Contacts of the helix formed by residues 113 - 145 (chain I) in PDB entry 3IS7
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 ASP 113 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I ASP* 5.8 2.3 + - + +
7I VAL* 3.4 16.8 - - + +
61I ARG* 3.0 15.0 + - - -
65I LEU* 4.0 11.5 - - - +
108I CYS* 2.9 23.3 + - + +
111I VAL* 3.3 13.0 + - + +
112I HIS* 1.3 73.9 - - - +
114I TYR* 1.3 61.4 + - - +
115I VAL* 3.6 1.9 + - - +
116I SER* 2.6 40.0 + - - -
117I ARG* 3.1 15.4 + - - +
102Q ARG* 4.0 5.3 + - - +
128Q GLU* 4.6 2.9 - - - +
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Residues in contact with TYR 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109I GLU* 3.4 38.1 + - - -
112I HIS* 3.2 45.1 + - + -
113I ASP* 1.3 71.2 - - - +
115I VAL* 1.3 62.4 + - - +
116I SER 3.4 0.2 - - - -
117I ARG* 3.7 8.8 - - - +
118I ASP* 3.1 26.0 + - - +
102Q ARG* 3.9 14.7 - - + +
105Q ILE* 3.4 45.4 - - + +
106Q VAL* 3.1 30.3 + - - +
117Q ARG* 3.7 12.8 - - - +
121Q LYS* 4.3 18.1 - - + +
124Q LEU* 4.2 15.0 - - + -
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Residues in contact with VAL 115 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I ARG* 3.4 25.4 - - - +
113I ASP* 3.2 1.2 + - - -
114I TYR* 1.3 75.0 - - - +
116I SER* 1.3 65.4 + - - +
118I ASP* 3.3 7.3 + - + +
119I LEU* 3.1 21.3 + - + +
121Q LYS* 5.0 4.0 - - + +
124Q LEU* 4.0 13.0 - - + -
125Q GLU* 3.8 45.8 - - + +
128Q GLU* 3.4 33.4 + - + +
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Residues in contact with SER 116 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I VAL* 3.8 9.7 - - - +
11I LEU* 4.3 8.9 - - - +
61I ARG* 3.2 23.7 + - - +
65I LEU* 4.0 3.6 - - - +
108I CYS* 3.7 16.6 - - - -
113I ASP* 2.6 37.8 + - - -
115I VAL* 1.3 76.5 - - - +
117I ARG* 1.3 59.2 + - - +
119I LEU* 3.4 7.6 + - - +
120I LEU* 3.0 32.4 + - - +
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Residues in contact with ARG 117 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I ILE* 3.8 26.6 - - + +
106I VAL* 6.0 0.2 - - - +
108I CYS* 3.9 16.3 - - + +
109I GLU* 2.9 40.7 + - - +
113I ASP 3.1 16.7 + - - +
114I TYR* 3.7 9.4 - - - +
116I SER* 1.3 79.3 - - - +
118I ASP* 1.3 58.3 + - - +
120I LEU* 3.3 5.7 + - - +
121I LYS* 2.9 36.8 + - + +
109P GLU* 2.5 41.6 + - - -
114P TYR* 3.9 18.4 + - - +
117P ARG* 4.4 13.9 - - - +
117Q ARG* 4.1 17.5 - - - +
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Residues in contact with ASP 118 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I TYR 3.1 16.1 + - - +
115I VAL* 3.6 10.1 - - + +
117I ARG* 1.3 72.8 - - - +
119I LEU* 1.3 66.8 + - - +
121I LYS* 3.2 17.7 + - - +
122I ASP* 3.0 38.1 + - - +
118Q ASP* 5.6 1.2 - - - +
121Q LYS* 3.7 25.0 - - + +
125Q GLU* 5.2 10.1 - - - +
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Residues in contact with LEU 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I LEU* 5.5 1.8 - - + -
57I LYS* 3.9 34.1 - - + +
58I LEU* 4.1 11.0 - - + -
61I ARG* 4.0 24.5 - - + -
115I VAL* 3.1 10.6 + - + +
116I SER* 3.4 9.6 - - - +
117I ARG 3.4 0.2 - - - -
118I ASP* 1.3 75.9 - - - +
120I LEU* 1.3 74.2 + - + +
122I ASP* 3.2 12.1 + - - +
123I ILE* 3.0 45.6 + - + +
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Residues in contact with LEU 120 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I LEU* 4.2 13.7 - - + -
14I ILE* 4.0 15.9 - - + -
58I LEU* 4.1 13.5 - - + -
101I LEU* 4.0 23.8 - - + +
104I ALA* 3.7 30.5 - - + -
105I ILE* 3.9 14.4 - - + +
108I CYS* 4.0 20.2 - - - -
116I SER 3.0 18.4 + - - +
117I ARG* 3.3 4.5 + - - +
119I LEU* 1.3 90.0 - - + +
121I LYS* 1.3 58.5 + - - +
123I ILE* 3.2 6.3 + - + +
124I LEU* 2.8 28.4 + - - +
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Residues in contact with LYS 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I ILE* 4.3 9.0 - - + -
117I ARG* 2.9 27.7 + - + +
118I ASP* 3.5 17.7 - - - +
119I LEU 3.2 0.4 - - - -
120I LEU* 1.3 78.7 - - - +
122I ASP* 1.3 60.2 + - - +
124I LEU* 3.1 9.8 + - + +
125I GLU* 3.0 29.7 + - + +
114P TYR* 4.6 23.3 - - + +
115P VAL* 5.0 2.8 - - + +
117P ARG* 6.4 2.0 - - - -
118P ASP* 4.2 31.2 - - + +
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Residues in contact with ASP 122 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I HIS* 4.9 1.7 + - + -
118I ASP* 3.0 27.8 + - - +
119I LEU* 3.2 10.0 + - - +
121I LYS* 1.3 75.4 - - - +
123I ILE* 1.3 68.4 + - + +
125I GLU* 3.4 14.2 + - - +
126I SER* 3.2 22.5 + - - -
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Residues in contact with ILE 123 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ILE* 4.9 1.3 - - + -
18I GLU* 3.6 22.2 - - - +
54I HIS* 3.9 35.7 - - + +
57I LYS* 5.5 2.0 - - + -
58I LEU* 4.0 28.5 - - + -
101I LEU* 4.2 12.6 - - + -
119I LEU* 3.0 36.7 + - + +
120I LEU* 3.5 12.1 - - + +
122I ASP* 1.3 77.0 - - + +
124I LEU* 1.3 57.3 + - - +
126I SER* 3.3 3.1 + - - -
127I GLU* 2.9 41.7 + - + +
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Residues in contact with LEU 124 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98I THR* 3.7 23.1 - - - +
101I LEU* 3.9 26.9 - - + +
102I ARG* 3.8 29.2 - - + +
105I ILE* 4.1 19.7 - - + -
120I LEU 2.8 14.5 + - - +
121I LYS* 3.1 9.4 + - - +
123I ILE* 1.3 74.7 - - - +
125I GLU* 1.3 59.8 + - - +
127I GLU* 3.2 1.9 + - - +
128I GLU* 2.9 43.0 + - + +
114P TYR* 4.2 13.7 - - + -
115P VAL* 4.0 13.0 - - + -
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Residues in contact with GLU 125 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121I LYS* 3.0 15.9 + - + +
122I ASP* 3.8 14.3 - - - +
123I ILE 3.4 0.2 - - - -
124I LEU* 1.3 76.2 - - - +
126I SER* 1.3 63.0 + - - +
128I GLU* 3.4 3.1 + - - +
129I GLU* 3.0 41.0 + - + +
115P VAL* 3.9 32.8 - - + +
118P ASP* 4.4 13.6 - - - +
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Residues in contact with SER 126 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I ASP* 5.3 4.2 + - - +
51I GLU* 4.7 0.2 + - - -
54I HIS* 2.7 37.7 - - - -
122I ASP 3.2 17.9 + - - -
123I ILE 3.7 1.1 - - - -
124I LEU 3.3 0.2 - - - -
125I GLU* 1.3 75.3 - - - +
127I GLU* 1.3 63.8 + - - +
129I GLU* 3.3 16.5 + - - +
130I HIS* 3.1 20.4 + - - +
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Residues in contact with GLU 127 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I GLU* 2.8 27.2 - - - +
51I GLU* 2.9 25.4 - - - +
94I GLU* 2.8 37.5 - - - +
97I ALA* 5.0 6.6 - - + +
98I THR* 4.0 14.1 - - - +
101I LEU* 3.9 18.6 - - + -
123I ILE* 2.9 26.5 + - - +
124I LEU* 3.2 4.7 + - - +
126I SER* 1.3 81.1 + - - +
128I GLU* 1.3 56.8 + - - +
130I HIS* 3.1 8.2 + - - +
131I ILE* 2.9 31.8 + - - +
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Residues in contact with GLU 128 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98I THR* 4.6 4.5 - - - +
102I ARG* 2.8 36.9 + - - +
124I LEU* 2.9 29.4 + - + +
125I GLU* 3.9 5.2 - - - +
127I GLU* 1.3 68.7 - - - +
129I GLU* 1.3 62.0 + - + +
131I ILE* 3.2 11.3 + - + -
132I ASP* 2.9 28.2 + - - +
61P ARG* 2.9 37.7 + - - +
64P PHE* 3.5 20.9 - - + -
113P ASP* 4.7 0.3 - - - +
115P VAL* 3.3 23.0 - - + +
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Residues in contact with GLU 129 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I GLU* 3.0 34.5 + - + +
126I SER* 3.5 16.8 - - - +
127I GLU 3.3 0.2 - - - -
128I GLU* 1.3 72.5 - - + +
130I HIS* 1.3 66.3 + - - +
132I ASP* 3.3 10.6 + - - +
133I TYR* 3.0 22.2 + - - +
----------------------------------------------------------
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Residues in contact with HIS 130 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I TYR* 3.4 37.1 - + - -
44I GLU* 4.5 3.6 + - - -
47I GLU* 3.2 46.2 + - + +
51I GLU* 5.8 0.6 - - - -
90I ASP* 4.6 2.4 + - - -
94I GLU* 2.8 24.0 + - - +
126I SER 3.1 12.9 + - - +
127I GLU* 3.3 12.7 + - - +
129I GLU* 1.3 77.9 - - - +
131I ILE* 1.3 62.6 + - - +
133I TYR* 3.1 8.7 + + - -
134I LEU* 2.8 50.5 + - + +
----------------------------------------------------------
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Residues in contact with ILE 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91I LEU* 4.0 14.1 - - + -
94I GLU* 3.6 24.5 - - + +
95I LEU* 4.0 22.7 - - + -
98I THR* 3.9 26.0 - - + +
127I GLU 2.9 16.8 + - - +
128I GLU* 3.2 15.5 + - + +
130I HIS* 1.3 74.4 - - - +
132I ASP* 1.3 64.2 + - - +
134I LEU* 3.2 8.2 + - - +
135I GLU* 2.9 45.2 + - - +
64P PHE* 4.3 10.5 - - + -
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Residues in contact with ASP 132 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128I GLU 2.9 14.1 + - - +
129I GLU* 3.3 14.1 - - - +
131I ILE* 1.3 77.3 - - - +
133I TYR* 1.3 59.1 + - - +
135I GLU* 3.9 3.7 - - - +
136I THR* 2.8 41.3 + - - -
34O ASP* 4.4 12.6 - - - +
64P PHE* 3.6 33.4 - - + +
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Residues in contact with TYR 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I LEU* 3.7 25.3 - - - +
43I HIS* 3.3 56.8 - + + +
44I GLU* 5.3 4.0 - - - -
47I GLU* 4.8 0.9 - - - +
87I LEU* 4.6 4.9 - - + -
129I GLU 3.0 14.0 + - - +
130I HIS* 3.5 17.9 - + + +
132I ASP* 1.3 76.0 - - - +
134I LEU* 1.3 81.2 + - + +
136I THR* 3.3 4.7 + - - -
137I GLN* 2.9 68.1 + - + +
153I HIS* 5.2 2.5 + - - -
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Residues in contact with LEU 134 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I GLU* 5.6 0.7 - - - +
87I LEU* 3.9 29.4 - - + +
90I ASP* 3.9 20.6 - - + +
91I LEU* 3.8 31.2 - - + +
94I GLU* 4.0 9.0 - - + -
130I HIS* 2.8 52.8 + - + +
131I ILE* 3.2 6.7 + - - +
133I TYR* 1.3 97.1 - - + +
135I GLU* 1.3 62.6 + - - +
137I GLN* 3.1 4.8 + - - +
138I LEU* 3.1 29.8 + - - +
----------------------------------------------------------
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Residues in contact with GLU 135 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91I LEU* 4.2 22.2 - - + +
95I LEU* 5.9 1.4 - - - +
131I ILE* 2.9 39.0 + - + +
132I ASP* 4.0 2.8 - - - +
134I LEU* 1.3 69.6 - - - +
136I THR* 1.3 66.6 + - - +
138I LEU* 4.0 6.8 - - - +
139I GLY* 3.0 21.0 + - - -
64P PHE* 4.3 15.4 - - - +
66P GLU* 3.8 21.5 - - - +
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Residues in contact with THR 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I ASP* 2.8 30.1 + - - -
133I TYR* 3.4 7.0 - - - -
135I GLU* 1.3 77.7 - - - +
137I GLN* 1.3 73.6 + - - +
139I GLY* 3.2 2.8 + - - -
140I LEU* 2.9 23.6 + - + +
33O ASN 5.0 0.7 - - - +
34O ASP 3.3 16.2 + - - +
35O TRP* 3.6 6.1 - - - +
36O GLY* 3.4 38.4 - - - +
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Residues in contact with GLN 137 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87I LEU* 3.9 17.7 - - + -
133I TYR* 2.9 69.0 + - + +
134I LEU 3.1 5.1 + - - +
136I THR* 1.3 88.3 - - - +
138I LEU* 1.3 59.4 + - - +
140I LEU* 2.9 12.5 + - - +
141I ILE* 2.8 32.4 + - - +
149I TYR* 2.4 43.4 + - - +
153I HIS* 3.8 12.3 + - - -
154O MET* 5.4 0.4 - - - +
----------------------------------------------------------
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Residues in contact with LEU 138 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I GLN* 4.0 34.7 + - + +
87I LEU* 3.9 37.0 - - + +
88I GLN* 4.4 14.4 - - + +
91I LEU* 4.3 20.2 - - + -
134I LEU 3.1 28.5 + - - +
135I GLU* 4.1 5.2 - - - +
137I GLN* 1.3 78.7 - - - +
139I GLY* 1.3 63.8 + - - +
141I ILE* 3.2 21.2 + - + +
142I GLN* 3.3 18.7 + - - +
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Residues in contact with GLY 139 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135I GLU 3.0 15.9 + - - -
136I THR* 3.6 4.3 - - - -
138I LEU* 1.3 74.9 - - - +
140I LEU* 1.3 62.9 + - - +
142I GLN* 3.3 9.1 + - - +
143I LYS* 3.1 41.2 + - - +
35O TRP 5.6 0.7 - - - -
----------------------------------------------------------
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Residues in contact with LEU 140 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I THR* 2.9 17.7 + - + +
137I GLN* 2.9 22.6 + - - +
139I GLY* 1.3 74.3 - - - +
141I ILE* 1.3 69.5 + - - +
142I GLN 3.1 0.2 + - - -
143I LYS* 4.3 7.0 - - + +
144I VAL* 3.0 34.9 + - + +
149I TYR* 3.9 11.2 - - + -
35O TRP 3.4 23.3 - - - +
36O GLY* 4.0 19.1 - - - +
37O LEU* 4.0 14.6 - - + -
154O MET* 3.7 41.3 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I THR* 5.1 1.3 - - + -
84I GLN* 3.8 27.8 - - + +
87I LEU* 3.9 24.9 - - + -
137I GLN 2.8 19.1 + - - +
138I LEU* 3.2 20.8 + - + +
140I LEU* 1.3 78.4 - - - +
142I GLN* 1.3 72.4 + - - +
145I GLY* 2.9 27.7 + - - -
146I LEU* 3.7 23.7 + - + +
149I TYR* 3.6 33.0 - - + -
----------------------------------------------------------
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Residues in contact with GLN 142 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I GLN* 3.6 26.1 + - - +
138I LEU 3.4 14.6 + - - +
139I GLY* 3.6 8.1 - - - +
140I LEU 3.1 0.6 - - - -
141I ILE* 1.3 84.1 - - - +
143I LYS* 1.3 63.0 + - + +
145I GLY* 4.2 3.3 + - - -
147O GLU* 4.7 4.5 - - - +
----------------------------------------------------------
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Residues in contact with LYS 143 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139I GLY* 3.1 31.3 + - - +
140I LEU* 3.1 7.6 + - + +
142I GLN* 1.3 79.9 - - + +
144I VAL* 1.4 60.9 + - + +
35O TRP* 3.7 54.3 + - + +
37O LEU* 4.5 17.3 - - + -
146O LEU* 5.6 0.5 - - - +
147O GLU* 3.6 15.0 - - - +
150O LEU* 3.7 26.3 - - + +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140I LEU* 3.0 32.1 + - + +
143I LYS* 1.4 74.2 - - + +
145I GLY* 1.3 71.0 + - - +
148I ASN* 3.3 27.1 + - + +
149I TYR* 3.7 22.4 - - + +
147O GLU* 3.4 26.2 - - - +
150O LEU* 3.8 13.5 - - + +
151O GLN* 3.6 28.9 - - + +
154O MET* 4.3 16.8 - - - -
----------------------------------------------------------
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Residues in contact with GLY 145 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141I ILE 2.9 18.6 + - - -
142I GLN 4.2 2.0 + - - -
143I LYS 3.6 1.4 - - - -
144I VAL* 1.3 81.3 - - - +
146I LEU* 1.3 66.7 + - - -
147I GLU 3.2 2.5 - - - -
148I ASN 3.1 2.5 + - - -
149I TYR* 2.9 19.6 + - - +
147O GLU* 3.8 14.0 + - - -
----------------------------------------------------------
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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