Contacts of the helix formed by residues 92 - 119 (chain Q) in PDB entry 1MFR
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 THR 92 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Q PHE* 3.6 19.7 - - - -
44Q LEU* 3.8 8.1 - - - +
47Q VAL* 4.1 17.9 - - + +
91Q ASN* 1.3 72.2 - - - +
93Q LEU* 1.3 58.2 + - - +
95Q ALA* 3.9 0.9 - - - +
96Q MET* 3.0 39.1 + - + +
151Q LEU* 4.1 7.2 - - + -
156Q LEU* 4.0 7.4 - - - -
163Q GLU* 2.8 30.5 + - + +
166Q PHE* 3.8 35.0 - - + -
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Residues in contact with LEU 93 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91Q ASN* 2.9 10.3 + - - +
92Q THR* 1.3 75.2 - - - +
94Q GLU* 1.3 62.0 + - - +
96Q MET* 3.3 1.6 + - - +
97Q GLN* 2.9 52.5 + - - +
148Q ILE* 3.9 29.4 - - + +
151Q LEU* 3.9 24.7 - - + -
152Q LYS* 4.3 16.4 - - + -
156Q LEU* 3.4 18.1 - - + +
157Q PRO* 3.7 35.7 - - + -
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Residues in contact with GLU 94 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86Q ARG* 3.0 39.8 + - - +
89Q TRP 3.4 12.1 - - - +
90Q GLY* 3.7 8.2 - - - -
91Q ASN* 3.1 27.5 + - - +
93Q LEU* 1.3 80.2 - - - +
95Q ALA* 1.3 57.9 + - - +
97Q GLN* 3.5 14.3 + - - +
98Q ALA* 3.0 26.9 + - - +
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Residues in contact with ALA 95 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Q MET* 3.8 10.1 - - - +
37Q PHE* 3.7 27.6 - - + -
51Q PHE* 4.1 11.4 - - + -
89Q TRP* 3.7 16.5 + - + -
91Q ASN 3.0 17.9 + - - +
92Q THR 3.9 2.7 - - - +
94Q GLU* 1.3 74.6 - - - +
96Q MET* 1.3 60.5 + - - +
98Q ALA* 3.4 7.9 + - - +
99Q ALA* 2.9 27.4 + - - +
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Residues in contact with MET 96 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47Q VAL* 4.6 3.8 - - + -
50Q PHE* 4.0 16.6 - - + -
51Q PHE* 3.7 31.2 - - + -
92Q THR* 3.0 26.8 + - + +
93Q LEU 3.7 3.6 - - - +
95Q ALA* 1.3 74.3 - - - +
97Q GLN* 1.3 61.0 + - - +
99Q ALA* 3.3 2.3 + - - +
100Q LEU* 2.8 23.9 + - - +
144Q ILE* 3.4 21.0 - - + +
147Q PHE* 3.9 32.5 - - + -
148Q ILE* 3.8 17.7 - - + -
151Q LEU* 3.8 17.5 - - + -
166Q PHE* 4.3 16.6 - - + -
171Q VAL* 5.3 1.3 - - + -
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Residues in contact with GLN 97 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93Q LEU* 2.9 42.0 + - + +
94Q GLU* 3.8 14.7 - - - +
96Q MET* 1.3 72.8 - - - +
98Q ALA* 1.3 66.2 + - - +
100Q LEU* 3.3 3.8 + - - +
101Q GLN* 3.1 25.1 + - - +
148Q ILE* 4.0 21.1 - - + +
152Q LYS* 4.1 21.8 + - - -
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Residues in contact with ALA 98 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Q MET* 4.0 4.6 - - + +
85Q GLU* 5.4 4.5 - - - +
86Q ARG* 5.6 2.5 - - - +
89Q TRP* 3.8 32.5 - - + -
94Q GLU 3.0 15.7 + - - +
95Q ALA 3.5 7.9 - - - +
97Q GLN* 1.3 75.7 - - - +
99Q ALA* 1.3 58.6 + - - +
101Q GLN* 3.4 6.6 + - - +
102Q LEU* 3.0 28.3 + - - +
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Residues in contact with ALA 99 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Q TYR* 3.9 27.8 - - + +
33Q MET* 4.2 5.1 - - + +
51Q PHE* 4.2 8.3 - - + -
95Q ALA 2.9 18.1 + - - +
96Q MET* 3.5 10.1 - - - +
98Q ALA* 1.3 74.3 - - - +
100Q LEU* 1.3 59.9 + - - +
102Q LEU* 3.2 6.0 + - - +
103Q GLU* 2.9 35.0 + - - +
144Q ILE* 4.1 12.1 - - + -
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Residues in contact with LEU 100 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J GLN* 3.7 38.1 - - + +
4J VAL* 4.9 0.7 - - + -
96Q MET 2.8 19.6 + - - +
97Q GLN* 3.3 6.5 + - + +
99Q ALA* 1.3 72.9 - - - +
101Q GLN* 1.3 59.6 + - + +
103Q GLU* 3.4 3.5 + - - +
104Q LYS* 3.0 41.4 + - + +
141Q ILE* 3.9 42.2 - - + +
144Q ILE* 3.9 11.8 - - + +
145Q GLY* 4.5 3.6 - - - +
148Q ILE* 3.7 22.4 - - + -
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Residues in contact with GLN 101 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97Q GLN 3.1 13.2 + - - +
98Q ALA* 3.7 9.0 - - - +
100Q LEU* 1.3 76.3 - - + +
102Q LEU* 1.3 59.9 + - - +
104Q LYS* 3.2 10.5 + - - +
105Q THR* 2.9 34.1 + - - +
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Residues in contact with LEU 102 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Q LEU* 5.4 1.8 - - + -
25Q TYR* 4.1 26.9 - - + -
26Q ALA* 3.9 24.7 - - + +
29Q THR* 3.7 28.3 - - + -
30Q TYR* 3.9 32.8 - - + +
33Q MET* 5.2 0.2 - - + -
98Q ALA 3.0 17.7 + - - +
99Q ALA* 3.2 5.8 + - - +
101Q GLN* 1.3 75.7 - - - +
103Q GLU* 1.3 59.4 + - + +
105Q THR* 3.4 10.9 + - + -
106Q VAL* 3.1 36.0 + - + +
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Residues in contact with GLU 103 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Q ALA* 6.5 0.4 - - - -
30Q TYR* 2.8 28.9 + - - +
54Q HIS* 3.6 14.4 + - - -
58Q GLU* 3.4 12.4 - - - +
99Q ALA 2.9 14.9 + - - +
100Q LEU* 3.8 5.6 - - - +
102Q LEU* 1.3 75.3 - - - +
104Q LYS* 1.3 60.2 + - - +
106Q VAL* 3.3 5.9 + - - +
107Q ASN* 2.8 25.5 + - - +
137Q GLN* 3.0 29.2 + - - +
140Q ASP* 4.4 7.4 - - + +
141Q ILE* 3.9 14.6 - - + -
144Q ILE* 3.9 14.6 - - + -
177Q MG 2.9 27.1 - - - -
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Residues in contact with LYS 104 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J SER 4.8 1.0 + - - -
3J GLN* 2.9 31.5 + - - +
4J VAL 4.4 6.3 - - - +
5J ARG 3.5 16.4 + - - -
6J GLN* 3.0 43.9 + - + +
100Q LEU* 3.0 29.5 + - + +
101Q GLN* 3.7 9.2 - - - +
103Q GLU* 1.3 75.0 - - - +
105Q THR* 1.3 55.8 + - - +
107Q ASN* 4.1 0.2 - - - -
108Q GLN* 2.9 25.8 + - - +
141Q ILE* 4.2 11.2 - - + -
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Residues in contact with THR 105 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Q LEU* 4.6 19.3 - - + -
25Q TYR* 6.5 0.4 - - + -
101Q GLN* 2.9 20.9 + - - +
102Q LEU* 3.5 12.5 - - + +
103Q GLU 3.2 0.2 - - - -
104Q LYS* 1.3 76.2 - - - +
106Q VAL* 1.3 63.5 + - - +
108Q GLN* 3.4 6.8 + - - +
109Q ALA* 3.1 21.3 + - - +
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Residues in contact with VAL 106 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Q MET* 5.1 1.8 - - - -
22Q LEU* 3.9 28.7 - - + +
23Q GLU* 4.0 10.1 - - - +
26Q ALA* 4.2 23.8 - - + -
58Q GLU* 4.9 0.9 - - - +
102Q LEU* 3.1 20.6 + - + +
103Q GLU* 3.7 9.9 - - - +
105Q THR* 1.3 71.6 - - - +
107Q ASN* 1.3 66.4 + - - +
109Q ALA* 3.2 3.5 + - - +
110Q LEU* 3.0 30.5 + - + +
137Q GLN* 3.9 11.4 - - - +
176Q MG 3.8 22.4 - - - -
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Residues in contact with ASN 107 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J GLN* 3.0 41.3 + - - +
103Q GLU 2.8 21.2 + - - +
106Q VAL* 1.3 72.6 - - - +
108Q GLN* 1.3 57.5 + - - +
110Q LEU* 3.1 9.5 + - - +
111Q LEU* 2.9 42.2 + - - +
134Q LEU* 4.8 8.8 - - - +
137Q GLN* 3.6 22.9 - - - +
138Q VAL* 5.0 9.7 - - - +
141Q ILE* 3.9 16.9 - - + +
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Residues in contact with GLN 108 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J GLN* 3.6 20.7 + - - +
7J ASN* 5.8 2.6 + - - +
104Q LYS 2.9 18.3 + - - +
105Q THR* 3.6 7.4 - - - +
107Q ASN* 1.3 79.1 - - - +
109Q ALA* 1.3 55.9 + - - +
111Q LEU* 3.4 16.4 + - - +
112Q ASP* 2.9 63.1 + - - +
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Residues in contact with ALA 109 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Q MET* 3.1 21.6 - - + +
22Q LEU* 3.7 22.2 - - + -
105Q THR 3.1 13.4 + - - +
106Q VAL 3.2 9.2 + - - +
108Q GLN* 1.3 78.1 - - - +
110Q LEU* 1.3 56.9 + - - +
112Q ASP* 3.4 10.0 + - - +
113Q LEU* 2.9 22.0 + - - +
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Residues in contact with LEU 110 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Q MET* 3.7 24.9 - - + -
23Q GLU* 4.9 1.3 - - - +
65Q PHE* 4.0 21.3 - - + -
106Q VAL* 3.0 26.2 + - + +
107Q ASN* 3.4 7.2 - - - +
109Q ALA* 1.3 75.4 - - - +
111Q LEU* 1.3 60.9 + - - +
113Q LEU* 3.4 3.6 + - - +
114Q HIS* 2.9 26.2 + - - +
129Q LEU* 4.2 14.5 - - + +
133Q TYR* 3.9 30.7 - - + -
134Q LEU* 3.9 15.7 - - + +
137Q GLN* 3.7 31.2 - - + +
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Residues in contact with LEU 111 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J GLN* 4.5 4.0 - - + -
7J ASN* 3.7 34.8 - - + +
123J PRO* 3.7 34.7 - - + +
124J HIS* 5.3 4.0 - - + +
107Q ASN* 2.9 43.5 + - - +
108Q GLN* 3.7 20.0 - - - +
109Q ALA 3.3 0.2 - - - -
110Q LEU* 1.3 75.0 - - - +
112Q ASP* 1.3 59.6 + - - +
114Q HIS* 3.2 7.1 + - - +
115Q LYS* 3.0 27.4 + - - +
134Q LEU* 4.6 15.7 - - + -
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Residues in contact with ASP 112 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108Q GLN* 2.9 49.6 + - - +
109Q ALA* 3.4 9.4 - - - +
111Q LEU* 1.3 77.1 - - - +
113Q LEU* 1.3 59.6 + - - +
115Q LYS* 3.3 7.8 + - - +
116Q LEU* 3.0 26.2 + - - +
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Residues in contact with LEU 113 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Q CYS* 4.3 9.6 - - - +
15Q ALA* 3.5 31.4 - - + +
16Q VAL* 4.3 16.8 - - + -
19Q MET* 3.7 35.2 - - + -
65Q PHE* 4.5 2.0 - - + -
109Q ALA 2.9 17.6 + - - +
110Q LEU* 3.7 5.6 - - + +
111Q LEU 3.3 0.2 - - - -
112Q ASP* 1.3 76.4 - - - +
114Q HIS* 1.3 59.4 + - - +
116Q LEU* 3.4 10.2 + - + +
117Q ALA* 3.0 26.2 + - - +
125Q LEU* 4.4 10.1 - - + -
129Q LEU* 3.9 25.8 - - + -
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Residues in contact with HIS 114 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J VAL* 6.0 1.6 - - - +
123J PRO* 3.5 36.7 - - + +
110Q LEU 2.9 14.7 + - - +
111Q LEU* 3.3 13.2 - - - +
112Q ASP 3.1 0.2 - - - -
113Q LEU* 1.3 74.5 - - - +
115Q LYS* 1.3 61.0 + - - +
117Q ALA* 3.3 4.3 + - - +
118Q THR* 2.9 43.2 + - - -
126Q CYS* 3.6 30.9 + - - +
129Q LEU* 3.8 18.5 - - + +
130Q GLU* 2.9 25.3 + - - -
134Q LEU* 4.2 6.5 - - + -
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Residues in contact with LYS 115 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J VAL* 4.2 25.6 - - + -
111Q LEU 3.0 12.6 + - - +
112Q ASP* 3.5 11.2 - - - +
114Q HIS* 1.3 74.4 + - - +
116Q LEU* 1.3 61.2 + - - +
118Q THR* 3.2 9.4 + - + +
119Q ASP* 2.9 29.2 + - - +
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Residues in contact with LEU 116 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q ASP* 3.6 39.5 - - + +
12Q CYS* 4.0 11.7 - - - -
15Q ALA* 3.7 20.2 - - + -
18Q ARG* 5.4 2.0 - - - +
112Q ASP 3.0 14.0 + - - +
113Q LEU* 3.6 11.2 - - + +
114Q HIS 3.3 0.2 - - - -
115Q LYS* 1.3 77.0 - - - +
117Q ALA* 1.3 55.7 + - - +
119Q ASP* 3.3 5.2 + - + +
120Q LYS* 2.9 50.2 + - + +
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Residues in contact with ALA 117 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Q CYS* 4.3 10.7 - - - -
113Q LEU 3.0 14.7 + - - +
114Q HIS* 3.3 10.3 + - - +
116Q LEU* 1.3 73.1 - - - +
118Q THR* 1.3 64.0 + - - +
120Q LYS 3.5 0.7 + - - -
121Q VAL 3.1 3.5 + - - -
122Q ASP* 2.9 34.9 + - + +
125Q LEU* 3.9 27.4 - - + -
126Q CYS* 3.6 18.2 - - - +
129Q LEU* 5.1 0.2 - - + -
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Residues in contact with THR 118 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J VAL* 6.3 2.5 - - + -
114Q HIS* 2.9 31.6 + - - -
115Q LYS* 3.2 10.5 + - + +
117Q ALA* 1.3 75.1 - - - +
119Q ASP* 1.3 62.3 + - - +
121Q VAL* 3.1 18.2 + - - +
126Q CYS* 3.5 15.5 - - - -
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Residues in contact with ASP 119 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115Q LYS 2.9 16.0 + - - +
116Q LEU* 3.6 9.4 - - + +
118Q THR* 1.3 78.5 - - - +
120Q LYS* 1.3 72.8 + - + +
121Q VAL* 3.2 9.2 + - - +
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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