Contacts of the helix formed by residues 46 - 73 (chain U) in PDB entry 6L49
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 46 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-132J G 4.8 1.4 + - - -
44U GLY* 3.2 1.0 - - - -
45U ALA* 1.3 76.2 - - - +
47U ALA* 1.3 59.6 + - - +
48U PRO 3.6 0.4 - - - -
49U VAL* 3.3 11.3 + - - +
50U TYR* 2.8 31.0 + - - +
88V SER* 3.3 18.1 + - - +
115V VAL* 3.3 12.2 - - - +
118V TYR* 4.4 6.2 - - - -
119V THR* 5.4 5.3 - - - +
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Residues in contact with ALA 47 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34U LEU* 4.1 3.4 - - + -
43U VAL* 3.8 19.7 - - + -
44U GLY 3.2 14.5 + - - +
46U GLY* 1.3 74.7 - - - +
48U PRO* 1.3 63.0 - - + +
50U TYR* 3.8 2.2 - - - +
51U LEU* 2.9 31.9 + - - +
86V ILE 3.9 3.4 - - - +
87V THR 3.8 11.9 - - - +
88V SER* 3.9 3.0 + - - +
91V ILE* 3.7 28.6 - - + +
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Residues in contact with PRO 48 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26U PRO 4.7 0.5 - - - +
27U VAL* 3.3 28.7 - - + +
30U VAL* 3.7 18.5 - - + +
31U HIS* 3.4 41.5 - - + +
34U LEU* 3.8 8.1 - - + -
44U GLY 3.3 14.1 - - - +
45U ALA 3.6 10.1 - - - +
47U ALA* 1.3 87.2 - - + +
49U VAL* 1.3 60.3 + - - +
51U LEU* 3.8 0.5 - - - +
52U ALA* 2.8 31.7 + - - +
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Residues in contact with VAL 49 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21U ALA* 3.7 19.3 - - + -
23U LEU* 3.3 12.4 - - + +
27U VAL* 3.8 23.3 - - + -
45U ALA 3.4 21.8 - - - +
46U GLY* 3.4 8.5 - - - +
47U ALA 3.2 0.4 - - - -
48U PRO* 1.3 76.6 - - - +
50U TYR* 1.3 56.0 + - - +
52U ALA 3.4 0.2 + - - -
53U ALA* 2.9 26.2 + - - +
114V ALA* 3.3 37.5 - - + +
115V VAL* 4.1 1.3 - - + +
118V TYR* 3.6 22.4 - - + -
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Residues in contact with TYR 50 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46U GLY 2.8 20.2 + - - +
47U ALA* 3.8 5.2 - - - +
48U PRO 3.3 0.2 - - - -
49U VAL* 1.3 73.7 - - - +
51U LEU* 1.3 57.9 + - - +
53U ALA* 3.3 4.5 + - - +
54U VAL* 3.0 40.3 + - + +
88V SER* 4.3 9.4 - - - -
91V ILE* 3.5 42.8 - - + -
92V GLN* 3.3 24.2 - - + +
95V VAL* 3.6 15.4 - - + +
107V ALA 3.8 6.8 + - - -
108V VAL* 3.3 35.9 + - - +
111V GLY* 3.4 33.0 - - - -
112V THR* 3.8 7.9 - - - -
115V VAL* 3.9 12.3 - - + +
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Residues in contact with LEU 51 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30U VAL* 3.8 8.5 - - + -
34U LEU* 3.8 25.1 - - + -
47U ALA 2.9 15.6 + - - +
48U PRO 3.8 4.3 - - - +
50U TYR* 1.3 77.0 - - - +
52U ALA* 1.3 56.0 + - - +
54U VAL* 3.9 3.5 - - + +
55U LEU* 2.9 37.8 + - + +
66V ILE* 6.3 0.2 - - + -
67V PHE* 3.7 46.7 - - + +
70V ILE* 4.0 25.1 - - + -
71V ALA* 4.3 11.9 - - + +
91V ILE* 3.7 26.5 - - + -
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Residues in contact with ALA 52 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23U LEU* 3.8 17.3 - - + -
25U PHE* 3.5 30.2 - - + +
26U PRO 3.9 16.2 - - - +
27U VAL* 5.1 0.4 - - + +
30U VAL* 4.7 4.4 - - + +
48U PRO 2.8 19.8 + - - +
49U VAL* 4.6 0.7 - - - -
51U LEU* 1.3 76.5 - - - +
53U ALA* 1.3 56.7 + - - +
55U LEU* 4.2 6.1 - - - -
56U GLU* 2.9 30.0 + - - +
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Residues in contact with ALA 53 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23U LEU* 3.5 15.9 - - + +
49U VAL 2.9 18.8 + - - +
50U TYR 3.7 0.7 - - - +
51U LEU 3.3 0.2 - - - -
52U ALA* 1.3 75.0 - - - +
54U VAL* 1.3 60.2 + - - +
56U GLU* 3.3 2.3 + - - +
57U TYR* 2.9 29.1 + - - +
110V GLU* 3.9 12.2 - - + +
111V GLY* 3.7 19.7 - - - +
114V ALA* 3.7 23.3 - - + -
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Residues in contact with VAL 54 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50U TYR* 3.0 42.3 + - + +
51U LEU* 4.1 4.7 - - + +
53U ALA* 1.3 74.4 - - - +
55U LEU* 1.3 58.3 + - + +
57U TYR* 3.4 5.7 + - - +
58U LEU* 2.9 33.5 + - + +
66V ILE* 5.2 0.7 - - + -
70V ILE* 3.9 17.5 - - + -
91V ILE* 6.4 0.2 - - + -
95V VAL* 3.8 20.2 - - + -
99V LEU* 4.1 8.1 - - + -
107V ALA* 3.6 37.7 - - + +
111V GLY* 4.7 1.3 - - - -
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Residues in contact with LEU 55 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25U PHE* 3.5 18.3 - - + -
30U VAL* 5.3 4.5 - - + -
51U LEU* 2.9 26.0 + - + +
52U ALA* 3.7 2.7 - - - +
54U VAL* 1.3 77.4 - - - +
56U GLU* 1.3 57.3 + - - +
58U LEU* 3.4 2.7 + - - +
59U THR* 2.9 32.6 + - - +
34V TYR* 5.1 7.9 - - + +
62V PHE* 5.2 1.0 - - + -
63V VAL* 3.3 47.3 - - + +
66V ILE* 3.8 27.4 - - + -
67V PHE* 3.8 27.6 - - + +
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Residues in contact with GLU 56 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22U GLY 4.9 1.2 - - - +
23U LEU* 3.4 23.1 - - + +
24U GLN* 2.9 47.2 + - - +
25U PHE* 3.4 16.7 + - + -
52U ALA 2.9 16.3 + - - +
53U ALA* 3.3 5.8 + - - +
55U LEU* 1.3 75.4 - - - +
57U TYR* 1.3 56.1 + - - +
59U THR* 3.4 2.7 - - - +
60U ALA* 2.9 32.9 + - + +
41V VAL* 4.2 17.3 - - + +
44V GLN* 3.9 8.0 - - - +
110V GLU* 5.9 1.8 - - - +
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Residues in contact with TYR 57 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53U ALA 2.9 17.0 + - - +
54U VAL* 3.8 4.0 - - - +
55U LEU 3.3 0.2 - - - -
56U GLU* 1.3 77.0 - - - +
58U LEU* 1.3 69.6 + - + +
60U ALA* 3.3 6.6 + - + +
61U GLU* 3.0 48.6 + - + +
103V LEU* 3.4 49.6 - - + +
106V HIS* 3.3 33.8 + - + +
107V ALA* 3.9 18.8 - - + -
110V GLU* 4.3 31.1 + - + +
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Residues in contact with LEU 58 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54U VAL* 2.9 22.2 + - + +
55U LEU* 3.9 3.6 - - - +
57U TYR* 1.3 94.8 - - + +
59U THR* 1.3 57.1 + - - +
61U GLU* 3.4 4.5 + - + +
62U ILE* 2.9 32.9 + - - +
93U LEU* 4.6 6.9 - - + +
96U LEU* 4.0 6.1 - - + -
62V PHE* 3.9 13.9 - - + -
66V ILE* 3.6 37.5 - - + -
99V LEU* 3.9 27.8 - - + -
103V LEU* 3.8 32.1 - - + -
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Residues in contact with THR 59 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25U PHE* 3.7 25.1 - - + -
55U LEU 2.9 21.6 + - - +
56U GLU* 3.4 7.9 - - - +
58U LEU* 1.3 76.1 - - - +
60U ALA* 1.3 60.1 + - - +
62U ILE* 4.3 2.5 - - - -
63U LEU* 2.9 31.3 + - - +
38V VAL* 3.3 14.8 - - + +
41V VAL* 3.7 17.3 - - + -
59V MET* 3.3 21.7 - - - +
62V PHE* 4.0 11.6 - - - -
63V VAL* 4.6 5.8 - - - +
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Residues in contact with ALA 60 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56U GLU* 2.9 22.1 + - + +
57U TYR* 3.6 8.1 - - + +
59U THR* 1.3 76.1 - - - +
61U GLU* 1.3 59.3 + - - +
63U LEU* 3.8 2.2 - - - +
64U GLU* 2.9 31.4 + - - +
41V VAL* 4.5 7.2 - - + -
45V VAL* 4.1 26.4 - - + +
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Residues in contact with GLU 61 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57U TYR* 3.0 42.1 + - + +
58U LEU* 3.8 5.8 - - - +
60U ALA* 1.3 78.4 - - - +
62U ILE* 1.3 56.9 + - - +
64U GLU* 3.3 8.0 + - - +
65U LEU* 3.0 38.9 + - + +
90U ASP* 4.4 8.5 - - - +
93U LEU* 3.8 26.7 - - + -
103V LEU* 4.9 5.6 - - + -
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Residues in contact with ILE 62 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58U LEU 2.9 20.0 + - - +
59U THR* 4.0 3.6 - - - +
61U GLU* 1.3 76.7 - - - +
63U LEU* 1.3 57.3 + - - +
65U LEU 3.5 0.2 + - - -
66U ALA* 2.9 29.5 + - - +
83U LEU* 3.8 16.6 - - + -
86U ALA* 3.5 8.8 - - + +
87U ILE* 4.0 30.7 - - + +
93U LEU* 3.7 33.2 - - + -
97U LEU* 4.8 4.3 - - + -
59V MET* 3.7 24.0 - - + -
62V PHE* 3.9 23.8 - - + -
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Residues in contact with LEU 63 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59U THR* 2.9 35.7 + - - +
60U ALA 4.2 2.0 - - - +
62U ILE* 1.3 72.0 - - - +
64U GLU* 1.3 59.9 + - - +
66U ALA* 3.7 5.5 - - + +
67U GLY* 2.9 25.5 + - - -
78U ILE* 3.8 17.3 - - + +
83U LEU* 5.2 0.9 - - + -
38V VAL* 3.7 15.3 - - + +
41V VAL* 4.4 6.1 - - + -
42V LEU* 3.7 46.9 - - + +
45V VAL* 4.2 10.3 - - + -
46V HIS* 4.1 6.6 + - - -
51V ILE* 4.1 14.8 - - + -
59V MET* 3.9 18.4 - - + -
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Residues in contact with GLU 64 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60U ALA 2.9 20.3 + - - +
61U GLU* 3.6 11.0 - - - +
63U LEU* 1.3 77.0 - - - +
65U LEU* 1.3 61.8 + - + +
67U GLY* 3.3 1.9 + - - -
68U ASN* 3.0 47.7 + - - +
71U ARG* 5.8 0.3 + - - -
45V VAL* 4.2 14.4 - - + +
46V HIS* 3.4 28.1 + - - -
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Residues in contact with LEU 65 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61U GLU* 3.0 25.0 + - + +
62U ILE 4.7 0.2 - - - -
64U GLU* 1.3 80.1 - - + +
66U ALA* 1.3 57.1 + - - +
68U ASN* 3.4 21.8 + - + +
69U ALA* 2.9 28.1 + - - +
85U LEU 5.3 0.2 - - - -
86U ALA* 3.4 37.2 - - + +
89U ASN* 5.0 7.2 + - + +
90U ASP* 3.7 29.2 - - + +
93U LEU* 3.8 12.3 - - + -
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Residues in contact with ALA 66 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62U ILE 2.9 19.0 + - - +
63U LEU* 3.7 8.3 - - - +
65U LEU* 1.3 74.6 - - - +
67U GLY* 1.3 59.7 + - - +
69U ALA 3.3 0.5 + - - -
70U ALA* 2.9 28.3 + - - +
78U ILE* 4.0 19.2 - - + +
82U HIS* 3.5 18.9 - - - +
83U LEU* 3.7 24.9 - - + -
86U ALA* 3.4 2.6 - - + +
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Residues in contact with GLY 67 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63U LEU 2.9 17.6 + - - -
64U GLU 3.8 1.8 - - - -
66U ALA* 1.3 72.2 - - - +
68U ASN* 1.3 61.3 + - - +
70U ALA* 3.7 6.9 - - - +
71U ARG* 2.9 35.8 + - - +
78U ILE* 4.5 1.0 - - - +
46V HIS* 4.2 18.8 - - - -
49V THR* 4.8 13.2 + - - -
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Residues in contact with ASN 68 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64U GLU* 3.0 29.4 + - - +
65U LEU* 3.6 24.4 - - + +
66U ALA 3.3 0.2 - - - -
67U GLY* 1.3 77.9 - - - +
69U ALA* 1.3 56.5 + - - +
71U ARG* 3.4 14.7 + - - +
72U ASP* 2.9 35.8 + - - +
46V HIS* 4.1 9.7 + - - -
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Residues in contact with ALA 69 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65U LEU 2.9 18.0 + - - +
66U ALA 3.3 2.0 + - - +
68U ASN* 1.3 73.9 - - - +
70U ALA* 1.3 59.8 + - - +
72U ASP* 3.4 9.5 + - - +
73U ASN* 2.4 38.1 + - - +
82U HIS* 3.6 27.1 - - - +
85U LEU* 3.7 25.4 - - + -
86U ALA 4.8 0.2 - - - +
89U ASN* 5.3 2.9 - - - +
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Residues in contact with ALA 70 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66U ALA 2.9 18.3 + - - +
67U GLY* 3.7 8.3 - - - +
68U ASN 3.3 0.2 - - - -
69U ALA* 1.3 74.8 - - - +
71U ARG* 1.3 60.2 + - + +
73U ASN 3.2 0.9 + - - -
74U LYS 3.0 8.3 + - - -
75U LYS 2.9 43.1 + - - +
76U THR* 5.0 4.0 - - - +
77U ARG 4.8 1.3 - - - +
78U ILE* 4.8 8.3 - - + -
82U HIS* 3.4 27.5 - - + +
49V THR* 5.5 2.2 - - + -
----------------------------------------------------------
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Residues in contact with ARG 71 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64U GLU* 5.8 0.4 + - - -
67U GLY 2.9 20.7 + - - +
68U ASN* 3.8 13.3 + - - +
70U ALA* 1.3 75.7 - - + +
72U ASP* 1.3 63.4 + - - +
74U LYS* 3.7 12.4 + - - +
75U LYS 4.4 4.7 - - - +
46V HIS* 3.3 39.8 + - - +
47V PRO* 5.6 4.2 - - - +
48V ASP* 5.0 8.1 + - - +
49V THR* 4.7 7.4 + - - +
----------------------------------------------------------
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Residues in contact with ASP 72 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68U ASN* 2.9 26.2 + - - +
69U ALA* 3.6 10.8 - - - +
70U ALA 3.2 0.4 - - - -
71U ARG* 1.3 80.0 - - - +
73U ASN* 1.3 61.5 + - - +
74U LYS* 3.3 10.0 + - - +
85U LEU* 6.0 0.9 - - + -
89U ASN* 5.9 0.9 + - - -
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Residues in contact with ASN 73 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69U ALA* 2.4 28.1 + - - +
70U ALA 3.2 0.8 + - - +
72U ASP* 1.3 80.7 - - - +
74U LYS* 1.3 63.8 + - - +
75U LYS* 2.6 35.7 + - + +
81U ARG* 3.3 34.0 + - - +
82U HIS* 3.4 27.1 - - - +
85U LEU* 3.6 19.7 - - - +
----------------------------------------------------------
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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