Contacts of the helix formed by residues 114 - 139 (chain A) in PDB entry 1HPL
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 TYR 114 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A THR 3.6 1.6 + - - -
113A ALA* 1.3 71.4 - - - +
115A SER* 1.3 64.4 + - - +
117A ALA* 3.2 2.7 + - - +
118A SER* 3.0 40.4 + - - -
153A LEU* 3.3 27.9 - - + +
178A ALA* 3.5 14.4 - - - +
180A PRO* 2.8 42.4 + - + +
181A CYS* 3.9 10.1 - - - -
215A PHE* 3.7 24.7 - + - -
248A ILE* 3.5 28.5 - - + -
249A ASP* 3.0 19.3 + - - +
252A TRP* 3.6 42.2 - + + -
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Residues in contact with SER 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.7 29.2 - - - +
27A ILE* 3.6 10.9 - - - +
113A ALA* 4.5 7.8 - - - +
114A TYR* 1.3 82.0 - - - +
116A GLN* 1.3 61.1 + - - +
118A SER* 3.6 8.9 + - - -
119A GLN* 3.3 26.2 + - - +
181A CYS* 4.9 11.4 - - - -
248A ILE* 5.8 0.4 - - - +
249A ASP* 4.4 3.5 + - - -
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Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 3.5 21.2 - - + +
28A LEU 2.9 26.3 + - - +
29A PRO* 3.7 1.2 - - - +
30A TRP* 3.3 40.6 + - + +
112A THR* 3.9 15.3 - - + +
113A ALA* 2.9 15.9 + - + +
115A SER* 1.3 79.3 + - - +
117A ALA* 1.3 60.2 + - - +
119A GLN* 3.1 4.9 + - - +
120A ASN* 2.8 54.1 + - - +
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TRP* 3.9 3.0 - - + -
109A GLY 3.8 17.3 - - - +
110A SER* 3.9 22.9 - - - +
112A THR* 3.8 2.1 - - + +
113A ALA 2.9 10.8 + - - +
114A TYR 3.5 8.1 - - - +
116A GLN* 1.3 75.8 - - - +
118A SER* 1.4 57.0 + - - +
120A ASN* 2.9 17.3 + - - +
121A VAL* 3.0 17.0 + - - +
153A LEU* 3.6 20.4 - - + -
252A TRP* 4.0 7.9 - - - +
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ARG* 4.5 9.2 + - - -
114A TYR* 3.0 37.4 + - - -
115A SER* 3.6 12.3 - - - -
116A GLN 3.2 0.4 - - - -
117A ALA* 1.4 72.6 - - - +
119A GLN* 1.3 65.5 + - - +
121A VAL* 3.2 23.1 - - - +
122A ARG* 4.6 1.7 - - - +
153A LEU* 3.7 6.1 - - - +
181A CYS* 4.1 9.3 - - - +
182A PHE* 3.6 29.7 - - - -
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Residues in contact with GLN 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 6.4 0.4 - - - -
17A TRP 2.9 25.8 + - - +
18A ALA* 4.3 6.9 - - - +
23A ARG* 3.5 15.3 + - - +
25A LEU 5.0 2.2 + - - -
27A ILE* 3.5 34.5 + - + +
29A PRO* 3.7 23.8 - - + +
115A SER 3.3 13.2 + - - +
116A GLN* 3.1 11.8 + - - +
118A SER* 1.3 79.5 - - - +
120A ASN* 1.3 62.0 + - - +
122A ARG* 3.0 56.9 + - - +
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Residues in contact with ASN 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PRO* 3.5 5.5 - - - +
30A TRP* 3.0 43.8 + - - -
34A VAL* 3.9 15.0 - - + +
106A TRP* 4.3 5.8 - - + -
109A GLY* 3.0 28.4 + - - +
112A THR* 4.3 0.2 - - - +
116A GLN* 2.8 44.5 + - - +
117A ALA 2.9 8.0 + - - +
119A GLN* 1.3 71.8 - - - +
121A VAL* 1.3 62.8 + - - +
123A ILE* 3.0 18.0 + - - +
124A VAL* 3.4 13.7 + - - +
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TRP* 4.0 11.9 - - + -
117A ALA 3.0 6.8 + - - +
118A SER 3.2 18.2 - - - +
120A ASN* 1.3 75.7 - - - +
122A ARG* 1.3 60.2 + - + +
124A VAL* 3.4 5.0 + - - -
125A GLY* 3.0 25.8 + - - -
153A LEU* 3.4 43.7 - - + +
156A HIS* 4.0 15.3 - - + +
157A ALA* 3.7 30.4 - - + +
160A GLU* 4.5 2.9 - - + +
182A PHE* 4.5 7.2 - - + -
189A VAL 5.8 1.3 - - - +
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Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A CYS 5.2 0.2 + - - -
11A PHE* 3.7 47.0 - - + +
12A SER 2.8 31.9 + - - +
13A ASP* 4.7 1.2 - - - +
17A TRP* 3.4 61.2 - - + +
23A ARG* 6.0 1.1 - - - +
28A LEU* 5.1 0.2 - - - +
29A PRO* 4.1 13.0 - - + +
118A SER 4.6 3.4 - - - +
119A GLN* 3.0 42.4 + - - +
121A VAL* 1.3 80.3 - - + +
123A ILE* 1.3 58.3 + - - +
126A ALA* 3.0 27.9 + - - +
160A GLU* 3.9 19.7 + - - +
164A ARG* 6.0 0.2 - - - +
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A TYR* 5.2 2.5 - - + -
8A LEU* 4.3 8.1 - - + -
11A PHE* 3.8 31.4 - - + -
29A PRO* 3.7 19.3 - - + -
30A TRP 3.5 26.2 - - - +
31A PRO* 4.0 34.3 - - + +
34A VAL* 4.0 22.2 - - + -
36A THR* 4.7 0.2 - - - +
120A ASN* 3.0 9.5 + - - +
122A ARG* 1.3 74.5 - - - +
124A VAL* 1.3 65.3 + - - +
126A ALA* 3.2 5.7 + - - +
127A GLU* 2.9 33.0 + - + +
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.9 9.2 - - + -
36A THR* 4.0 11.4 - - + +
74A ILE* 4.2 9.4 - - + -
104A VAL* 3.9 27.8 - - + -
106A TRP* 3.6 40.6 - - + -
120A ASN 3.4 12.8 + - - +
121A VAL* 3.7 8.3 - - - +
123A ILE* 1.3 75.0 - - - +
125A GLY* 1.3 61.4 + - - +
127A GLU* 3.2 4.3 + - - +
128A VAL* 3.0 30.8 + - + +
157A ALA* 4.1 15.7 - - + -
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Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A VAL 3.0 15.3 + - - -
124A VAL* 1.3 75.1 - - - +
126A ALA* 1.3 60.5 + - - +
128A VAL* 3.3 2.1 + - - -
129A ALA* 3.1 20.3 + - - +
157A ALA 3.5 23.9 + - - -
160A GLU* 3.9 13.0 - - - -
161A ALA* 3.5 17.5 - - - +
164A ARG* 4.6 0.7 - - - -
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Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 3.8 16.9 - - + +
11A PHE* 4.0 14.4 - - + -
122A ARG 3.0 19.2 + - - +
123A ILE 3.5 4.9 - - - +
125A GLY* 1.3 74.9 - - - +
127A GLU* 1.3 57.3 + - - +
129A ALA* 3.6 2.2 + - - +
130A TYR* 2.9 30.1 + - - +
164A ARG* 3.7 36.3 + - - +
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Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ARG* 2.8 33.9 + - - -
8A LEU* 3.7 16.7 - - + +
31A PRO* 3.8 14.2 - - - +
36A THR* 3.8 27.4 + - + +
38A PHE* 3.8 24.8 - - + -
54A ALA* 5.8 0.2 - - - +
123A ILE* 2.9 21.2 + - + +
124A VAL 3.2 8.0 + - - +
126A ALA* 1.3 77.1 - - - +
128A VAL* 1.3 57.1 + - - +
130A TYR* 3.4 11.0 + - - +
131A LEU* 3.0 22.9 + - - +
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 4.1 22.4 - - + -
72A PHE* 4.1 25.8 - - + -
74A ILE* 4.3 20.0 - - + -
104A VAL* 4.5 10.8 - - + -
124A VAL 3.0 18.2 + - - +
125A GLY* 3.8 4.3 - - - +
127A GLU* 1.3 72.0 - - - +
129A ALA* 1.4 62.5 + - - +
131A LEU* 3.1 4.5 + - - +
132A VAL* 2.9 35.8 + - + +
148A ILE* 4.2 12.6 - - + -
161A ALA* 4.0 14.8 - - + -
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A GLY 3.1 16.1 + - - +
126A ALA* 3.7 5.4 - - - +
128A VAL* 1.4 75.1 - - - +
130A TYR* 1.3 58.5 + - - +
132A VAL* 3.3 8.2 + - - +
133A GLY* 2.9 27.5 + - - -
161A ALA* 4.0 11.1 - - - +
164A ARG* 3.7 31.2 - - + +
165A THR* 4.3 11.8 - - + +
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Residues in contact with TYR 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ARG* 3.7 57.1 - - + +
8A LEU* 4.1 10.1 - - + -
54A ALA* 3.8 27.8 + - + -
126A ALA 2.9 19.7 + - - +
127A GLU* 3.5 10.3 - - - +
128A VAL 3.2 0.2 - - - -
129A ALA* 1.3 75.9 - - - +
131A LEU* 1.4 61.4 + - - +
133A GLY* 3.3 3.2 + - - -
134A VAL* 3.1 34.1 + - + +
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 4.0 30.1 - - + -
52A ILE* 4.6 7.9 - - + -
53A VAL 4.4 0.4 - - - +
54A ALA* 3.8 33.6 - - + +
59A ILE* 3.9 20.6 - - + -
72A PHE* 3.9 27.6 - - + -
102A ILE* 4.5 11.0 - - + -
127A GLU 3.0 14.0 + - - +
128A VAL 3.1 6.3 + - - +
130A TYR* 1.4 73.6 - - - +
132A VAL* 1.3 65.0 + - - +
134A VAL* 3.1 6.0 + - + +
135A LEU* 3.0 33.9 + - + +
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A PHE* 4.1 26.0 - - + -
128A VAL* 2.9 31.3 + - + +
129A ALA* 3.7 8.3 - - - +
131A LEU* 1.3 69.3 - - - +
133A GLY* 1.3 62.8 + - - +
135A LEU* 3.3 12.3 + - + +
136A GLN* 3.1 23.2 + - - +
141A TYR 5.1 0.9 - - - +
143A PRO* 4.2 25.7 - - + +
146A VAL* 4.4 20.4 - - + -
148A ILE* 5.6 1.1 - - + -
161A ALA* 6.3 0.2 - - + -
165A THR* 4.2 18.6 - - + -
169A VAL* 4.6 4.7 - - + -
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Residues in contact with GLY 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ALA 2.9 17.0 + - - -
130A TYR* 3.6 3.1 - - - -
132A VAL* 1.3 76.3 - - - +
134A VAL* 1.3 59.9 + - - +
136A GLN* 3.2 12.6 + - - +
137A SER* 3.0 25.8 + - - -
165A THR* 5.9 0.2 - - - +
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA* 4.0 37.7 - - + +
55A ASP 4.3 4.3 - - - +
56A PRO* 4.3 14.6 - - + -
59A ILE* 5.2 5.2 - - + -
130A TYR* 3.1 28.4 + - + +
131A LEU* 3.1 11.4 + - + +
133A GLY* 1.3 73.3 - - - +
135A LEU* 1.3 57.9 + - + +
137A SER* 3.1 7.1 + - - +
138A SER* 2.8 46.1 + - - +
139A PHE* 5.2 0.9 - - + -
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 4.2 19.5 - - + -
64A PHE* 3.9 36.3 - - + -
70A THR* 5.0 7.4 - - + -
72A PHE* 5.1 5.6 - - + -
102A ILE* 5.9 1.1 - - + -
131A LEU* 3.0 33.1 + - + +
132A VAL* 3.6 13.7 - - - +
134A VAL* 1.3 74.2 - - - +
136A GLN* 1.3 57.0 + - - +
139A PHE* 2.8 48.3 + - + +
141A TYR* 3.3 36.2 + - + +
146A VAL* 5.4 3.8 - - + -
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Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A VAL* 3.1 14.0 + - - +
133A GLY* 3.2 13.8 + - - +
135A LEU* 1.3 76.5 - - - +
137A SER* 1.3 64.0 + - - +
140A ASP* 3.1 23.8 + - - -
141A TYR 3.4 20.4 + - - +
142A SER* 5.2 0.6 - - - +
143A PRO* 3.7 32.1 - - + +
168A ALA* 6.2 0.2 - - - +
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Residues in contact with SER 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLY 3.0 17.3 + - - -
134A VAL* 3.1 10.0 + - - +
136A GLN* 1.3 77.3 - - - +
138A SER* 1.3 64.7 + - - +
140A ASP* 4.6 1.2 + - - -
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Residues in contact with SER 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO* 3.5 32.2 - - - +
134A VAL* 2.8 23.9 + - - +
137A SER* 1.3 78.8 + - - +
139A PHE* 1.3 75.9 + - - +
140A ASP 3.5 0.7 - - - -
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Residues in contact with PHE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO* 3.5 37.5 - - + -
59A ILE* 3.8 31.2 - - + -
60A GLN* 3.6 27.4 - - + -
64A PHE* 6.4 0.2 - + - -
66A THR* 3.8 32.6 - - + +
134A VAL* 4.9 1.8 - - + -
135A LEU* 2.8 37.8 + - + +
138A SER* 1.3 86.0 - - - +
140A ASP* 1.4 73.6 + - - +
141A TYR* 3.4 5.2 + - + +
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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