
42A ASN* 5.3 6.5 - - - +
43A PRO* 3.9 24.6 + - - -
44A ARG* 5.1 4.0 - - - +
64A THR* 3.0 31.2 + - + +
65A GLN* 3.8 24.3 + - - +
67A ALA* 1.3 72.6 - - - +
69A GLY* 1.3 66.2 + - - +
71A GLU* 3.3 15.9 + - - +
72A GLN* 3.1 28.0 + - - +
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Residues in contact with GLY 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLN 3.0 14.1 + - - -
66A LYS* 3.6 3.6 - - - -
68A LYS* 1.3 76.0 - - - +
70A ASN* 1.3 63.4 + - - +
72A GLN* 3.1 10.0 + - - +
73A SER* 3.0 24.7 + - - -
5P PHE 5.4 0.9 - - - -
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Residues in contact with ASN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 3.2 16.2 - - - +
24A GLU* 3.2 16.9 + - - +
66A LYS* 2.7 27.4 + - - +
67A ALA 3.5 4.5 - - - +
69A GLY* 1.3 73.4 - - - +
71A GLU* 1.3 62.4 + - - +
73A SER* 3.1 7.7 + - - -
74A PHE* 3.0 30.6 + - + -
2P GLN* 3.5 9.7 - - - +
3P TYR 3.1 21.3 + - - +
4P LYS* 3.7 4.3 - - - +
5P PHE* 2.9 39.3 + - + +
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 5.7 3.5 - - - +
20A PRO 4.4 7.0 - - - +
22A TYR* 3.6 33.8 - - + +
36A PHE* 4.2 10.2 - - - -
38A SER* 3.3 29.9 + - - -
67A ALA 2.7 20.3 + - - +
68A LYS* 3.4 15.7 - - - +
70A ASN* 1.3 73.7 - - - +
72A GLN* 1.3 74.9 + - - +
74A PHE* 3.5 2.3 + - - +
75A ARG* 3.0 24.0 + - + +
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Residues in contact with GLN 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS 3.1 17.1 + - - +
69A GLY* 3.5 10.1 - - - +
71A GLU* 1.3 91.9 - - - +
73A SER* 1.3 63.6 + - - +
75A ARG* 3.2 40.7 + - - +
76A VAL* 3.0 30.0 + - + +
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Residues in contact with SER 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLY 3.0 12.7 + - - -
70A ASN* 3.4 8.7 - - - -
72A GLN* 1.3 76.5 - - - +
74A PHE* 1.3 60.9 + - - +
76A VAL* 3.2 10.3 + - - +
77A ASP* 2.8 31.6 + - - +
5P PHE 3.0 22.7 + - - -
6P TYR* 3.2 26.1 + - - +
7P SER* 4.5 2.1 - - - -
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Residues in contact with PHE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.9 10.1 - - + -
11A ALA* 3.7 18.8 - - + -
22A TYR* 3.4 31.6 - + + -
70A ASN* 3.0 26.2 + - + +
71A GLU 4.0 2.0 - - - +
73A SER* 1.3 74.5 - - - +
75A ARG* 1.3 61.6 + - - +
77A ASP* 3.2 21.5 - - - +
78A LEU* 2.9 35.4 + - - +
95A ILE* 3.7 20.4 - - + +
97A VAL* 3.6 33.0 - - + -
116A TYR* 3.8 9.4 - + - -
5P PHE* 3.6 41.7 - + + -
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Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA* 5.9 0.2 - - - -
19A GLU* 3.0 42.9 + - - -
20A PRO* 3.8 22.8 - - + +
71A GLU* 3.0 16.1 + - + +
72A GLN* 3.4 35.0 + - - +
74A PHE* 1.3 78.2 - - - +
76A VAL* 1.3 63.3 + - - +
78A LEU* 3.3 18.6 + - - +
79A ARG* 3.4 38.7 + - - +
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLN* 3.0 19.5 + - + +
73A SER* 3.3 12.6 - - - +
75A ARG* 1.3 74.5 - - + +
77A ASP* 1.3 59.7 + - - +
79A ARG* 3.2 30.8 + - - +
80A THR* 2.9 36.1 + - - +
7P SER* 4.5 16.2 - - - +
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A SER 2.8 19.4 + - - +
74A PHE* 3.2 32.2 - - - +
76A VAL* 1.3 76.9 - - - +
78A LEU* 1.3 58.1 + - - +
80A THR* 3.1 7.2 + - - -
81A LEU* 2.8 34.0 + - - +
95A ILE* 3.3 19.4 - - + +
116A TYR* 4.4 1.4 + - - -
6P TYR 4.3 5.2 - - - +
7P SER* 3.4 7.3 - - - -
8P VAL* 2.9 47.1 + - + +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA* 4.0 17.9 - - + +
13A SER* 3.9 17.5 - - - +
20A PRO* 3.5 38.1 - - + -
74A PHE 2.9 19.4 + - - +
75A ARG* 3.6 6.7 - - - +
76A VAL 3.3 0.2 - - - -
77A ASP* 1.3 75.8 - - - +
79A ARG* 1.3 62.2 + - - +
81A LEU* 3.5 4.3 + - - +
82A LEU* 3.2 25.7 + - - +
93A HIS* 3.8 34.6 - - + +
95A ILE* 3.6 26.7 - - + -
118A TYR* 4.7 4.6 + - + -
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Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG* 3.4 50.0 + - - +
76A VAL* 3.2 36.5 + - - +
78A LEU* 1.3 75.0 - - - +
80A THR* 1.3 67.0 + - - +
82A LEU* 3.2 24.6 + - + +
83A GLY* 3.4 3.8 + - - -
89A LYS* 3.6 27.7 - - - +
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Residues in contact with THR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 2.9 26.2 + - - +
77A ASP* 3.1 11.8 + - - -
79A ARG* 1.3 77.4 - - - +
81A LEU* 1.3 57.7 + - - +
83A GLY* 3.1 5.4 + - - -
84A TYR* 3.0 63.1 + - + +
146A LYS* 4.7 3.5 + - - +
7P SER* 6.0 0.3 - - - -
8P VAL* 4.0 16.0 + - + +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASP 2.8 19.9 + - - +
78A LEU 3.9 2.2 - - - +
80A THR* 1.3 68.2 - - - +
82A LEU* 1.3 66.6 + - - +
83A GLY 3.0 2.0 - - - -
84A TYR* 3.6 15.0 - - + -
85A TYR* 2.9 33.1 + - + +
95A ILE* 3.9 19.3 - - + -
118A TYR* 3.3 53.4 - - + -
123A TYR* 3.3 39.5 - - + +
8P VAL* 3.8 14.4 - - + -
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU 3.2 15.1 + - - +
79A ARG* 3.2 16.0 + - + +
81A LEU* 1.3 75.1 - - - +
83A GLY* 1.3 58.1 + - - +
86A ASN* 2.9 7.8 + - - -
87A GLN* 2.8 55.5 + - + +
88A SER 3.2 29.2 - - - +
89A LYS* 3.7 37.0 - - + +
91A GLY 5.4 0.9 - - - +
93A HIS* 3.7 24.5 - - + -
118A TYR* 4.3 1.3 + - - +
----------------------------------------------------------
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Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG 3.4 4.3 + - - -
80A THR* 3.1 8.0 + - - -
81A LEU 3.0 0.4 - - - -
82A LEU* 1.3 78.8 - - - +
84A TYR* 1.3 66.9 + - - +
86A ASN* 3.1 13.3 + - - +
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A THR* 3.0 34.0 + - + -
81A LEU* 3.2 17.9 + - + +
83A GLY* 1.3 77.3 - - - +
85A TYR* 1.3 62.0 + - + +
86A ASN* 5.1 0.9 - - - +
123A TYR* 3.3 27.1 - - - -
139A ALA* 3.9 28.4 - - + +
142A ILE* 3.5 34.6 - - + +
143A THR* 3.6 9.9 - - - -
146A LYS* 3.0 36.6 + - - -
8P VAL* 3.5 8.3 + - + -
----------------------------------------------------------
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Residues in contact with TYR 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 2.9 28.9 + - + +
84A TYR* 1.3 79.1 - - + +
86A ASN* 1.3 73.8 + - - +
87A GLN* 3.4 27.9 + - + +
118A TYR* 3.4 35.4 - + - +
122A ASP 5.5 0.3 + - - -
123A TYR* 3.2 29.4 - + - -
137A ASP* 2.6 31.3 + - - -
139A ALA* 3.5 21.5 - - + -
----------------------------------------------------------
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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