Contacts of the helix formed by residues 92 - 128 (chain B) in PDB entry 5AJI
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 GLN 92 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ILE* 5.8 2.4 - - + +
93A THR* 3.7 35.0 + - - +
90B GLY 3.2 7.8 + - - +
91B VAL* 1.3 78.1 - - - +
93B THR* 1.3 71.9 + - + +
94B ALA* 3.3 9.3 - - + +
95B SER* 3.3 27.1 + - - +
96B VAL* 3.3 12.8 + - - +
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Residues in contact with THR 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 3.8 23.0 - - - +
87B GLY* 6.3 0.7 - - - -
91B VAL 3.8 1.0 + - - -
92B GLN* 1.3 81.2 - - + +
94B ALA* 1.3 65.8 + - + +
96B VAL* 3.7 5.9 + - - +
97B ILE* 3.4 27.4 + - + +
92C GLN* 3.6 33.1 + - - +
94C ALA* 6.1 3.2 - - + +
95C SER* 4.0 8.8 + - - -
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A THR* 6.2 2.0 - - + +
97A ILE* 4.0 12.9 - - + +
92B GLN* 3.3 8.1 - - + +
93B THR* 1.3 83.6 - - + +
95B SER* 1.3 66.8 + - - +
97B ILE* 3.4 8.8 + - - +
98B ALA* 3.0 24.1 + - - +
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 3.8 12.6 - - - -
83A ILE* 3.7 39.3 - - - +
93A THR* 4.0 6.2 + - - -
97A ILE* 3.9 11.4 - - - +
91B VAL* 4.4 4.3 - - - -
92B GLN* 3.3 23.0 + - - +
94B ALA* 1.3 79.5 - - - +
96B VAL* 1.3 56.7 + - - +
98B ALA* 3.3 1.6 + - - +
99B VAL* 2.9 34.1 + - - +
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 3.7 7.9 - - + -
83B ILE* 3.4 42.2 - - + +
86B LEU* 4.0 27.4 - - + -
91B VAL* 3.6 23.1 - - + +
92B GLN 3.3 15.3 + - - +
93B THR* 4.1 4.7 - - - +
94B ALA 3.3 0.6 - - - -
95B SER* 1.3 75.2 - - - +
97B ILE* 1.3 58.1 + - - +
100B LEU* 2.9 47.8 + - + +
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 4.3 15.7 - - + -
93B THR* 3.4 19.2 + - + +
94B ALA* 3.4 10.0 + - - +
95B SER 3.2 0.6 - - - -
96B VAL* 1.3 76.1 - - - +
98B ALA* 1.3 54.8 + - - +
100B LEU* 3.9 3.9 - - - +
101B GLY* 2.7 34.9 + - - -
94C ALA* 3.9 18.6 - - + +
95C SER* 3.8 30.1 - - - +
98C ALA* 3.7 23.1 - - + -
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ILE* 6.3 0.4 - - + -
97A ILE* 3.8 34.1 - - + -
94B ALA 3.0 17.2 + - - +
95B SER 3.6 4.5 - - - +
97B ILE* 1.3 77.1 - - - +
99B VAL* 1.3 59.8 + - + +
101B GLY* 3.5 0.7 - - - -
102B ALA* 2.9 28.8 + - - +
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLY* 3.5 26.9 - - - -
79A ALA* 3.8 25.8 - - + -
80A PHE* 3.5 31.6 - - + -
83A ILE* 5.1 4.9 - - + -
95B SER 2.9 23.3 + - - +
96B VAL 4.0 0.2 - - - +
98B ALA* 1.3 76.0 - - + +
100B LEU* 1.3 69.2 + - + +
102B ALA* 3.1 8.6 + - - +
103B ALA* 2.9 23.5 + - + +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 5.7 2.0 - - + -
79B ALA* 4.3 31.2 - - + +
82B LEU* 4.5 21.3 - - + -
83B ILE* 4.8 3.1 - - + -
96B VAL* 2.9 42.1 + - + +
97B ILE* 4.0 3.6 - - - +
99B VAL* 1.3 82.9 - - + +
101B GLY* 1.3 53.8 + - - +
103B ALA* 3.2 9.5 + - + +
104B GLY* 2.7 34.1 + - - -
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Residues in contact with GLY 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ILE* 2.7 23.0 + - - -
98B ALA* 3.5 2.2 - - - -
99B VAL 3.2 0.2 - - - -
100B LEU* 1.3 74.5 - - - +
102B ALA* 1.3 56.0 + - - +
104B GLY* 3.2 1.7 + - - -
105B LEU* 2.8 31.1 + - - +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 5.7 0.4 - - - -
98B ALA 2.9 15.0 + - - +
99B VAL* 3.1 11.0 + - - +
101B GLY* 1.3 70.7 - - - +
103B ALA* 1.3 65.9 + - - +
105B LEU* 3.0 11.3 + - - +
106B ALA* 2.8 24.7 + - - +
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 4.2 26.0 - - + +
99B VAL* 2.9 15.4 + - + +
100B LEU* 3.5 16.6 - - + +
102B ALA* 1.3 74.6 - - - +
104B GLY* 1.3 64.1 + - - +
106B ALA* 3.1 9.2 + - - +
107B VAL* 3.0 28.6 + - + +
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Residues in contact with GLY 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU 2.7 18.8 + - - -
101B GLY* 3.6 2.2 - - - -
103B ALA* 1.3 73.2 - - - +
105B LEU* 1.3 51.0 + - - +
107B VAL* 3.4 6.5 + - - +
108B GLY* 2.7 33.1 + - - -
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 6.4 1.8 - - + -
101B GLY 2.8 17.4 + - - +
102B ALA* 3.4 9.4 - - - +
104B GLY* 1.3 73.1 - - - +
106B ALA* 1.3 59.2 + - - +
108B GLY* 3.2 3.0 + - - +
109B LEU* 2.9 58.0 + - + +
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 4.0 12.6 - - + -
72A LEU* 3.9 23.8 - - + -
115A LEU* 3.8 10.2 - - + +
102B ALA 2.8 14.8 + - - +
103B ALA 3.1 8.7 + - - +
105B LEU* 1.3 73.4 - - - +
107B VAL* 1.3 63.2 + - - +
109B LEU* 3.3 10.0 + - - +
110B ALA* 3.2 21.0 + - - +
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 4.4 9.9 - - + -
69A LEU* 4.1 18.2 - - + -
72A LEU* 3.8 19.7 - - + -
103B ALA* 3.0 17.5 + - + +
104B GLY* 3.6 9.2 - - - +
106B ALA* 1.3 73.4 - - - +
108B GLY* 1.3 60.3 + - - +
110B ALA* 3.2 2.8 + - - +
111B LEU* 2.9 55.7 + - + +
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Residues in contact with GLY 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B GLY 2.7 22.1 + - - -
105B LEU* 3.5 5.8 - - - -
106B ALA 3.2 0.2 - - - -
107B VAL* 1.3 75.1 - - - +
109B LEU* 1.3 63.6 + - - +
111B LEU* 3.3 3.5 + - - +
112B GLN* 3.1 23.4 + - - +
109C LEU* 5.4 9.4 - - - +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLY* 5.6 8.5 - - - +
112A GLN* 5.3 15.3 - - + +
115A LEU* 3.8 20.2 - - + -
116A SER* 5.8 3.7 - - - -
105B LEU* 2.9 42.0 + - + +
106B ALA* 3.8 6.3 - - - +
107B VAL 3.3 0.2 - - - -
108B GLY* 1.3 75.2 - - - +
110B ALA* 1.3 63.8 + - - +
112B GLN* 3.3 32.7 + - - +
113B GLY 4.9 0.3 + - - -
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 4.3 13.5 - - + -
115A LEU* 3.9 25.9 - - + +
116A SER* 5.7 1.5 - - - +
118A LEU* 6.3 0.7 - - + -
119A ALA* 3.5 30.9 - - + +
106B ALA 3.2 9.4 + - - +
107B VAL* 3.2 8.4 + - - +
109B LEU* 1.3 80.5 - - - +
111B LEU* 1.3 62.9 + - + +
112B GLN 3.3 1.1 + - - -
113B GLY 4.8 1.9 + - - -
114B SER* 5.2 2.9 + - - -
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B VAL* 2.9 42.2 + - + +
108B GLY* 3.7 4.3 - - - +
110B ALA* 1.3 80.0 - - + +
112B GLN* 1.3 57.4 + - - +
113B GLY 3.5 0.9 - - - -
114B SER* 3.4 18.1 + - - +
115B LEU* 2.9 34.1 + - + +
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Residues in contact with GLN 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLY 3.1 11.6 + - - +
109B LEU* 3.3 30.3 - - - +
110B ALA 3.3 2.6 - - - -
111B LEU* 1.3 78.7 - - - +
113B GLY* 1.3 63.9 + - - +
115B LEU* 3.4 9.9 + - + +
116B SER* 3.2 21.1 + - - -
109C LEU* 5.1 15.5 - - + +
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Residues in contact with GLY 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ILE* 6.0 6.3 - - - -
110B ALA 4.8 1.8 + - - -
111B LEU 3.5 0.4 - - - -
112B GLN* 1.3 79.0 - - - +
114B SER* 1.3 57.4 + - - +
116B SER* 3.1 9.1 + - - -
117B ASN* 2.9 37.4 + - - -
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 3.4 32.6 - - - +
110B ALA 5.2 2.8 + - - -
111B LEU* 3.4 23.6 + - - +
112B GLN 3.3 0.4 - - - -
113B GLY* 1.3 74.5 - - - +
115B LEU* 1.3 53.7 + - - +
117B ASN* 3.2 7.5 + - - +
118B LEU* 2.7 36.6 + - - +
151B PHE* 3.5 29.2 - - - -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 3.7 33.9 - - + -
111B LEU* 2.9 21.6 + - + +
112B GLN* 3.5 8.3 - - + +
113B GLY 3.3 0.2 - - - -
114B SER* 1.3 77.5 - - - +
116B SER* 1.3 61.7 + - - +
118B LEU* 3.4 17.1 - - + +
119B ALA* 3.2 21.3 + - - +
106C ALA* 3.7 22.7 - - + +
109C LEU* 3.7 27.8 - - + -
110C ALA* 3.7 16.3 - - + +
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLN* 3.2 9.0 + - - -
113B GLY* 3.1 12.1 + - - -
115B LEU* 1.3 78.6 - - - +
117B ASN* 1.3 65.2 + - - +
119B ALA* 3.4 6.4 + - - +
120B ALA* 3.1 22.0 + - - +
168B GLY* 4.4 11.1 - - - -
109C LEU 5.6 4.3 - - - -
110C ALA* 5.5 4.0 - - - +
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Residues in contact with ASN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 6.3 0.6 - - - +
171A ILE* 5.4 8.9 + - - +
113B GLY* 2.9 27.2 + - - -
114B SER* 3.6 9.2 + - - +
116B SER* 1.3 73.6 + - - +
118B LEU* 1.3 60.8 + - - +
120B ALA 3.4 0.2 + - - -
121B GLY 2.9 24.4 + - - -
150B ILE 3.5 4.7 - - - +
151B PHE* 3.4 29.8 + - + +
166B PRO* 3.5 14.8 - - - +
167B ASN* 3.4 11.8 + - - +
168B GLY* 2.9 33.0 + - - +
169B LYS 4.5 0.2 + - - -
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B THR* 3.4 30.2 - - + +
68B PHE* 4.4 30.3 - - + -
114B SER 2.7 21.2 + - - +
115B LEU* 3.4 17.3 - - + +
117B ASN* 1.3 73.4 - - - +
119B ALA* 1.3 63.0 + - + +
121B GLY* 3.2 3.3 + - - -
122B VAL* 3.1 23.3 + - + +
150B ILE* 3.4 42.2 - - + +
151B PHE* 3.9 7.1 - - + -
110C ALA* 6.2 0.7 - - + -
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU 3.2 12.5 + - - +
116B SER* 3.7 6.1 - - - +
117B ASN 3.2 0.2 - - - -
118B LEU* 1.3 80.3 - - + +
120B ALA* 1.3 65.3 + - - +
122B VAL* 3.1 11.5 + - - +
123B LEU* 3.1 31.1 + - + +
110C ALA* 3.4 32.8 - - + +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B SER 3.1 9.0 + - - +
119B ALA* 1.3 77.3 - - - +
121B GLY* 1.3 61.8 + - - +
123B LEU* 3.1 5.0 + - - +
124B LEU* 2.9 28.6 + - - +
167B ASN* 3.4 37.7 - - + +
168B GLY* 3.5 8.7 - - - +
171B ILE* 3.5 26.9 - - + -
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Residues in contact with GLY 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASN 2.9 11.7 + - - -
118B LEU 3.5 4.3 - - - -
120B ALA* 1.3 75.9 - - - +
122B VAL* 1.3 62.3 + - - +
124B LEU* 3.4 2.0 + - - +
125B VAL* 3.1 29.9 + - - +
148B VAL* 4.4 5.3 - - - +
149B GLN 4.6 1.3 - - - -
150B ILE* 4.2 4.3 - - - -
167B ASN* 3.2 26.3 - - - +
----------------------------------------------------------
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP* 4.2 14.1 - - + +
64B THR* 4.0 29.8 - - + +
65B VAL* 3.8 28.0 - - + -
118B LEU* 3.1 18.0 + - + +
119B ALA* 3.5 10.1 - - - +
121B GLY* 1.3 74.6 - - - +
123B LEU* 1.3 61.4 + - + +
125B VAL* 3.3 6.4 + - - +
126B MET* 2.8 47.8 + - - +
----------------------------------------------------------
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ALA* 3.1 20.7 + - + +
120B ALA* 3.1 1.8 + - - +
122B VAL* 1.3 79.8 - - + +
124B LEU* 1.3 58.8 + - - +
126B MET* 4.1 9.4 - - - -
127B PHE* 2.9 45.8 + - + +
129B PRO* 4.6 0.7 - - - +
171B ILE* 3.4 31.9 - - + -
114C SER* 3.3 22.9 - - - +
117C ASN* 6.4 0.4 - - - +
151C PHE* 3.8 32.1 - - + -
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ALA 2.9 19.7 + - - +
121B GLY 3.8 3.6 - - - +
123B LEU* 1.3 73.4 - - - +
125B VAL* 1.3 60.3 + - - +
128B ARG* 2.9 30.5 + - - +
129B PRO* 3.7 25.6 - - + +
130B PHE* 4.1 17.9 - - + +
148B VAL* 4.3 11.9 - - + -
153B THR* 4.1 9.9 - - - +
167B ASN* 3.8 32.8 - - + +
170B ILE* 4.1 29.6 - - + -
171B ILE* 4.2 15.9 - - + -
175B ILE* 4.2 3.8 - - + -
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP* 4.4 15.3 - - - +
121B GLY 3.1 15.0 + - - +
122B VAL* 3.5 9.0 - - - +
124B LEU* 1.3 77.6 - - - +
126B MET* 1.3 63.6 + - - +
128B ARG* 3.1 23.2 - - - +
148B VAL* 4.3 23.3 - - + +
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Residues in contact with MET 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP* 5.6 8.3 - - + +
65B VAL* 6.3 0.4 - - - -
122B VAL* 2.8 36.5 + - + +
123B LEU* 4.1 6.1 - - - -
124B LEU 3.3 0.2 - - - -
125B VAL* 1.3 78.8 - - + +
127B PHE* 1.3 87.4 + - + +
128B ARG* 4.7 2.8 - - - +
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Residues in contact with PHE 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 2.9 44.1 + - + +
126B MET* 1.3 102.5 - - + +
128B ARG* 1.3 72.4 + - - +
129B PRO* 3.2 8.3 - - + +
149C GLN* 5.3 12.3 - - + -
150C ILE* 3.8 21.5 - - + -
151C PHE* 3.8 23.8 - + + -
152C SER* 6.0 1.6 - - - -
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU 2.9 15.7 + - - +
125B VAL* 3.1 22.9 - - - +
126B MET 4.6 2.7 - - - -
127B PHE* 1.3 79.1 - - - +
129B PRO* 1.3 69.4 - - - +
130B PHE 3.0 12.2 + - - +
131B ARG* 3.1 43.5 + - + +
180B ARG* 3.4 18.0 + - - -
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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