Contacts of the helix formed by residues 110 - 139 (chain J) in PDB entry 1UMN
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 110 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J ARG 4.3 2.9 - - - -
108J ASN 3.6 5.1 + - - +
109J VAL* 1.3 79.8 - - - +
111J ILE* 1.3 66.6 + - - +
112J GLU* 3.4 16.4 + - - +
113J GLU* 3.1 25.6 + - - +
114J GLN* 2.9 22.5 + - - +
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Residues in contact with ILE 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F ARG* 3.6 27.4 - - - +
50J MET* 3.3 40.2 - - + -
51J ARG 3.3 18.7 + - - +
52J GLY* 3.6 11.6 - - - +
53J ARG 3.5 13.7 - - - +
54J GLY 4.1 2.5 - - - +
55J PHE 3.9 17.5 - - - +
58J TRP* 4.8 3.4 - - + -
110J THR* 1.3 73.1 - - - +
112J GLU* 1.3 66.9 + - - +
114J GLN* 3.0 9.3 + - - +
115J LEU* 2.9 41.5 + - + +
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Residues in contact with GLU 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F ARG* 3.5 35.3 + - + +
110J THR* 3.4 21.2 - - - +
111J ILE* 1.3 79.6 + - - +
113J GLU* 1.3 56.5 + - - +
115J LEU* 3.5 2.5 + - - +
116J ALA* 3.0 26.9 + - - +
166J LEU* 4.0 24.0 - - + +
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Residues in contact with GLU 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J VAL* 3.6 28.9 - - + +
110J THR* 3.1 22.8 + - - +
112J GLU* 1.3 74.5 - - - +
114J GLN* 1.3 66.7 + - - +
116J ALA* 3.2 9.0 + - + +
117J ARG* 3.0 22.6 + - + +
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Residues in contact with GLN 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45J GLN* 5.5 1.0 - - - +
46J VAL* 3.7 37.9 - - + +
49J TYR* 4.2 24.5 + - - +
50J MET* 4.3 16.0 - - + +
51J ARG 5.7 0.2 - - - +
106J ASP 4.1 10.3 + - - +
109J VAL* 3.6 29.0 + - + +
110J THR 2.9 20.3 + - - +
111J ILE* 3.0 10.3 + - - +
113J GLU* 1.3 76.9 - - - +
115J LEU* 1.3 63.3 + - - +
117J ARG* 3.0 12.9 + - - +
118J VAL* 3.0 25.4 + - - +
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Residues in contact with LEU 115 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F ARG* 5.4 0.9 - - - +
50J MET* 4.7 7.0 - - + -
58J TRP* 3.6 64.4 - - + +
62J MET* 4.1 13.7 - - + -
111J ILE* 2.9 29.4 + - + +
112J GLU 4.0 4.3 - - - +
114J GLN* 1.3 78.0 - - - +
116J ALA* 1.3 57.8 + - - +
118J VAL* 3.2 5.9 + - + +
119J VAL* 2.9 31.7 + - - +
162J LEU* 4.1 13.3 - - + +
165J GLU* 4.1 13.2 - - + -
166J LEU* 4.1 19.7 - - + -
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Residues in contact with ALA 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J GLU 3.0 18.1 + - - +
113J GLU* 3.5 11.2 - - + +
114J GLN 3.2 0.2 - - - -
115J LEU* 1.3 76.9 - - - +
117J ARG* 1.3 62.7 + - - +
119J VAL* 3.4 6.4 + - - +
120J GLU* 3.1 30.6 + - - +
166J LEU* 4.0 15.0 - - + +
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Residues in contact with ARG 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J ILE* 3.7 46.6 - - + +
45J GLN* 4.6 8.7 + - - -
46J VAL* 4.4 11.4 - - + -
100J LEU* 5.7 1.8 - - - +
101J LYS 3.1 28.1 + - - +
102J GLU* 3.9 8.9 - - - +
103J VAL* 4.1 20.4 - - - +
113J GLU 3.0 13.4 + - - +
114J GLN* 3.0 16.4 + - - +
116J ALA* 1.3 74.0 - - - +
118J VAL* 1.3 66.2 + - - +
120J GLU* 3.1 25.3 + - - +
121J VAL* 3.1 27.4 + - - +
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Residues in contact with VAL 118 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J ILE* 6.1 1.1 - - + -
43J LEU* 4.1 13.0 - - + -
46J VAL* 4.2 13.0 - - + -
62J MET* 3.8 28.9 - - + -
65J TYR* 4.3 6.7 - - + -
114J GLN 3.0 17.8 + - - +
115J LEU* 3.2 11.4 + - - +
117J ARG* 1.3 77.9 - - - +
119J VAL* 1.3 64.4 + - - +
121J VAL* 3.2 9.3 + - - +
122J PHE* 2.9 44.1 + - + -
162J LEU* 3.7 23.1 - - + -
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Residues in contact with VAL 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115J LEU 2.9 21.8 + - - +
116J ALA* 3.6 8.7 - - - +
117J ARG 3.2 0.2 - - - -
118J VAL* 1.3 76.4 - - - +
120J GLU* 1.3 52.5 + - + +
122J PHE* 3.1 7.4 + - - +
123J ARG* 2.7 63.5 + - + +
159J ILE* 4.4 9.2 - - + +
162J LEU* 3.6 30.3 - - + -
163J GLN* 3.6 28.9 - - + +
166J LEU* 4.4 3.8 - - + -
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Residues in contact with GLU 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100J LEU* 5.8 0.2 - - - -
116J ALA* 3.1 19.8 + - + +
117J ARG* 3.1 24.7 + - - +
119J VAL* 1.3 76.6 - - + +
121J VAL* 1.3 66.2 + - + +
123J ARG* 3.2 9.6 + - - +
124J TYR* 3.0 22.9 + - - +
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Residues in contact with VAL 121 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J ALA* 3.7 33.9 - - + +
42J ILE* 4.0 35.9 - - + -
43J LEU* 5.6 4.0 - - + -
100J LEU* 4.3 18.8 - - + -
117J ARG* 3.1 22.1 + - - +
118J VAL* 3.2 9.2 + - - +
120J GLU* 1.3 77.6 - - + +
122J PHE* 1.3 70.5 + - + +
124J TYR* 3.3 3.3 + - - +
125J LEU* 3.0 28.6 + - + +
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Residues in contact with PHE 122 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J LEU* 4.2 19.1 - - + -
65J TYR* 3.8 31.9 - + + -
69J ILE* 4.8 3.6 - - + -
118J VAL* 2.9 33.4 + - + +
119J VAL* 3.6 7.4 - - - +
121J VAL* 1.3 83.8 - - + +
123J ARG* 1.3 66.6 + - - +
125J LEU* 3.3 12.6 + - + +
126J ALA* 2.9 21.1 + - - +
155J ILE* 3.4 34.4 - - + +
158J HIS* 3.9 27.1 - + + -
159J ILE* 3.8 12.3 - - + -
162J LEU* 3.8 24.0 - - + -
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Residues in contact with ARG 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J VAL* 2.7 34.8 + - + +
120J GLU* 3.7 8.1 - - - +
122J PHE* 1.3 73.0 - - - +
124J TYR* 1.3 64.9 + - - +
126J ALA* 3.3 3.9 + - - +
127J ALA* 3.0 22.9 + - - +
159J ILE* 3.8 22.1 - - + +
163J GLN* 3.2 30.9 + - - +
170J PRO 2.9 23.4 + - - -
171J LYS* 2.8 34.9 + - - +
172J LEU* 3.9 8.6 + - + +
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Residues in contact with TYR 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J GLN* 3.9 2.1 + - - +
35J ASP* 2.8 46.0 + - + -
99J GLN* 3.6 42.1 + - + +
100J LEU* 3.6 32.8 - - + -
120J GLU 3.0 12.7 + - - +
121J VAL 3.4 7.4 - - - +
123J ARG* 1.3 77.1 - - - +
125J LEU* 1.3 65.7 - - + +
127J ALA* 3.0 10.5 + - + +
128J LEU* 2.8 40.9 + - + +
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Residues in contact with LEU 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J ASP* 4.2 25.8 - - + +
36J LEU* 4.2 16.8 - - + -
39J ALA* 3.9 14.6 - - + -
69J ILE* 3.7 30.1 - - + -
100J LEU* 4.8 0.7 - - + -
121J VAL* 3.0 26.3 + - + +
122J PHE* 3.3 13.4 + - + +
124J TYR* 1.3 88.2 - - + +
126J ALA* 1.3 52.2 + - - +
128J LEU* 3.1 11.7 + - + +
129J PHE* 2.7 51.9 + - + -
155J ILE* 4.5 7.4 - - + -
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Residues in contact with ALA 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122J PHE 2.9 17.0 + - - +
123J ARG* 3.6 5.2 - - - +
125J LEU* 1.3 75.8 - - - +
127J ALA* 1.3 57.7 + - - +
129J PHE* 4.4 8.3 - - - -
130J GLN* 3.1 22.0 + - - +
152J LYS* 3.6 16.9 - - + +
155J ILE* 4.1 9.8 - - + +
156J GLU* 4.1 29.8 - - + +
159J ILE* 4.4 5.6 - - + -
172J LEU* 6.0 0.7 - - + -
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Residues in contact with ALA 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123J ARG 3.0 12.2 + - - +
124J TYR* 3.0 15.5 + - + +
126J ALA* 1.3 73.0 - - - +
128J LEU* 1.3 65.4 + - - +
130J GLN* 3.1 8.4 + - - +
131J LYS* 3.0 20.8 + - - +
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Residues in contact with LEU 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J VAL* 4.2 16.8 - - + +
31J GLN* 3.7 26.7 - - + -
32J ALA* 3.7 28.0 - - + +
35J ASP* 3.7 24.2 - - + +
124J TYR* 2.8 23.5 + - + +
125J LEU* 3.4 13.5 - - + +
127J ALA* 1.3 77.8 - - - +
129J PHE* 1.3 71.0 + - + +
131J LYS* 3.1 9.6 + - + +
132J GLY* 2.8 24.4 + - - -
148J PHE* 4.6 1.0 - - + -
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Residues in contact with PHE 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J ALA* 4.7 0.4 - - + -
36J LEU* 4.0 25.6 - - + -
72J TYR* 4.2 8.1 - + - -
76J MET* 3.8 19.5 - - + -
125J LEU* 2.7 34.2 + - + +
126J ALA* 3.8 5.4 - - - +
127J ALA 3.2 0.2 - - - -
128J LEU* 1.3 87.8 - - + +
130J GLN* 1.3 61.3 + - - +
132J GLY 3.2 0.3 + - - -
133J PHE* 2.9 25.8 + - - +
148J PHE* 3.5 34.0 - + + +
151J ALA* 3.6 27.4 - - + -
152J LYS* 3.6 26.4 - - + +
155J ILE* 3.8 23.3 - - + -
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Residues in contact with GLN 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H GLY 5.2 7.9 + - - +
142H SER* 4.8 4.7 + - - -
126J ALA 3.1 14.5 + - - +
127J ALA* 3.1 11.6 + - - +
129J PHE* 1.3 73.5 - - - +
131J LYS* 1.3 66.7 + - - +
133J PHE* 3.3 14.1 + - - +
134J ASP* 2.9 53.4 + - - +
152J LYS* 3.2 36.1 - - + +
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Residues in contact with LYS 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J VAL* 4.4 7.9 - - + -
127J ALA 3.0 12.8 + - - +
128J LEU* 3.3 13.9 - - + +
130J GLN* 1.3 77.8 - - - +
132J GLY* 1.3 64.2 + - - +
134J ASP* 3.2 8.6 + - - +
135J VAL* 2.9 34.2 + - + +
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Residues in contact with GLY 132 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J VAL* 3.6 17.3 - - - +
128J LEU 2.8 12.7 + - - -
129J PHE 3.2 2.8 + - - -
131J LYS* 1.3 77.5 - - - +
133J PHE* 1.3 57.3 + - - +
135J VAL* 4.1 0.9 - - - +
136J SER* 2.8 30.8 + - - -
148J PHE* 3.4 30.7 - - - -
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Residues in contact with PHE 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H GLY 5.7 2.0 - - - -
142H SER* 3.3 35.2 - - - -
129J PHE 2.9 13.4 + - - +
130J GLN* 3.4 19.3 - - - +
131J LYS 3.1 0.2 - - - -
132J GLY* 1.3 75.7 - - - +
134J ASP* 1.3 71.5 + - - +
136J SER* 3.0 5.2 + - - -
137J ASP* 2.8 40.5 + - + +
145J ASN* 2.9 50.6 + - - +
148J PHE* 3.8 7.5 - - + +
149J ASN* 3.7 24.7 - - + +
152J LYS* 5.9 1.8 - - - -
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Residues in contact with ASP 134 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130J GLN* 2.9 45.7 + - - +
131J LYS* 3.7 7.3 - - - +
133J PHE* 1.3 84.7 - - - +
135J VAL* 1.3 59.5 + - + +
137J ASP* 3.3 4.6 + - - +
138J GLU* 2.9 29.9 + - - +
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Residues in contact with VAL 135 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J ASP* 3.3 50.7 - - + +
25J SER* 3.7 4.0 - - - +
28J VAL* 4.6 10.3 - - + -
131J LYS* 2.9 24.7 + - + +
132J GLY 4.1 2.5 - - - +
134J ASP* 1.3 78.4 - - + +
136J SER* 1.3 64.1 + - - +
138J GLU* 3.1 9.9 + - - +
139J GLU* 3.1 22.3 + - + +
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Residues in contact with SER 136 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J SER* 3.3 20.9 - - - -
132J GLY 2.8 22.7 + - - -
133J PHE 3.0 8.1 + - - -
135J VAL* 1.3 77.9 - - - +
137J ASP* 1.3 60.8 + - - +
139J GLU 3.3 1.0 + - - -
140J GLY 3.1 3.1 + - - -
141J ASP* 2.9 42.2 + - - +
144J THR* 3.7 19.0 - - - -
145J ASN* 3.1 19.5 - - - -
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Residues in contact with ASP 137 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133J PHE* 2.8 32.2 + - + +
134J ASP* 3.6 6.7 - - - +
136J SER* 1.3 77.5 + - - +
138J GLU* 1.3 64.6 + - - +
140J GLY* 3.1 13.9 + - - -
141J ASP 5.7 0.2 - - - -
145J ASN* 3.5 19.8 + - - +
----------------------------------------------------------
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Residues in contact with GLU 138 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J ASP 2.9 14.1 + - - +
135J VAL* 3.1 11.9 + - - +
137J ASP* 1.3 78.0 - - - +
139J GLU* 1.3 61.9 + - + +
140J GLY 3.5 0.7 + - - -
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Residues in contact with GLU 139 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J SER 3.6 20.2 - - - +
22J LEU* 3.2 23.0 - - + +
23J ALA* 3.6 5.0 + - - +
24J ASP* 3.0 35.7 + - + +
25J SER* 2.6 44.9 + - - +
135J VAL 3.1 13.8 + - - +
136J SER 3.3 0.9 + - - +
137J ASP 3.2 0.2 - - - -
138J GLU* 1.3 77.9 - - + +
140J GLY* 1.3 62.3 + - - +
141J ASP 3.3 1.0 + - - +
----------------------------------------------------------
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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