Contacts of the helix formed by residues 56 - 87 (chain A) in PDB entry 4DJH
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 PRO 56 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER* 1.3 90.7 - - - +
57A ALA* 1.3 60.4 + - + +
58A ILE 3.4 0.2 - - - -
59A PRO* 3.5 11.9 - - + +
60A VAL* 4.0 3.3 - - - +
125B PRO* 4.2 20.0 - - + +
126B PHE* 3.4 46.7 - - + +
130B LEU* 5.0 10.3 - - + -
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER* 3.2 12.6 + - - +
56A PRO* 1.3 80.0 - - + +
58A ILE* 1.3 69.0 + - + +
60A VAL* 3.1 9.0 + - + +
61A ILE* 2.8 38.4 + - + +
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Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER* 3.8 30.1 - - - +
56A PRO 3.4 0.2 - - - -
57A ALA* 1.3 78.5 - - + +
59A PRO* 1.3 71.1 - - + +
61A ILE* 3.2 4.5 + - + +
62A ILE* 2.8 56.7 + - + +
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Residues in contact with PRO 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER 3.7 7.2 - - - +
56A PRO* 3.5 16.2 - - + +
58A ILE* 1.3 101.9 - - + +
60A VAL* 1.3 50.7 + - + +
62A ILE* 3.6 5.6 - - + +
63A THR* 2.6 44.1 + - - +
117B THR* 3.8 25.6 - - + +
121B MET* 5.6 6.5 - - - -
125B PRO* 6.5 0.2 - - + -
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO 4.0 2.7 - - - +
57A ALA* 3.1 11.8 + - - +
59A PRO* 1.3 79.3 - - - +
61A ILE* 1.3 73.4 + - + +
63A THR* 3.7 2.6 - - - -
64A ALA* 3.0 24.5 + - + +
113B PRO* 3.9 32.1 - - + +
114B PHE* 3.9 32.8 - - + -
117B THR* 4.7 0.4 - - - +
126B PHE* 3.8 31.9 - - + -
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Residues in contact with ILE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA* 2.8 34.8 + - + +
58A ILE* 3.7 5.2 - - + +
60A VAL* 1.3 82.2 - - + +
62A ILE* 1.3 60.3 + - + +
64A ALA* 3.3 6.0 + - + +
65A VAL* 2.9 42.9 + - + +
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 2.8 47.9 + - + +
59A PRO* 3.7 4.9 - - + +
61A ILE* 1.3 74.2 - - + +
63A THR* 1.3 60.7 + - - +
65A VAL* 3.9 4.3 - - - +
66A TYR* 2.8 39.8 + - + +
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PRO* 2.6 30.1 + - - +
60A VAL* 3.7 4.6 - - - -
62A ILE* 1.3 75.2 - - - +
64A ALA* 1.3 64.4 + - - +
66A TYR* 3.4 8.8 - - + +
67A SER* 3.0 26.5 + - - +
66B TYR* 3.2 35.9 - - + +
70B PHE* 6.5 0.2 - - + -
113B PRO* 4.1 9.6 - - + -
116B SER* 3.8 15.1 + - - +
117B THR* 4.4 5.4 + - - -
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL* 3.0 19.5 + - + +
61A ILE* 3.6 7.2 - - + +
63A THR* 1.3 78.6 - - - +
65A VAL* 1.3 64.5 + - + +
67A SER* 3.1 13.0 + - - -
68A VAL* 3.1 18.7 + - + +
70B PHE* 3.8 31.7 - - + -
113B PRO* 4.8 5.4 - - + +
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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 ILE* 2.9 32.0 + - + +
62A ILE* 3.9 4.7 - - - +
64A ALA* 1.3 77.5 - - + +
66A TYR* 1.3 66.6 + - - +
68A VAL* 3.2 6.6 + - - +
69A VAL* 3.0 40.5 + - + +
321A THR* 5.8 0.9 - - - +
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Residues in contact with TYR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 2.8 29.6 + - + +
63A THR* 3.4 10.1 - - + +
65A VAL* 1.3 76.8 - - - +
67A SER* 1.3 64.0 + - - +
69A VAL* 3.3 5.6 + - - +
70A PHE* 3.0 31.5 + + + +
112A MET* 3.1 31.1 + - + +
113A PRO* 3.0 35.0 - - - +
115A GLN* 5.7 1.6 - - + -
116A SER* 3.3 24.8 + - - -
320A TYR* 6.4 1.1 - + - -
63B THR* 3.4 13.7 - - + +
66B TYR* 6.3 0.9 - + - -
67B SER* 3.8 16.4 - - - -
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Residues in contact with SER 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 3.0 14.4 + - - +
64A ALA 3.4 7.9 - - - -
66A TYR* 1.3 80.1 - - - +
68A VAL* 1.3 64.9 + - - +
70A PHE* 3.2 2.2 + - - +
71A VAL* 2.9 29.1 + - - +
66B TYR* 3.8 18.0 - - - -
67B SER* 3.6 25.7 + - - -
70B PHE* 3.8 20.0 - - - -
71B VAL* 3.6 4.9 - - - -
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ALA* 3.1 12.6 + - + +
65A VAL* 3.6 10.1 - - - +
67A SER* 1.3 77.2 - - - +
69A VAL* 1.3 70.2 + - + +
71A VAL* 3.9 0.3 - - - +
72A VAL* 3.0 38.3 + - + +
70B PHE* 4.9 7.2 - - + -
71B VAL* 3.6 24.9 - - + +
75B VAL* 5.5 6.1 - - + -
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 3.0 29.7 + - + +
66A TYR* 3.7 7.2 - - - +
68A VAL* 1.3 80.5 - - + +
70A PHE* 1.3 58.7 + - - +
73A GLY* 2.8 27.5 + - - -
112A MET* 3.6 14.3 - - + +
320A TYR* 3.4 22.4 - - + +
321A THR* 3.7 21.1 - - + +
324A SER* 3.2 31.9 - - - +
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Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 3.0 23.7 + - + +
67A SER* 3.6 4.5 - - - +
69A VAL* 1.3 77.2 - - - +
71A VAL* 1.3 64.5 + - + +
74A LEU* 2.8 64.6 + - + +
109A THR* 3.3 32.4 - - + +
110A THR* 4.4 4.0 - - + -
112A MET* 3.7 23.1 - - + -
113A PRO* 3.8 14.8 - - + -
64B ALA* 3.7 43.1 - - + -
67B SER* 3.7 19.5 - - - -
68B VAL* 5.8 1.6 - - + -
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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 SER 2.9 20.2 + - - +
68A VAL 4.0 1.6 - - - +
70A PHE* 1.3 83.8 - - + +
72A VAL* 1.3 60.5 + - + +
74A LEU* 4.7 1.3 - - - -
75A VAL* 2.6 58.8 + - + +
67B SER 3.8 1.3 - - - -
68B VAL* 3.6 35.9 - - + +
71B VAL* 3.5 33.9 - - + -
72B VAL* 5.3 4.9 - - + -
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL* 3.0 32.8 + - + +
71A VAL* 1.3 79.5 - - + +
73A GLY* 1.3 55.0 + - - +
75A VAL* 5.0 0.9 - - - -
76A GLY* 2.7 34.7 + - - +
324A SER* 2.9 34.3 - - - +
327A PRO* 4.0 6.0 - - + +
328A ILE* 4.3 19.5 - - + -
71B VAL* 5.5 5.8 - - + -
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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 VAL 2.8 18.9 + - - -
70A PHE 3.8 0.4 - - - -
72A VAL* 1.3 79.5 - - - +
74A LEU* 1.3 58.4 + - - +
77A ASN* 2.7 28.9 + - - +
105A ASP 4.4 1.2 - - - +
106A ALA* 4.4 0.9 - - - -
109A THR* 3.7 17.9 + - - -
112A MET* 5.8 0.2 - - - -
323A SER 3.8 4.7 - - - -
324A SER* 3.5 18.8 - - - -
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PHE* 2.8 45.3 + - + +
71A VAL* 4.1 1.8 - - - +
73A GLY* 1.3 76.5 - - - +
75A VAL* 1.3 62.0 + - + +
77A ASN* 4.7 0.2 - - - +
78A SER* 2.6 40.5 + - - +
106A ALA* 4.1 13.7 - - + +
109A THR* 3.5 8.4 - - + +
110A THR* 3.5 32.8 - - + +
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 2.6 43.4 + - + +
72A VAL* 5.0 1.1 - - - -
74A LEU* 1.3 77.8 - - + +
76A GLY* 1.3 65.4 + - - +
78A SER* 3.2 7.3 + - - +
79A LEU* 3.2 24.4 + - + +
68B VAL* 6.0 4.5 - - + -
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Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A VAL* 2.7 28.3 + - - +
75A VAL* 1.3 79.0 - - - +
77A ASN* 1.3 61.7 + - - +
79A LEU* 3.2 15.6 + - - +
80A VAL* 3.2 15.4 + - - +
327A PRO* 3.7 17.0 - - - +
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Residues in contact with ASN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLY 2.7 26.0 + - - +
76A GLY* 1.3 71.6 - - - +
78A SER* 1.3 61.6 + - - +
80A VAL* 3.1 4.9 + - - +
81A MET* 2.9 35.1 + - - +
102A ALA* 3.3 42.6 - - + +
105A ASP* 3.5 18.4 - - - +
106A ALA* 3.9 5.8 - - + -
323A SER 2.8 24.2 + - - -
327A PRO* 3.4 17.4 - - - +
330A TYR* 4.3 5.0 - - - -
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Residues in contact with SER 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 2.6 27.9 + - - +
75A VAL* 3.2 14.0 + - - +
77A ASN* 1.3 79.3 - - - +
79A LEU* 1.3 61.0 + - - +
81A MET* 3.4 20.4 - - - +
82A PHE* 3.2 23.4 + - - +
106A ALA* 4.6 2.4 - - - +
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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 VAL* 3.2 23.7 + - + +
76A GLY* 3.2 9.6 + - - +
77A ASN 3.1 0.4 - - - -
78A SER* 1.3 74.9 + - - +
80A VAL* 1.3 59.8 + - - +
82A PHE* 3.4 5.3 + - + +
83A VAL* 2.9 30.8 + - + +
341A PHE* 3.8 37.7 - - + -
344A PHE* 3.2 42.8 - - + -
345A CYS* 5.1 10.8 - - + -
346B PHE* 5.6 5.2 - - + -
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLY 3.2 13.0 + - - +
77A ASN* 3.1 9.6 + - - +
79A LEU* 1.3 74.4 - - - +
81A MET* 1.3 69.2 + - - +
82A PHE 3.1 0.7 + - - -
83A VAL* 3.2 12.7 + - - +
84A ILE* 3.2 22.9 + - + +
98A ILE* 4.2 12.3 - - + +
99A PHE* 5.2 0.2 - - - -
102A ALA* 4.1 15.7 - - + -
327A PRO* 4.6 4.0 - - + -
330A TYR* 3.8 20.2 - - + -
337A PHE* 4.0 17.7 - - + -
341A PHE* 3.7 29.6 - - + -
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Residues in contact with MET 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASN 2.9 12.7 + - - +
78A SER* 3.4 28.9 - - - +
80A VAL* 1.3 77.7 - - - +
82A PHE* 1.3 64.1 + - - +
84A ILE* 3.4 1.0 + - - +
85A ILE* 3.1 20.5 + - - +
99A PHE* 3.6 36.4 - - + +
102A ALA* 3.8 14.1 - - + -
103A LEU* 3.4 44.2 - - + +
106A ALA* 3.7 22.4 - - + -
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Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER 3.2 14.7 + - - +
79A LEU* 3.8 5.2 - - - +
80A VAL 3.2 0.8 - - - -
81A MET* 1.3 76.9 - - - +
83A VAL* 1.3 72.7 + - - +
84A ILE 2.9 1.4 + - - -
85A ILE* 3.2 7.0 + - + +
86A ARG* 3.0 54.4 + - + +
87A TYR* 5.3 2.9 - + - -
344A PHE* 3.3 42.2 - + - -
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 2.9 17.9 + - + +
80A VAL* 3.2 13.2 + - - +
82A PHE* 1.3 82.3 - - - +
84A ILE* 1.3 71.9 + - + +
86A ARG* 5.0 0.9 - - - -
87A TYR* 3.3 34.8 + - + +
90A MET* 4.5 4.7 - - - +
337A PHE* 4.3 15.5 - - + -
340A CYS* 3.5 44.1 - - + +
341A PHE* 4.4 12.6 - - + -
344A PHE* 4.5 16.4 - - + -
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 3.2 28.7 + - + +
81A MET 3.8 4.9 - - - +
82A PHE 2.9 1.0 + - - -
83A VAL* 1.3 86.7 - - + +
85A ILE* 1.3 70.6 + - - +
86A ARG 2.8 2.9 + - - -
87A TYR 3.0 22.8 + - - +
90A MET* 4.0 22.7 - - + +
91A LYS* 3.4 18.7 - - + -
95A ASN* 3.8 30.1 - - + +
96A ILE* 5.6 4.3 - - + -
98A ILE* 5.0 0.4 - - + -
99A PHE* 4.2 22.4 - - + +
337A PHE* 4.2 15.5 - - + -
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Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A MET 3.1 14.4 + - - +
82A PHE* 3.9 8.1 - - + +
84A ILE* 1.3 80.4 - - - +
86A ARG* 1.3 58.4 + - - +
91A LYS* 3.2 22.1 + - - +
99A PHE* 4.7 11.6 - - + -
----------------------------------------------------------
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Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PHE* 3.0 44.0 + - + +
83A VAL 4.2 0.2 - - - +
84A ILE 2.8 2.2 + - - -
85A ILE* 1.3 80.6 - - + +
87A TYR* 1.3 84.1 + - + +
88A THR* 3.5 3.5 + - - -
91A LYS* 5.4 0.2 - - - -
----------------------------------------------------------
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Residues in contact with TYR 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PHE* 5.3 6.1 - + - -
83A VAL* 3.3 16.1 + - + +
84A ILE 3.0 14.9 + - - +
86A ARG* 1.3 101.5 - - + +
88A THR* 1.3 65.3 + - - +
89A LYS* 3.2 13.3 + - + +
90A MET* 3.3 20.1 + - + +
91A LYS* 3.7 6.0 - - - +
340A CYS* 3.4 29.2 - - - -
343A ASP* 5.1 8.7 + - + +
344A PHE* 4.5 23.8 + + + +
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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