Contacts of the helix formed by residues 120 - 144 (chain A) in PDB entry 3N1Z
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 ALA 120 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TRP* 3.1 34.4 - - + +
47A TYR* 3.2 31.4 - - + -
118A ALA* 3.4 0.8 - - + -
119A LYS* 1.3 76.6 - - - +
121A PRO* 1.3 64.2 - - - +
123A ASN* 2.9 25.4 + - + +
124A ARG* 3.1 12.2 + - - +
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Residues in contact with PRO 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 3.0 30.7 - - + +
16A THR* 3.7 9.7 + - - +
17A ASN* 3.4 18.6 - - + +
45A GLU* 3.9 19.5 - - + +
47A TYR* 6.0 0.7 - - + +
119A LYS 3.1 10.9 - - - +
120A ALA* 1.3 82.0 - - + +
122A GLY* 1.3 62.3 + - - +
124A ARG* 3.3 36.2 + - - +
125A ASN* 3.3 20.6 + - - -
133B HIS* 5.4 0.2 + - - -
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Residues in contact with GLY 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 4.1 18.2 - - - +
47A TYR* 3.8 10.3 + - - -
49A GLU* 3.4 23.7 - - - -
120A ALA* 3.1 1.8 - - - +
121A PRO* 1.3 82.1 - - - +
123A ASN* 1.3 62.1 + - - +
125A ASN* 3.4 2.6 + - - +
126A MET* 3.1 28.6 + - - +
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Residues in contact with ASN 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TRP* 6.3 0.4 - - - -
47A TYR* 3.3 29.6 + - + -
114A MET* 3.9 10.5 - - - +
118A ALA* 3.6 21.7 - - + +
120A ALA* 2.9 17.9 + - + +
122A GLY* 1.3 76.8 - - - +
124A ARG* 1.3 56.9 + - - +
126A MET* 4.6 2.2 - - - -
127A ALA* 2.9 27.1 + - - +
185A SER* 4.6 3.6 + - - -
186A VAL* 5.7 2.8 - - - +
189A SER* 4.5 10.5 + - - -
237A GLN* 3.0 20.9 + - - -
241A SER* 4.0 18.2 + - - -
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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
----------------------------------------------------------
16A THR* 2.9 30.1 + - - -
17A ASN* 2.7 30.1 + - - +
18A TRP* 5.7 1.2 - - - -
29A PHE* 4.5 7.2 - - - -
114A MET 3.8 5.8 - - - +
115A ALA* 3.3 36.1 - - - +
116A ARG 4.3 9.0 - - - -
118A ALA* 2.9 32.6 + - + +
119A LYS* 3.3 13.9 + - - +
120A ALA 3.1 8.0 + - - +
121A PRO* 3.6 16.7 - - - +
122A GLY 3.3 0.4 - - - -
123A ASN* 1.3 78.4 - - - +
125A ASN* 1.3 60.0 + - - +
127A ALA 3.6 0.2 + - - -
128A THR* 2.8 26.1 + - - -
133B HIS* 2.7 31.6 + - + +
136B GLN* 4.7 0.4 - - - -
137B MET* 4.1 12.1 - - - -
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Residues in contact with ASN 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 2.7 38.0 + - - -
14A ARG* 3.8 12.3 - - + +
16A THR* 5.3 0.6 + - - +
121A PRO 3.3 9.7 + - - +
122A GLY* 4.1 2.9 - - - +
123A ASN 3.3 0.4 - - - -
124A ARG* 1.3 71.4 - - - +
126A MET* 1.3 72.6 + - + +
127A ALA 3.1 1.3 - - - -
128A THR* 2.8 24.3 + - - -
129A PHE* 3.1 16.6 + - + -
133B HIS* 3.5 14.6 + - - -
136B GLN* 3.1 20.0 + - - +
163B LEU* 3.7 20.5 - - + +
166B LEU* 4.3 0.4 - - - +
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Residues in contact with MET 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TYR* 3.5 22.0 - - - +
47A TYR* 5.5 0.2 - - + -
49A GLU* 3.6 26.0 - - + +
51A TYR 3.7 9.2 - - - +
53A ILE* 3.8 18.6 - - + +
122A GLY 3.1 21.0 + - - +
123A ASN* 4.0 0.7 - - - +
125A ASN* 1.3 81.0 - - + +
127A ALA* 1.3 58.1 + - - +
129A PHE* 3.2 28.4 + - + +
130A GLY* 2.8 24.1 + - - -
233A ARG* 4.3 7.3 - - - +
234A HIS* 4.6 3.5 - - - +
236A GLN* 3.5 23.1 - - - +
237A GLN* 3.6 23.6 + - + +
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLU* 3.5 32.5 - - - +
114A MET* 3.7 6.7 - - + -
115A ALA* 3.5 15.9 - - - +
123A ASN 2.9 19.6 + - - +
124A ARG 3.7 1.8 - - - +
126A MET* 1.3 76.5 - - - +
128A THR* 1.3 52.0 + - - +
130A GLY* 3.4 0.7 - - - -
131A MET* 2.6 32.9 + - - +
237A GLN* 3.1 17.3 - - - +
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Residues in contact with THR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ALA* 3.8 11.1 - - - +
124A ARG 2.8 19.9 + - - -
125A ASN* 2.8 10.1 + - - -
127A ALA* 1.3 74.8 - - - +
129A PHE* 1.3 63.4 + - + +
131A MET* 3.4 14.4 - - + +
132A MET* 3.2 23.0 + - + +
136B GLN* 3.0 24.0 + - - +
159B THR* 3.8 27.0 - - + +
160B ALA* 4.7 5.8 - - + -
163B LEU* 4.2 18.8 - - + -
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Residues in contact with PHE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 3.7 23.3 - - + -
54A THR* 3.9 2.7 - - - -
55A TYR* 3.5 31.2 - + + -
58A TYR* 3.4 42.8 - + + -
125A ASN* 3.1 21.0 + - + -
126A MET* 3.7 24.5 - - + +
128A THR* 1.3 75.3 - - - +
130A GLY* 1.3 62.0 + - - +
131A MET 3.1 0.4 - - - -
132A MET* 3.3 8.5 + - + +
133A ASP* 2.9 35.9 + - - +
233A ARG* 4.1 17.9 - - + -
163B LEU* 3.3 32.1 - - + -
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Residues in contact with GLY 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLU* 3.4 27.1 - - - -
126A MET 2.8 13.7 + - - -
127A ALA 3.1 1.0 + - - -
129A PHE* 1.3 79.7 - - - +
131A MET* 1.3 60.6 + - - +
133A ASP* 3.2 3.8 + - - +
134A GLU* 3.2 29.3 + - - +
234A HIS* 3.7 17.2 + - - -
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Residues in contact with MET 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A SER* 3.8 26.5 + - - +
111A GLU* 3.5 14.3 - - + +
112A ALA* 4.8 2.7 - - - +
115A ALA* 5.7 0.2 - - + -
127A ALA 2.6 19.5 + - - +
128A THR* 3.4 22.7 - - + +
130A GLY* 1.3 74.6 - - - +
132A MET* 1.3 70.5 + - + +
134A GLU 3.5 0.7 + - - -
135A ASN* 3.2 19.2 + - - +
140B VAL* 3.7 25.6 - - - -
143B HIS* 3.8 11.9 - - + -
156B THR* 3.3 49.6 - - + +
159B THR* 4.0 9.4 - - - -
160B ALA 4.6 0.9 - - - +
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Residues in contact with MET 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 3.2 32.3 - - + +
128A THR* 3.2 13.6 + - + +
129A PHE* 3.3 9.8 + - + +
131A MET* 1.3 83.5 - - + +
133A ASP* 1.3 63.3 + - - +
135A ASN* 3.0 15.7 + - - +
136A ARG 3.1 9.9 + - - -
83B TYR* 3.3 23.8 - - + -
86B TYR* 3.6 38.4 - - + -
87B ASN* 4.8 0.7 - - - +
156B THR* 3.9 22.0 - - - -
157B TYR* 4.0 13.9 - - + -
160B ALA* 4.0 20.0 - - + -
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Residues in contact with ASP 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 2.8 21.8 + - - -
129A PHE 2.9 17.3 + - - +
130A GLY 3.2 7.4 + - - +
132A MET* 1.3 74.2 - - - +
134A GLU* 1.3 63.4 + - - +
136A ARG* 2.9 15.4 + - - +
137A HIS* 3.0 27.3 + - - +
230A ASP* 3.8 7.4 - - - +
233A ARG* 2.8 43.7 + - - +
234A HIS* 3.0 31.5 + - + +
83B TYR* 4.4 0.5 + - - -
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Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU* 3.2 23.2 - - - +
105A TYR* 4.3 0.9 - - - -
107A ALA* 3.6 24.6 - - + +
108A SER* 3.5 15.0 - - - +
111A GLU* 4.0 6.3 - - + +
130A GLY 3.2 15.1 + - - +
133A ASP* 1.3 75.9 - - - +
135A ASN* 1.3 57.8 + - - +
137A HIS* 3.3 2.6 + - - +
138A GLY* 2.8 28.6 + - - -
192A LEU* 5.7 0.3 - - - +
197A GLU* 3.1 4.7 - - - +
234A HIS* 3.0 13.5 + - - -
501A P6G 3.1 6.7 + - - -
503A FE 2.2 27.0 - - - -
504A FE 2.4 24.7 - - - -
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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
----------------------------------------------------------
105A TYR* 4.4 10.8 - - - -
108A SER* 4.4 8.2 + - - +
131A MET 3.2 13.0 + - - +
132A MET* 3.0 18.0 + - - +
134A GLU* 1.3 77.6 - - - +
136A ARG* 1.3 59.6 + - - +
138A GLY* 3.3 1.4 + - - -
139A GLN* 3.0 42.6 + - - +
83B TYR* 3.4 8.4 - - + +
153B ASN* 3.6 25.9 - - - +
156B THR* 4.0 18.4 + - + +
157B TYR* 2.6 35.5 + - + -
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Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN* 4.1 5.9 - - - +
65A LYS* 3.5 24.7 + - - +
66A ASP* 2.9 29.2 + - - +
69A ALA* 4.6 0.8 - - - +
132A MET 3.1 4.6 + - - -
133A ASP* 2.9 10.2 + - - +
135A ASN* 1.3 77.5 + - - +
137A HIS* 1.3 59.6 + - + +
139A GLN* 3.1 2.2 + - - -
140A ILE* 2.7 49.5 + - + +
226A SER* 2.5 42.4 + - - -
227A ILE* 3.6 16.5 - - - +
230A ASP* 2.5 37.7 + - - -
83B TYR* 3.6 46.2 - - + -
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Residues in contact with HIS 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU* 3.5 21.9 + - - +
133A ASP 3.0 17.7 + - - -
134A GLU* 3.2 7.9 + - - +
136A ARG* 1.3 80.7 - - + +
138A GLY* 1.3 64.4 + - - +
140A ILE* 4.0 5.6 - - - -
141A GLN* 2.9 36.0 + - - +
227A ILE* 3.2 45.3 - - + +
230A ASP* 3.4 29.7 + - + +
231A GLU* 4.3 7.4 - - - -
234A HIS* 4.4 7.6 - + - -
503A FE 2.1 28.5 - - - -
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Residues in contact with GLY 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ALA 3.7 19.4 - - - +
104A GLU* 4.0 0.2 - - - +
105A TYR* 4.0 18.4 - - - -
134A GLU 2.8 20.6 + - - -
135A ASN 3.8 1.3 - - - -
137A HIS* 1.3 75.6 - - - +
139A GLN* 1.3 63.6 + - - +
141A GLN* 3.9 1.4 - - - +
142A LEU* 3.4 27.5 + - - +
35B LEU* 5.7 0.7 - - - -
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Residues in contact with GLN 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 4.8 3.3 + - - +
105A TYR* 5.7 4.5 - - + -
135A ASN* 3.0 25.0 + - - +
136A ARG* 3.7 2.2 - - - +
138A GLY* 1.3 74.1 - - - +
140A ILE* 1.3 60.2 + - - +
142A LEU* 2.8 6.9 + - - +
143A TYR* 2.8 28.8 + - - +
31B VAL* 3.6 38.9 - - + +
32B SER* 4.2 3.5 + - - -
81B LEU 5.1 0.2 - - - +
82B VAL* 3.2 21.0 - - - +
83B TYR* 2.9 30.6 + - - +
153B ASN* 3.8 14.5 - - - +
157B TYR* 2.9 19.6 + - - -
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Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASP* 3.7 11.0 - - - +
69A ALA* 4.1 12.6 - - + -
70A TYR* 3.4 41.0 + - + +
136A ARG* 2.7 34.9 + - + +
137A HIS 3.9 3.4 - - - +
139A GLN* 1.3 74.4 - - - +
141A GLN* 1.3 60.6 + - + +
142A LEU 3.1 0.2 - - - -
143A TYR* 4.1 1.3 - - - -
144A PHE* 3.0 55.5 + - + +
223A LEU* 3.7 20.0 - - + +
226A SER* 5.7 0.4 - - - +
227A ILE* 3.5 26.7 - - + -
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Residues in contact with GLN 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A HIS* 3.1 24.7 + - - -
97A PHE* 3.2 42.1 - - + -
100A ILE* 4.2 3.3 - - - +
101A ALA* 3.7 16.2 - - + +
104A GLU* 3.0 38.0 + - - +
137A HIS* 2.9 25.7 + - - +
138A GLY 3.9 2.7 - - - +
139A GLN 3.1 1.0 - - - -
140A ILE* 1.3 81.6 - - + +
142A LEU* 1.3 58.7 + - - +
144A PHE* 5.0 0.2 - - - -
145A PRO* 3.2 7.2 - - - +
205A PHE* 4.2 5.2 - - - -
223A LEU* 4.2 10.8 - - + -
224A ILE* 4.1 9.9 - - - +
227A ILE* 4.4 9.7 - - - +
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ALA* 4.2 8.3 - - + -
102A LEU* 4.2 4.5 - - + -
105A TYR* 6.4 0.2 - - + -
138A GLY* 3.4 16.3 + - - +
139A GLN 2.8 6.4 + - - +
141A GLN* 1.3 77.9 - - - +
143A TYR* 1.3 69.6 + - - +
144A PHE 3.2 1.1 - - - -
145A PRO* 3.0 16.3 - - - +
146A TYR* 3.0 13.0 + - - +
158A ALA 3.7 24.7 - - - +
159A HIS* 4.1 14.1 - - + -
15B TRP* 3.5 25.8 - - + -
30B VAL* 4.1 14.1 - - - +
31B VAL* 3.9 19.3 - - + +
35B LEU* 3.6 30.7 - - + -
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Residues in contact with TYR 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 3.3 37.5 - + - +
73A LYS* 3.5 31.4 + - - -
139A GLN 2.8 15.1 + - - +
140A ILE* 3.7 8.7 - - - +
142A LEU* 1.3 77.3 - - - +
144A PHE* 1.3 64.5 + + - +
146A TYR* 3.1 25.8 + + - +
147A ALA* 3.8 2.3 + - - +
27B GLU* 4.0 31.1 + - + +
30B VAL* 4.5 9.6 - - + -
31B VAL* 3.9 22.1 - - + +
----------------------------------------------------------
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Residues in contact with PHE 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA* 3.9 17.7 - - + -
70A TYR* 4.7 7.0 - + - -
73A LYS* 3.6 36.8 - - + +
97A PHE* 4.3 0.2 - - + -
140A ILE* 3.0 47.5 + - + +
143A TYR* 1.3 80.8 - + - +
145A PRO* 1.3 73.1 - - + +
146A TYR 3.2 0.7 + - - -
147A ALA* 3.2 19.9 + - - +
148A ASN* 4.5 1.7 + - - -
219A THR* 3.6 26.0 - - + -
222A SER* 6.0 0.4 - - - -
223A LEU* 3.5 45.1 - - + -
500A GOL 3.5 25.0 + - - +
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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