Contacts of the helix formed by residues 53 - 83 (chain B) in PDB entry 4LT6
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 ASP 53 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PHE 4.2 0.4 + - - -
52B GLU* 1.3 75.5 - - - +
54B GLU* 1.3 64.9 + - - +
55B GLU* 3.3 16.5 - - + +
56B GLU* 2.7 44.1 + - - +
57B LEU* 3.0 23.4 + - - +
109B LYS* 4.1 10.8 + - - +
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLU 4.8 2.1 - - - +
53B ASP* 1.3 73.2 - - - +
55B GLU* 1.3 62.4 + - + +
57B LEU* 3.9 20.1 - - - +
58B ASN* 2.9 43.7 + - - +
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Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ASP* 3.1 16.8 - - + +
54B GLU* 1.3 78.9 - - + +
56B GLU* 1.3 57.7 + - + +
58B ASN* 3.4 7.5 + - - +
59B HIS* 3.0 28.6 + - - +
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Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLU* 3.3 30.9 - - - +
53B ASP* 2.7 46.1 + - - +
55B GLU* 1.3 78.9 - - + +
57B LEU* 1.3 65.4 + - - +
59B HIS* 3.4 7.8 + - - +
60B ARG* 3.4 24.6 + - - +
109B LYS* 3.2 40.7 + - - +
110B GLY 5.4 0.5 + - - -
163B ILE* 5.6 0.5 - - - +
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLU* 3.9 22.4 - - + +
53B ASP 3.0 20.2 + - - +
54B GLU* 3.9 25.4 - - - +
56B GLU* 1.3 75.2 - - - +
58B ASN* 1.3 63.5 + - - +
60B ARG* 3.3 7.6 + - - +
61B LEU* 3.0 35.5 + - + +
102B TYR* 5.3 5.4 - - + -
107B HIS* 3.7 33.0 - - + +
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Residues in contact with ASN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLU* 2.9 41.2 + - - +
55B GLU* 3.6 6.9 - - - +
57B LEU* 1.3 76.8 - - - +
59B HIS* 1.3 65.7 + - - +
61B LEU* 3.0 15.2 + - - +
62B VAL* 3.0 26.5 + - + +
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Residues in contact with HIS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLU 3.0 16.1 + - - +
56B GLU* 3.6 7.4 - - - +
57B LEU 3.3 0.2 - - - -
58B ASN* 1.3 76.6 - - - +
60B ARG* 1.3 63.6 + - - +
62B VAL* 2.9 19.1 + - + +
63B VAL* 2.8 29.5 + - + +
161B ASP* 2.7 46.0 + - + +
163B ILE* 3.7 25.6 - - + -
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Residues in contact with ARG 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLU* 2.8 41.7 + - - -
56B GLU 3.4 7.8 + - - +
57B LEU* 3.3 9.4 + - - +
59B HIS* 1.3 78.3 - - - +
61B LEU* 1.3 57.9 + - - +
63B VAL* 3.1 7.8 + - - +
64B LEU* 2.8 35.5 + - - +
102B TYR* 3.6 32.8 - - + -
107B HIS* 3.8 8.4 + - - -
108B THR 3.9 1.8 + - - -
110B GLY* 3.9 3.8 - - - +
111B ALA* 2.7 46.2 + - - +
112B ASP 4.1 2.0 + - - -
113B ILE* 3.5 31.5 - - + +
163B ILE* 4.1 28.6 - - + +
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 3.0 32.9 + - + +
58B ASN* 3.0 17.6 + - - +
60B ARG* 1.3 75.3 - - - +
62B VAL* 1.3 58.6 + - + +
64B LEU* 3.5 7.5 + - + +
65B GLY* 2.8 26.3 + - - -
102B TYR* 3.2 24.7 - - + +
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASN* 3.0 18.1 + - + +
59B HIS* 2.9 20.7 + - + +
61B LEU* 1.3 78.0 - - + +
63B VAL* 1.3 63.6 + - + +
65B GLY* 3.1 4.4 + - - -
66B LYS* 3.1 39.2 + - + +
161B ASP* 5.4 0.9 - - - +
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B HIS* 2.8 26.0 + - + +
60B ARG* 3.6 7.4 - - - +
62B VAL* 1.3 77.8 - - + +
64B LEU* 1.3 64.2 + - + +
66B LYS* 3.1 10.5 + - - +
67B LEU* 3.0 21.3 + - - +
113B ILE* 5.5 0.2 - - + -
160B PHE* 3.9 31.7 - - + +
161B ASP* 3.7 33.4 - - + +
163B ILE* 3.9 20.0 - - + -
165B ILE* 3.9 15.9 - - + -
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG 2.8 18.8 + - - +
61B LEU* 3.8 8.1 - - + +
63B VAL* 1.3 69.7 - - - +
65B GLY* 1.3 67.0 - - - +
67B LEU* 3.8 22.2 - - + +
68B ASN* 3.1 25.8 + - - +
96B ILE* 4.7 9.9 - - + +
98B THR* 3.5 32.8 - - + -
102B TYR* 3.7 27.6 - - + +
113B ILE* 4.1 23.1 - - + -
115B ALA* 5.2 1.8 - - + -
165B ILE* 4.9 5.8 - - + -
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Residues in contact with GLY 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU 2.8 16.6 + - - -
62B VAL* 3.1 6.7 + - - -
64B LEU* 1.3 79.6 - - - +
66B LYS* 1.3 60.5 + - - +
68B ASN* 3.2 6.2 + - - +
69B ASN* 3.1 19.7 + - - +
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Residues in contact with LYS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 3.1 28.8 + - + +
63B VAL* 3.1 8.5 + - - +
65B GLY* 1.3 70.8 - - - +
67B LEU* 1.3 60.9 + - - +
69B ASN* 3.0 18.6 + - - +
70B LEU* 2.9 32.3 + - + +
139B GLN* 5.5 4.5 - - - +
140B ASP* 6.3 1.0 - - - +
141B GLY 5.9 0.8 - - - +
160B PHE* 3.8 24.0 - - + -
161B ASP* 3.1 30.1 + - - +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B VAL 3.0 14.9 + - - +
64B LEU* 3.8 13.9 - - + +
66B LYS* 1.3 75.5 - - - +
68B ASN* 1.3 63.5 + - - +
70B LEU* 3.2 11.3 + - + +
71B VAL* 3.2 24.2 + - + +
96B ILE* 3.8 31.0 - - + -
115B ALA* 4.6 1.1 - - + -
132B PHE* 4.2 22.7 - - + -
136B LEU* 4.7 1.6 - - + -
158B PHE* 4.5 15.0 - - + -
160B PHE* 4.0 10.4 - - + -
165B ILE* 4.3 27.1 - - + -
167B LEU* 4.0 16.8 - - + -
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Residues in contact with ASN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU 3.1 16.2 + - - +
65B GLY* 3.4 6.7 - - - +
67B LEU* 1.3 79.6 - - - +
69B ASN* 1.3 61.3 + - - +
71B VAL* 3.6 2.8 + - - +
72B LYS* 3.3 39.5 + - - +
94B GLY 5.2 0.2 - - - -
95B LYS* 4.3 12.7 - - - +
96B ILE* 3.4 45.8 + - + +
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Residues in contact with ASN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLY 3.1 11.7 + - - +
66B LYS* 3.0 25.2 + - - +
68B ASN* 1.3 75.8 - - - +
70B LEU* 1.3 75.5 + - - +
72B LYS* 3.6 8.5 + - - +
73B GLU* 3.1 30.7 + - - +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LYS* 2.9 18.9 + - + +
67B LEU* 3.2 9.8 + - + +
69B ASN* 1.3 86.7 - - - +
71B VAL* 1.3 52.3 + - - +
73B GLU* 3.1 17.6 + - - +
74B TRP* 2.6 36.7 + - - +
132B PHE* 4.1 11.9 - - + -
135B LYS* 4.5 14.7 - - + +
136B LEU* 3.9 24.5 - - + -
139B GLN* 3.4 50.0 - - + +
160B PHE* 4.4 15.3 - - + -
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.2 12.9 + - + +
68B ASN 3.8 8.3 - - - +
70B LEU* 1.3 76.4 - - - +
72B LYS* 1.3 58.6 + - - +
74B TRP* 3.0 2.3 + - + -
75B ILE* 2.8 49.7 + - + +
94B GLY 4.7 0.7 - - - -
95B LYS 4.5 13.7 - - - +
96B ILE* 3.6 25.6 - - + -
117B CYS* 3.6 27.1 - - + -
132B PHE* 3.7 28.5 - - + -
167B LEU* 5.7 0.2 - - + -
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Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASN* 3.3 28.2 + - - +
69B ASN* 3.9 7.4 - - - +
70B LEU 3.4 0.2 - - - -
71B VAL* 1.3 78.1 - - - +
73B GLU* 1.3 59.4 - - - +
75B ILE* 4.2 1.0 - - - +
76B SER* 3.3 24.3 + - - -
92B VAL 5.5 1.0 - - - +
93B GLY* 4.0 23.4 - - - +
94B GLY 3.9 25.8 - - - +
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASN* 3.1 25.0 + - - +
70B LEU* 3.1 20.5 + - - +
72B LYS* 1.3 72.6 - - - +
74B TRP* 1.3 68.2 + - - +
76B SER* 3.7 6.0 + - - -
77B ASP* 3.4 19.5 + - - +
135B LYS* 3.0 40.2 + - - +
139B GLN* 5.5 3.0 + - - -
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Residues in contact with TRP 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU 2.6 19.8 + - - +
71B VAL* 3.0 6.9 + - + +
73B GLU* 1.3 69.6 - - - +
75B ILE* 1.3 80.5 + - + +
76B SER 2.6 5.3 + - - -
77B ASP* 2.3 52.0 + - + +
78B VAL* 3.3 16.1 + - + +
117B CYS* 4.3 18.2 - - - -
123B VAL* 3.4 33.0 - - + -
127B ASP* 3.4 21.1 - - + -
128B PHE* 3.8 14.8 - + + -
131B SER* 3.5 34.4 + - - -
132B PHE* 3.4 37.1 - + + +
135B LYS* 4.5 10.7 - - + +
169B PHE* 4.1 9.9 - + - -
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Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 2.8 28.4 + - + +
72B LYS 4.3 1.1 - - - +
74B TRP* 1.3 99.2 - - + +
76B SER* 1.3 59.0 + - - +
78B VAL* 3.6 9.4 + - - +
79B SER* 3.3 19.1 + - - -
92B VAL* 3.6 22.8 - - + +
93B GLY 3.4 17.3 - - - +
94B GLY* 3.6 26.5 - - - -
117B CYS* 5.0 0.2 - - - -
118B VAL 4.0 1.8 - - - +
119B ALA* 3.9 13.9 - - + -
120B PRO* 3.6 22.2 - - + -
122B HIS* 5.0 2.5 - - + -
123B VAL* 4.5 6.8 - - + +
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Residues in contact with SER 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LYS 3.3 17.0 + - - -
73B GLU* 3.8 7.4 - - - -
74B TRP 2.6 4.9 + - - -
75B ILE* 1.3 76.3 - - - +
77B ASP* 1.3 63.4 + - - -
78B VAL 3.2 0.4 - - - -
79B SER* 3.2 19.3 + - - -
80B GLU* 3.3 17.4 + - - +
89B VAL* 3.9 23.1 + - - +
90B ALA* 5.5 1.2 - - - -
92B VAL* 5.5 2.9 - - - -
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Residues in contact with ASP 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 3.4 13.1 + - - +
74B TRP* 2.3 35.1 + - + +
76B SER* 1.3 68.8 - - - +
78B VAL* 1.3 58.7 + - + +
80B GLU* 3.8 17.0 + - - +
81B SER* 3.1 26.2 + - - -
135B LYS* 3.6 27.9 + - - -
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TRP* 3.3 38.0 + - + +
75B ILE* 4.0 6.7 - - - +
76B SER 3.2 0.2 - - - -
77B ASP* 1.3 77.4 - - + +
79B SER* 1.3 58.9 + - - +
81B SER* 3.7 9.9 - - - +
82B LYS* 3.0 47.9 + - + +
122B HIS* 3.5 26.2 - - - +
123B VAL* 4.5 7.4 - - + -
127B ASP* 3.8 13.7 - - + +
131B SER* 4.6 8.3 - - - +
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Residues in contact with SER 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ILE 3.3 14.5 + - - -
76B SER* 3.2 12.8 + - - -
77B ASP 3.1 0.4 - - - -
78B VAL* 1.3 76.8 - - - +
80B GLU* 1.3 65.8 + - - +
82B LYS* 3.5 0.4 + - - -
83B ASN 3.3 14.4 + - - -
84B LEU* 3.6 23.0 + - - +
89B VAL* 3.5 28.5 + - - -
92B VAL* 3.7 27.9 - - - +
122B HIS* 4.1 7.0 - - - -
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Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B SER* 3.3 13.8 + - - +
77B ASP* 3.9 22.0 - - - +
79B SER* 1.3 77.5 - - - +
81B SER* 1.3 54.2 + - - +
83B ASN* 2.8 35.3 + - - +
84B LEU 5.3 0.9 - - - +
89B VAL* 4.3 17.7 - - + +
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Residues in contact with SER 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASP 3.1 18.8 + - - -
78B VAL* 3.7 12.6 - - - +
79B SER 3.2 0.4 - - - -
80B GLU* 1.3 78.9 - - - +
82B LYS* 1.3 61.1 + - - +
83B ASN* 3.9 7.8 + - - +
----------------------------------------------------------
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 3.0 39.6 + - + +
79B SER* 4.1 1.6 - - - +
80B GLU 3.3 0.2 - - - -
81B SER* 1.3 78.3 + - - +
83B ASN* 1.3 72.6 + - - +
84B LEU* 3.8 20.3 - - + +
122B HIS* 3.7 30.4 + - + +
123B VAL* 5.2 0.2 - - - +
124B GLU* 5.6 4.6 + - - +
127B ASP* 3.6 13.7 + - - -
----------------------------------------------------------
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Residues in contact with ASN 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B SER 3.3 1.2 + - - -
80B GLU* 2.8 25.0 + - - +
81B SER* 3.9 7.7 + - - +
82B LYS* 1.3 84.2 + - - +
84B LEU* 1.3 68.7 + - - +
----------------------------------------------------------
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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