Contacts of the helix formed by residues 112 - 143 (chain A) in PDB entry 1J30
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 PHE 112 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ALA* 2.8 18.6 + - + +
110A GLU* 3.5 38.1 - - + -
111A GLY* 1.3 81.2 - - - +
113A PRO* 1.3 65.2 - - - +
114A GLU* 3.2 3.1 - - - -
115A VAL* 3.1 19.5 + - + +
116A ALA* 3.0 19.6 + - - +
3B ASP 4.0 17.9 - - - -
4B LEU* 3.4 32.8 - - + -
7B THR* 3.7 25.6 - - + -
9B THR* 3.8 10.5 - - - -
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Residues in contact with PRO 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 4.2 15.8 + - + +
111A GLY* 3.2 11.2 - - - +
112A PHE* 1.3 88.9 - - - +
114A GLU* 1.3 62.9 + - + +
116A ALA* 3.2 9.3 + - + +
117A GLU* 2.9 37.3 + - + +
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE 3.2 1.6 + - - -
113A PRO* 1.3 82.4 - - + +
115A VAL* 1.3 63.9 + - + +
117A GLU* 3.4 10.4 + - - +
118A TRP* 3.2 20.3 + - - +
63B PHE* 4.0 18.3 - - + -
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ALA* 4.3 1.3 - - + -
112A PHE* 3.1 23.6 + - + +
114A GLU* 1.3 76.0 - - + +
116A ALA* 1.3 60.0 + - - +
118A TRP* 3.1 10.0 + - + +
119A PHE* 2.9 57.8 + - + -
4B LEU* 4.7 13.7 - - + -
9B THR* 3.7 18.4 - - + -
13B LEU* 4.3 9.2 - - + -
63B PHE* 3.8 25.4 - - + -
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA* 3.6 14.4 - - - +
107A ALA* 3.7 9.8 - - + +
108A ARG* 3.3 40.2 - - + +
112A PHE 3.0 13.1 + - - +
113A PRO 3.4 8.1 - - - +
115A VAL* 1.3 77.4 - - - +
117A GLU* 1.3 58.4 + - - +
119A PHE* 3.2 3.1 + - - +
120A GLU* 2.8 34.4 + - - +
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Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 3.7 20.3 + - - +
113A PRO* 2.9 23.5 + - + +
114A GLU* 3.8 9.1 - - - +
116A ALA* 1.3 76.5 - - - +
118A TRP* 1.3 57.7 + - - +
120A GLU* 3.2 5.7 + - - +
121A THR* 2.9 33.1 + - - +
124A ARG* 5.0 0.7 + - - -
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Residues in contact with TRP 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU 3.2 8.4 + - - +
115A VAL* 3.1 10.0 + - + +
117A GLU* 1.3 77.0 - - - +
119A PHE* 1.3 73.2 + + - +
121A THR* 3.2 13.0 + - + -
122A LEU* 3.0 56.4 + - + +
13B LEU* 4.7 1.8 - - + -
55B ALA* 3.8 16.8 - - + -
56B HIS* 3.4 28.5 - + - -
59B GLY* 3.4 17.0 - - - -
60B HIS* 3.0 34.7 + + - +
63B PHE* 3.4 34.9 - + + -
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Residues in contact with PHE 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TYR* 3.6 26.3 - + + +
103A PHE* 3.4 50.9 - + + -
104A ALA* 3.7 17.5 - - + +
107A ALA* 4.2 2.2 - - + -
115A VAL* 2.9 29.8 + - + -
116A ALA 3.5 6.7 - - - +
118A TRP* 1.3 84.7 - + - +
120A GLU* 1.3 57.0 + - - +
122A LEU* 3.4 2.3 + - + +
123A ALA* 2.9 27.5 + - - +
9B THR* 4.3 9.4 - - + -
12B ASN* 4.4 4.9 - - + -
13B LEU* 3.7 34.5 - - + -
60B HIS* 3.7 23.3 - + - -
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PRO* 4.9 7.6 - - - +
104A ALA* 3.4 21.0 - - + +
105A LYS* 5.1 0.5 + - - -
108A ARG* 4.1 22.2 + - - +
116A ALA 2.8 20.3 + - - +
117A GLU* 3.5 7.4 - - - +
118A TRP 3.2 0.2 - - - -
119A PHE* 1.3 74.8 - - - +
121A THR* 1.3 64.9 + - - +
123A ALA* 3.2 12.0 + - - +
124A ARG* 3.2 43.4 + - - +
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Residues in contact with THR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLU* 2.9 17.2 + - - +
118A TRP* 3.5 19.1 - - + -
120A GLU* 1.3 74.7 - - - +
122A LEU* 1.3 68.4 + - + +
124A ARG* 3.3 26.6 + - - +
125A ALA* 3.0 28.1 + - + +
56B HIS* 6.0 0.2 - - - +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TYR* 3.7 25.1 - - + +
118A TRP* 3.0 53.1 + - + +
119A PHE* 3.7 4.5 - - + +
121A THR* 1.3 81.4 - - + +
123A ALA* 1.3 64.7 + - - +
125A ALA* 3.5 5.0 - - - +
126A GLU* 2.8 31.1 + - - +
56B HIS* 3.5 37.5 - - + +
60B HIS* 3.4 36.6 - - + +
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TRP* 3.2 20.0 - - - +
100A TYR* 3.8 20.8 - - + +
101A PRO* 4.3 18.8 - - + -
119A PHE 2.9 14.8 + - - +
120A GLU* 3.2 19.0 + - - +
122A LEU* 1.3 75.6 - - - +
124A ARG* 1.3 64.1 + - + +
127A LYS* 3.1 18.4 + - - +
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Residues in contact with ARG 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLU 5.0 0.4 + - - -
120A GLU* 3.2 33.6 + - - +
121A THR* 3.5 32.2 + - - +
123A ALA* 1.3 78.8 - - + +
125A ALA* 1.3 63.4 + - - +
127A LYS* 3.3 10.8 + - + +
128A SER* 3.1 24.3 + - - -
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A THR* 3.0 15.5 + - + +
122A LEU* 3.1 8.3 + - + +
124A ARG* 1.3 78.0 - - - +
126A GLU* 1.3 58.9 + - - +
128A SER* 3.1 9.6 + - - -
129A HIS* 2.9 34.8 + - - +
56B HIS* 3.7 27.8 - - + +
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Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU* 2.4 20.3 - - - +
95A GLU* 3.3 10.1 - - + +
96A TRP* 4.0 11.7 - - + -
100A TYR* 3.9 15.7 - - + -
122A LEU 2.8 19.5 + - - +
123A ALA 3.9 3.6 - - - +
125A ALA* 1.3 72.8 - - - +
127A LYS* 1.3 61.7 + - - +
129A HIS* 3.0 2.2 + - - +
130A ALA* 2.8 29.6 + - - +
405A ZN 2.1 33.7 - - - -
406A OXY 2.7 9.5 + - - -
20B GLU* 3.0 4.9 - - - +
56B HIS* 2.9 13.0 + - - -
404B FE 1.9 30.4 - - - -
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Residues in contact with LYS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TRP* 3.5 61.4 - - + +
123A ALA 3.1 10.7 + - - +
124A ARG* 3.5 13.7 - - - +
125A ALA 3.2 0.2 - - - -
126A GLU* 1.3 77.9 - - - +
128A SER* 1.3 63.2 + - - +
130A ALA* 3.3 3.1 + - - +
131A GLU* 3.0 49.5 + - + +
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Residues in contact with SER 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG 3.1 13.0 + - - -
125A ALA* 3.1 12.3 + - - -
127A LYS* 1.3 77.7 - - - +
129A HIS* 1.3 65.6 + - - +
131A GLU* 3.2 16.8 + - - +
132A LYS* 2.9 29.2 + - - +
----------------------------------------------------------
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Residues in contact with HIS 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU* 3.4 17.5 - - + +
125A ALA* 2.9 18.9 + - - +
126A GLU* 3.0 7.9 + - - +
128A SER* 1.3 79.6 - - - +
130A ALA* 1.3 62.5 + - - +
132A LYS* 3.1 9.7 + - + +
133A PHE* 2.9 30.0 + - + -
405A ZN 2.0 32.5 - - - -
49B ILE* 3.6 38.3 + - + +
52B GLY* 4.7 7.5 - - - -
53B GLU* 3.2 15.9 + - - -
56B HIS* 4.2 12.8 - + - -
----------------------------------------------------------
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 4.7 3.6 - - + +
92A GLU* 3.7 20.8 - - + +
93A THR* 4.2 10.5 - - - +
96A TRP* 4.0 18.8 - - + +
126A GLU 2.8 20.1 + - - +
127A LYS 3.6 5.2 - - - +
129A HIS* 1.3 73.0 - - - +
131A GLU* 1.3 57.9 + - + +
133A PHE* 3.3 5.2 + - - +
134A GLN* 2.9 41.6 + - - +
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LYS* 3.0 39.2 + - + +
128A SER* 3.2 18.4 + - - +
130A ALA* 1.3 75.1 - - + +
132A LYS* 1.3 66.1 + - + +
134A GLN* 3.4 14.5 + - - +
135A ASN* 3.1 32.0 + - - +
----------------------------------------------------------
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Residues in contact with LYS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A SER* 2.9 20.6 + - - +
129A HIS* 3.1 10.3 + - + +
131A GLU* 1.3 77.7 - - + +
133A PHE* 1.3 62.2 + - - +
135A ASN* 3.2 13.6 + - + +
136A VAL* 3.1 23.9 + - - +
45B LEU* 4.1 34.6 - - + +
49B ILE* 4.2 9.4 - - + -
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Residues in contact with PHE 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 3.4 20.9 - - + +
88A ALA* 3.7 19.3 - - + -
89A ILE* 3.5 19.6 - - + +
92A GLU* 3.8 19.3 - - + -
129A HIS* 2.9 20.9 + - + +
130A ALA 3.8 1.8 - - - +
132A LYS* 1.3 74.7 - - - +
134A GLN* 1.3 60.5 + - - +
136A VAL* 3.2 7.5 + - + +
137A LEU 2.9 23.6 + - - -
27B TYR* 3.7 36.1 - + - -
45B LEU* 5.0 6.7 - - + -
46B LEU* 3.5 37.7 - - + -
49B ILE* 3.4 31.2 - - + -
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Residues in contact with GLN 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 3.6 36.8 - - + +
93A THR* 4.6 5.3 + - - -
130A ALA* 2.9 32.1 + - - +
131A GLU* 3.7 17.9 + - - +
132A LYS 3.3 0.2 - - - -
133A PHE* 1.3 75.6 - - - +
135A ASN* 1.3 63.8 + - - +
137A LEU* 3.2 4.1 + - - +
138A LYS* 2.9 31.5 + - + +
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Residues in contact with ASN 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLU* 3.1 18.0 + - - +
132A LYS* 3.4 15.7 + - + +
133A PHE 3.2 0.2 - - - -
134A GLN* 1.3 78.6 - - - +
136A VAL* 1.3 63.8 + - + +
138A LYS* 3.3 31.5 + - - +
139A GLN* 3.1 20.6 + - - +
----------------------------------------------------------
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Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 4.0 20.9 - - + -
132A LYS 3.1 7.4 + - - +
133A PHE* 3.2 13.2 + - + +
135A ASN* 1.3 76.1 - - + +
137A LEU* 1.3 66.1 + - - +
139A GLN* 3.1 11.9 + - - +
140A LEU* 3.0 22.6 + - + +
42B ILE* 3.5 46.0 - - + -
45B LEU* 3.5 32.1 - - + -
----------------------------------------------------------
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 4.0 17.7 - - + +
85A ILE* 4.0 9.9 - - + -
86A GLU* 3.8 32.1 - - + +
89A ILE* 3.9 18.2 - - + -
133A PHE 2.9 13.8 + - - +
134A GLN 3.6 8.1 - - - +
136A VAL* 1.3 77.1 - - - +
138A LYS* 1.3 59.1 + - + +
140A LEU* 3.3 2.9 + - + -
141A LYS* 2.9 58.6 + - + +
----------------------------------------------------------
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Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLN* 2.9 18.7 + - + +
135A ASN* 3.4 29.7 - - - +
136A VAL 3.2 0.2 - - - -
137A LEU* 1.3 77.8 - - + +
139A GLN* 1.3 58.0 + - - +
141A LYS* 5.1 2.2 - - - -
142A GLY* 2.9 29.0 + - - +
----------------------------------------------------------
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Residues in contact with GLN 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ASN 3.1 13.3 + - - +
136A VAL* 3.1 12.4 + - - +
138A LYS* 1.3 77.8 - - - +
140A LEU* 1.3 63.2 + - - +
142A GLY* 4.0 0.4 - - - -
143A GLY* 3.1 27.9 + - - +
39B TYR* 4.2 15.6 - - - -
41B GLU* 5.6 5.9 - - - +
42B ILE* 3.5 34.4 - - - +
----------------------------------------------------------
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 4.0 17.5 - - + -
82A GLU* 3.9 34.4 - - + +
85A ILE* 3.9 28.7 - - + -
136A VAL* 3.0 22.8 + - + +
137A LEU* 3.8 4.9 - - - +
139A GLN* 1.3 80.4 - - + +
141A LYS* 1.3 61.4 + - - +
143A GLY* 3.5 9.0 + - - -
39B TYR* 3.9 34.1 - - + +
42B ILE* 3.7 21.3 - - + -
----------------------------------------------------------
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 2.6 40.7 + - - +
86A GLU* 2.9 29.5 + - - -
137A LEU* 2.9 42.3 + - + +
138A LYS* 4.7 2.0 - - - +
140A LEU* 1.3 72.5 - - - +
142A GLY* 1.3 62.1 + - - +
143A GLY* 3.4 0.4 - - - -
----------------------------------------------------------
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Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LYS 2.9 19.8 + - - -
139A GLN 4.0 0.2 - - - -
141A LYS* 1.3 78.8 - - - +
143A GLY* 1.3 63.0 + - - +
----------------------------------------------------------
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Residues in contact with GLY 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLN* 3.1 21.3 + - - +
140A LEU 3.5 6.7 + - - -
141A LYS 3.4 3.2 - - - -
142A GLY* 1.3 81.6 - - - +
----------------------------------------------------------
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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