Contacts of the helix formed by residues 52 - 80 (chain A) in PDB entry 4XNW
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 TYR 52 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLY* 2.8 35.5 + - - +
51A PHE* 1.3 89.5 - + + +
53A TYR* 1.3 63.9 + + + +
55A PRO* 3.2 17.0 - - - +
56A ALA 3.5 4.9 + - - -
112A PHE* 3.8 5.4 - + - -
114A LYS* 3.0 30.8 + - - -
256C ARG* 3.3 43.0 + - + -
260C TYR* 3.3 31.9 + - + +
1050C GLU* 5.7 0.5 + - - -
1051C GLU 5.0 4.1 + - - -
1053C GLU* 3.2 42.8 + - + +
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Residues in contact with TYR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLY* 3.1 32.1 + - - -
49A PHE* 3.2 21.2 + + + +
52A TYR* 1.3 87.0 - - + +
54A LEU* 1.3 64.9 + - - +
56A ALA* 3.4 7.0 + - - +
57A VAL* 3.2 27.8 + - + +
256C ARG* 3.6 18.2 - - + -
259C ILE* 2.9 53.5 - - + +
260C TYR* 4.0 10.5 - + - -
263C ILE* 4.5 11.6 - - + +
1053C GLU* 2.6 35.0 + - - +
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 2.6 51.8 + - + +
50A GLN* 4.6 4.0 - - - -
53A TYR* 1.3 69.4 - - - +
55A PRO* 1.3 71.2 - - + +
57A VAL* 3.2 10.4 + - + +
58A TYR* 3.0 53.6 + - + +
111A TYR* 4.0 33.2 - - + +
307A GLN* 4.6 11.7 - - - +
310A ARG* 6.3 0.7 - - + +
311A GLY* 3.9 18.6 - - - -
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Residues in contact with PRO 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLN 3.3 15.3 - - - +
51A PHE 3.6 13.7 - - - +
52A TYR 3.2 21.8 - - - +
54A LEU* 1.3 95.4 - - + +
56A ALA* 1.3 54.3 + - - +
58A TYR* 3.3 13.1 + - + +
59A ILE* 2.9 32.4 + - - +
108A ILE* 3.8 19.0 - - + +
111A TYR* 3.8 12.6 - - + -
112A PHE* 3.8 27.1 - - + -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR 3.5 11.9 + - - +
53A TYR* 3.4 10.5 + - - +
54A LEU 3.2 0.6 - - - -
55A PRO* 1.3 75.0 - - - +
57A VAL* 1.3 66.5 + - + +
59A ILE* 3.1 7.5 + - - +
60A LEU* 3.1 25.2 + - - +
112A PHE* 4.4 0.8 - - - -
260C TYR* 3.9 24.5 - - + -
263C ILE* 5.2 10.1 - - + -
264C ILE* 5.9 3.1 - - + -
322C ILE* 4.3 2.8 - - + +
326C LEU* 4.1 18.2 - - + -
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Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 5.6 5.8 - - + -
53A TYR 3.2 15.0 + - - +
54A LEU* 3.2 15.2 + - + +
56A ALA* 1.3 76.6 - - - +
58A TYR* 1.3 61.7 + - + +
60A LEU* 3.1 13.5 + - + +
61A VAL* 2.8 39.2 + - + +
311A GLY 5.5 5.2 - - - +
315A LEU* 4.6 12.6 - - + -
263C ILE* 4.7 20.0 - - + -
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Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.0 51.9 + - + +
55A PRO* 3.6 7.0 - - + +
57A VAL* 1.3 77.7 - - + +
59A ILE* 1.3 54.4 + - - +
61A VAL* 3.6 6.5 - - + +
62A PHE* 2.6 37.6 + - - +
104A LEU* 3.9 18.1 - - + +
107A LEU* 3.2 36.9 - - + +
108A ILE* 3.4 23.5 - - + +
111A TYR* 4.2 8.6 + + - -
310A ARG* 3.9 13.0 + - - +
311A GLY* 3.8 19.5 + - - -
314A SER* 3.4 30.6 + - - -
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Residues in contact with ILE 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PRO 2.9 20.1 + - - +
56A ALA* 3.1 6.7 + - - +
58A TYR* 1.3 74.7 - - - +
60A LEU* 1.3 58.2 + - - +
62A PHE* 3.1 7.3 + - + +
63A ILE* 2.9 42.8 + - + +
108A ILE* 3.6 22.2 - - + +
112A PHE* 3.9 22.7 - - + -
322C ILE* 3.4 25.1 - - + -
326C LEU* 4.1 22.0 - - + -
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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
----------------------------------------------------------
56A ALA 3.1 12.5 + - - +
57A VAL* 3.1 13.9 + - + +
59A ILE* 1.3 72.8 - - - +
61A VAL* 1.3 65.8 + - + +
63A ILE* 3.9 4.4 - - + +
64A ILE* 3.0 41.4 + - + +
263C ILE* 4.0 21.1 - - + -
264C ILE* 4.6 13.2 - - + -
267C THR* 3.7 36.1 - - + +
319C VAL* 3.9 28.9 - - + -
322C ILE* 4.3 14.8 - - + -
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Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 2.8 26.4 + - + +
58A TYR* 3.6 11.2 - - + +
60A LEU* 1.3 70.9 - - + +
62A PHE* 1.3 56.9 + - - +
65A GLY* 2.7 35.5 + - - -
100A TYR* 5.6 0.4 - - + -
101A VAL* 4.8 1.0 - - + +
104A LEU* 3.7 16.8 - - + +
314A SER* 3.5 29.4 - - - +
315A LEU* 3.8 29.4 - - + -
317A SER* 4.8 9.4 - - - -
318A CYS* 4.1 20.6 - - - -
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Residues in contact with PHE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR 2.6 22.2 + - - +
59A ILE* 3.1 11.0 + - + +
61A VAL* 1.3 73.2 - - - +
63A ILE* 1.3 74.0 + - + +
66A PHE* 2.8 49.5 + + + +
101A VAL* 3.3 40.8 - - + +
102A LEU* 4.7 5.2 - - + -
104A LEU* 3.6 16.6 - - + +
105A PRO* 4.0 25.4 - - + -
108A ILE* 4.4 4.9 - - + -
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 2.9 34.6 + - + +
60A LEU* 4.0 4.3 - - - +
62A PHE* 1.3 89.8 - - + +
64A ILE* 1.3 66.7 + - + +
66A PHE* 3.0 16.2 + - - +
67A LEU* 3.1 28.4 + - + +
64C ILE* 5.8 7.4 - - + -
318C CYS* 4.0 20.2 - - + +
319C VAL* 3.9 34.1 - - + -
322C ILE* 5.0 9.2 - - + +
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.0 36.4 + - + +
61A VAL* 5.3 0.7 - - - -
63A ILE* 1.3 82.3 - - + +
65A GLY* 1.3 52.6 - - - +
67A LEU* 3.2 7.7 + - + +
68A GLY* 2.8 35.5 + - - +
318A CYS* 3.7 28.0 - - + +
267C THR* 4.5 18.4 - - + -
271C VAL* 5.0 17.0 - - + -
315C LEU* 5.2 16.2 - - + -
319C VAL* 4.9 11.4 - - + -
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Residues in contact with GLY 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL 2.7 23.5 + - - -
62A PHE 3.9 0.2 - - - -
64A ILE* 1.3 72.1 - - - +
66A PHE* 1.3 61.8 + - - +
68A GLY 4.6 0.2 - - - -
69A ASN* 2.9 31.6 + - - +
98A PHE* 5.3 0.2 - - - -
101A VAL* 4.1 13.7 - - - +
317A SER 3.7 20.4 - - - -
318A CYS* 3.8 5.7 - - - +
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Residues in contact with PHE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE* 2.8 38.1 + + + +
63A ILE* 3.0 7.4 + - - +
65A GLY* 1.3 74.9 - - - +
67A LEU* 1.3 59.5 + - + +
70A SER* 2.7 49.9 + - - -
98A PHE* 3.5 30.6 - + - -
101A VAL* 3.9 5.9 - - + +
102A LEU* 3.8 22.9 - - + -
60C LEU* 4.6 14.1 - - + -
64C ILE* 4.6 19.5 - - + -
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 3.1 28.9 + - + +
64A ILE* 3.6 6.5 - - - +
66A PHE* 1.3 78.7 - - + +
68A GLY* 1.3 67.9 + - - +
71A VAL* 3.1 31.8 + - + +
60C LEU* 3.8 27.1 - - + -
61C VAL* 4.9 2.0 - - + +
64C ILE* 3.4 32.1 - - + -
315C LEU* 3.9 38.1 - - + -
318C CYS* 4.0 17.0 - - - -
319C VAL* 5.5 0.9 - - + -
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Residues in contact with GLY 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 2.8 21.2 + - - -
65A GLY 4.1 0.2 - - - -
67A LEU* 1.3 74.1 - - - +
69A ASN* 1.3 58.2 + - - +
71A VAL* 3.7 4.1 + - - +
72A ALA* 3.1 25.8 + - - +
321A PRO* 4.0 24.3 - - - +
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Residues in contact with ASN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLY* 2.9 22.0 + - - +
68A GLY* 1.3 75.1 - - - +
70A SER* 1.3 61.6 + - - +
71A VAL 3.3 0.2 - - - -
72A ALA* 3.7 4.2 - - - +
73A ILE* 2.9 36.3 + - - +
94A ALA* 3.8 14.7 - - - +
97A ASP* 3.8 21.7 + - - +
98A PHE* 4.2 11.7 - - + -
101A VAL* 4.8 0.2 - - - +
317A SER 2.7 29.7 + - - -
321A PRO* 3.8 7.6 - - - +
324A TYR* 3.5 30.0 + - - -
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 2.7 34.4 + - - -
69A ASN* 1.3 76.4 - - - +
71A VAL* 1.3 62.1 + - - +
73A ILE* 3.4 6.5 + - - +
74A TRP* 3.1 40.0 + - - -
98A PHE* 3.2 25.3 - - - -
60C LEU* 3.8 21.3 - - - -
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 3.1 18.2 + - + +
68A GLY* 3.9 3.6 - - - +
70A SER* 1.3 72.6 - - - +
72A ALA* 1.3 67.7 + - - +
74A TRP* 3.0 11.7 + - - +
75A MET* 2.9 30.9 + - + +
325A PHE* 5.8 1.3 - - + -
53C TYR* 4.0 33.9 - - + +
56C ALA* 4.3 6.5 - - + -
57C VAL* 3.8 30.1 - - + +
60C LEU* 3.5 20.4 - - + -
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY 3.1 17.2 + - - +
69A ASN* 3.7 5.8 - - - +
71A VAL* 1.3 78.8 - - - +
73A ILE* 1.3 57.6 + - - +
75A MET* 2.9 23.7 + - - +
76A PHE* 2.9 26.0 + - + -
94A ALA* 4.3 3.1 - - + -
321A PRO* 5.5 0.9 - - + -
324A TYR* 3.5 37.7 - - + -
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Residues in contact with ILE 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ASN 2.9 25.0 + - - +
70A SER* 3.7 5.8 - - - +
72A ALA* 1.3 71.7 - - - +
74A TRP* 1.3 66.0 + - + +
76A PHE* 4.6 5.4 - - - +
77A VAL* 3.0 41.4 + - + +
78A PHE* 6.3 0.9 - - + -
91A PHE* 4.2 12.6 - - + -
94A ALA* 3.9 22.7 - - + +
95A LEU* 4.3 14.8 - - + +
98A PHE* 3.8 36.6 - - + -
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Residues in contact with TRP 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A SER* 3.1 46.8 + - - -
71A VAL* 3.0 12.8 + - - +
73A ILE* 1.3 79.2 - - + +
75A MET* 1.3 73.6 + - + +
78A PHE* 3.2 57.8 + + + +
79A HIS* 3.5 5.2 - - + +
56C ALA* 5.0 10.5 - - + -
60C LEU* 4.1 24.5 - - + -
----------------------------------------------------------
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Residues in contact with MET 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 2.9 26.7 + - + +
72A ALA* 2.9 9.6 + - - +
74A TRP* 1.3 90.0 - - + +
76A PHE* 1.3 60.0 + - + +
79A HIS* 3.1 45.3 + - + +
80A MET* 3.3 19.3 + - + +
325A PHE* 5.9 4.7 - - + -
49C PHE* 5.0 1.3 - - - +
52C TYR* 3.3 28.7 - - + +
53C TYR* 3.6 30.1 - - + -
56C ALA* 4.2 9.9 - - + -
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Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA* 2.9 29.5 + - + +
73A ILE* 4.0 1.6 - - - +
75A MET* 1.3 79.3 - - + +
77A VAL* 1.3 67.9 + - - +
78A PHE 3.0 3.1 + - - -
80A MET* 3.3 31.0 + - + -
81A LYS 4.3 0.5 + - - -
83A TRP* 3.0 31.3 + - + -
87A SER* 3.7 38.6 - - - -
90A MET* 3.7 31.4 - - + -
91A PHE* 3.9 22.2 - + + -
94A ALA* 4.7 1.8 - - + -
324A TYR* 4.0 36.3 - + + -
328A GLY* 6.4 0.4 - - - -
329A ASP 6.3 0.2 - - - -
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 3.0 22.5 + - + +
76A PHE* 1.3 80.5 - - - +
78A PHE* 1.3 94.8 + - + +
81A LYS* 3.7 27.1 + - - +
83A TRP* 3.7 10.5 - - + -
91A PHE* 3.2 37.0 - - + -
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Residues in contact with PHE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 6.3 1.3 - - + -
74A TRP* 3.2 45.5 + + + +
76A PHE 3.1 0.4 - - - -
77A VAL* 1.3 106.9 - - + +
79A HIS* 1.3 82.1 + - + +
81A LYS 5.7 0.2 - - - -
----------------------------------------------------------
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Residues in contact with HIS 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 3.5 17.4 + - - +
75A MET* 3.1 38.0 + - + +
78A PHE* 1.3 101.3 + - + +
80A MET* 1.3 61.8 + - - +
81A LYS 3.7 3.3 - - - +
331A PHE* 3.6 35.8 - - + +
52C TYR* 3.6 35.4 - + + +
----------------------------------------------------------
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Residues in contact with MET 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A MET* 3.6 17.9 - - + +
76A PHE* 3.3 27.9 + - + +
79A HIS* 1.3 79.3 - - - +
81A LYS* 1.3 67.3 + - - +
82A PRO* 2.9 19.6 - - - +
83A TRP* 3.4 21.5 - - + +
87A SER* 4.3 12.3 - - - +
324A TYR 5.9 1.8 - - - +
329A ASP* 3.7 24.5 - - - +
330A THR 4.4 2.5 - - - +
331A PHE* 3.6 46.2 - - + +
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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