Contacts of the helix formed by residues 129 - 154 (chain E) in PDB entry 4N3E
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 ASN 129 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E ARG* 2.9 26.0 + - - +
95E ASN* 3.7 13.5 - - - +
127E THR* 3.4 8.6 + - + +
128E VAL* 1.3 70.2 - - - +
130E GLU* 1.3 57.9 + - - +
131E GLU* 2.9 27.9 + - - +
132E GLU* 3.0 31.6 + - + +
133E VAL* 3.7 3.1 + - - +
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Residues in contact with GLU 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E TYR* 4.7 13.2 - - + -
128E VAL 3.4 7.6 + - - -
129E ASN* 1.3 68.4 - - - +
131E GLU* 1.3 55.8 + - - +
132E GLU 3.5 0.4 - - - -
133E VAL* 3.4 12.7 + - + +
134E LYS* 3.2 59.6 + - + +
2F ALA* 6.3 2.9 - - + -
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Residues in contact with GLU 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E ARG* 3.3 24.9 + - - +
129E ASN* 2.9 15.7 + - - +
130E GLU* 1.3 73.6 + - - +
132E GLU* 1.3 53.2 + - - +
133E VAL 3.1 5.2 - - - -
134E LYS* 3.5 13.1 + - - +
135E ILE* 2.8 48.6 + - + +
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Residues in contact with GLU 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E LEU 4.3 4.3 - - - +
93E ARG* 3.3 35.0 - - - +
95E ASN* 5.0 0.2 - - - +
96E ILE* 2.8 45.2 - - - +
120E TYR* 3.5 29.8 + - - -
128E VAL* 3.6 14.0 - - - +
129E ASN* 3.0 30.3 + - + +
131E GLU* 1.3 77.2 - - - +
133E VAL* 1.3 58.5 + - - +
135E ILE* 3.8 9.9 - - + -
136E GLY* 3.2 16.3 + - - -
201E 2AN 4.0 10.2 - - + -
204E 2AN 5.9 1.6 - - + -
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Residues in contact with VAL 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E TYR* 4.5 13.9 - - + -
6E ILE* 3.8 29.8 - - + +
120E TYR* 3.8 35.5 + - + -
128E VAL* 4.2 13.7 - - + -
129E ASN 4.0 11.7 - - - +
130E GLU* 3.4 11.6 + - + +
131E GLU 3.1 0.6 - - - -
132E GLU* 1.3 77.7 - - - +
134E LYS* 1.3 67.4 + - + +
136E GLY* 3.3 1.4 + - - -
137E GLU* 3.2 25.0 + - - +
1F MET 5.7 4.9 - - - +
2F ALA* 6.5 0.9 - - - -
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Residues in contact with LYS 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E GLU* 3.2 46.7 + - + +
131E GLU* 4.1 10.3 - - - +
133E VAL* 1.3 75.1 - - + +
135E ILE* 1.3 63.5 + - - +
137E GLU* 4.0 15.1 - - - +
138E LYS* 3.3 26.0 + - - +
1F MET* 5.4 15.9 - - + +
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Residues in contact with ILE 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E ARG* 3.8 26.7 - - - +
131E GLU* 2.8 37.5 + - + +
132E GLU* 3.8 11.2 - - + +
133E VAL 3.3 0.2 - - - -
134E LYS* 1.3 75.1 - - - +
136E GLY* 1.3 66.7 + - - +
138E LYS* 3.4 9.4 + - - +
139E LYS* 3.2 30.5 + - + +
201E 2AN 3.9 15.0 - - + -
204E 2AN 4.2 18.2 - - + +
205E 2AN 3.4 31.4 - - + +
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Residues in contact with GLY 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E TYR* 5.5 3.5 + - - -
120E TYR* 3.5 22.7 - - - -
132E GLU 3.2 8.1 + - - -
133E VAL 3.3 0.4 + - - -
134E LYS 3.2 0.6 - - - -
135E ILE* 1.3 82.5 - - - +
137E GLU* 1.3 58.9 - - - +
139E LYS* 3.5 2.9 - - - +
140E ALA* 3.3 21.7 + - - +
201E 2AN 3.6 27.2 + - - -
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Residues in contact with GLU 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ILE* 4.0 24.3 - - + +
8E LYS* 3.6 33.2 + - - +
120E TYR* 4.5 0.6 + - - -
133E VAL* 3.2 16.9 + - - +
134E LYS* 4.1 12.1 - - - +
136E GLY* 1.3 74.6 - - - +
138E LYS* 1.3 60.7 + - + +
140E ALA* 4.0 3.7 - - - +
141E TYR* 3.1 31.9 + - + +
202E 2AN 4.7 1.3 + - - -
1F MET* 3.0 52.5 - - - +
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Residues in contact with LYS 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E LYS 3.3 14.4 + - - +
135E ILE* 4.2 13.2 - - - +
137E GLU* 1.3 80.2 - - + +
139E LYS* 1.3 82.0 + - - +
141E TYR* 4.0 6.5 - - - -
142E GLU* 3.2 37.0 + - - +
205E 2AN 2.8 37.3 + - - -
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Residues in contact with LYS 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E GLN* 4.8 4.0 - - - +
135E ILE* 3.2 21.6 + - + +
136E GLY 3.5 4.9 - - - +
138E LYS* 1.3 100.6 - - - +
140E ALA* 1.3 61.2 - - - +
142E GLU* 3.8 12.9 - - - +
143E PHE 3.3 16.6 + - - -
201E 2AN 3.6 72.0 - - + +
204E 2AN 3.7 3.4 + - - +
205E 2AN 2.6 61.3 + - - -
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Residues in contact with ALA 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ARG* 3.9 11.1 + - - +
101E TYR* 5.8 5.6 - - + -
136E GLY 3.3 12.7 + - - +
137E GLU* 4.1 4.0 - - - +
139E LYS* 1.3 78.4 - - - +
141E TYR* 1.3 57.8 + - - +
143E PHE* 3.8 5.7 - - - +
144E TYR* 3.1 25.6 + - - +
201E 2AN 3.5 24.2 + - - +
202E 2AN 3.8 22.5 + - + +
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Residues in contact with TYR 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E LYS* 3.9 19.3 - - - +
10E GLU* 4.1 24.3 + - + -
137E GLU* 3.1 22.4 + - + +
138E LYS* 4.4 4.3 - - - -
139E LYS 3.4 0.2 - - - -
140E ALA* 1.3 75.0 - - - +
142E GLU* 1.3 58.8 - - - +
144E TYR* 3.3 26.2 - + - +
145E LYS* 3.0 51.4 + - + +
202E 2AN 3.7 13.9 + - - +
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Residues in contact with GLU 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E GLN* 4.1 10.2 + - - +
37E HIS* 6.1 0.7 - - - -
138E LYS* 3.2 33.8 + - + +
139E LYS* 3.8 12.4 - - - +
141E TYR* 1.3 80.0 - - - +
143E PHE* 1.3 58.4 + - - +
145E LYS* 3.2 10.4 + - + +
146E GLN* 2.9 48.6 + - + +
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Residues in contact with PHE 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ALA 4.2 1.6 - - - -
23E LEU* 3.5 24.5 - - + -
27E ARG* 3.5 47.6 - - + -
30E VAL* 4.0 13.5 - - + -
31E LEU* 3.4 46.2 - - + -
34E ALA* 4.0 13.5 - - + -
35E GLN* 4.0 4.5 + - - +
139E LYS 3.3 15.6 + - - +
140E ALA 3.8 4.3 - - - +
142E GLU* 1.3 74.0 - - - +
144E TYR* 1.3 68.6 + - + +
146E GLN* 3.1 13.0 + - - +
147E VAL* 3.0 40.1 + - + +
201E 2AN 4.0 10.1 - + + -
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Residues in contact with TYR 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E GLU* 5.4 1.5 - - + +
11E GLU 3.6 8.3 + - - -
12E SER* 3.5 6.6 + - - -
19E LEU* 4.7 7.9 - - + -
23E LEU* 4.0 25.8 - - + -
140E ALA 3.1 10.1 + - - +
141E TYR* 3.3 29.8 - + - +
143E PHE* 1.3 77.0 - - + +
145E LYS* 1.3 86.3 + - + +
147E VAL* 3.4 2.1 + - - +
148E GLU* 2.4 54.6 + - + -
202E 2AN 2.9 66.6 - + - +
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Residues in contact with LYS 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E TYR* 3.0 41.1 + - + +
142E GLU* 3.2 11.2 + - - +
144E TYR* 1.3 103.1 + - + +
146E GLN* 1.3 61.9 + - + +
148E GLU* 2.6 30.8 + - - +
149E GLU* 3.2 21.5 + - - +
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Residues in contact with GLN 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ALA* 3.2 33.5 + - + +
35E GLN* 2.6 31.5 - - - +
37E HIS* 5.8 2.2 - - - -
142E GLU* 2.9 34.1 + - + +
143E PHE* 3.1 16.2 + - - +
145E LYS* 1.3 79.6 - - + +
147E VAL* 1.3 58.3 + - - +
149E GLU* 3.6 7.6 + - - +
150E TYR* 3.3 24.3 + - - +
203E 2AN 4.6 3.2 - - + -
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Residues in contact with VAL 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E LEU* 4.7 4.3 - - + -
22E ALA* 3.9 4.0 - - + -
23E LEU* 3.7 30.3 - - + -
30E VAL* 3.9 14.8 - - + -
34E ALA* 4.9 2.0 - - + -
143E PHE* 3.1 32.1 - - + +
144E TYR 3.7 3.8 - - - +
146E GLN* 1.3 74.4 - - - +
148E GLU* 1.3 56.3 + - - +
149E GLU 3.3 0.2 - - - -
150E TYR* 3.0 1.7 + - - +
151E LEU* 2.7 51.2 + - + +
203E 2AN 3.6 28.9 - - + -
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Residues in contact with GLU 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E GLU 4.3 0.2 - - - +
12E SER* 2.6 21.7 + - - +
13E PRO* 3.4 21.2 - - + +
14E ILE* 4.2 17.1 - - + +
19E LEU* 5.4 1.1 - - - -
144E TYR* 2.4 47.2 + - + +
145E LYS* 2.6 36.1 + - - +
147E VAL* 1.3 74.3 - - - +
149E GLU* 1.3 64.4 + - - +
151E LEU* 4.7 0.2 - - - -
152E ALA* 3.0 28.6 + - + +
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Residues in contact with GLU 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E LYS 3.2 10.7 + - - +
146E GLN* 3.7 11.2 - - - +
147E VAL 3.3 0.2 - - - -
148E GLU* 1.3 78.5 - - - +
150E TYR* 1.3 75.2 + - - +
152E ALA* 3.6 6.3 + - - +
153E ALA* 3.2 28.7 + - - +
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Residues in contact with TYR 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E GLN 3.3 6.4 + - - +
147E VAL 3.0 8.2 + - - +
149E GLU* 1.3 85.8 + - - +
151E LEU* 1.3 70.4 + - + +
153E ALA* 3.0 16.0 + - + +
154E ASN* 3.2 34.0 + - - +
157E VAL* 4.2 14.5 - - + +
203E 2AN 3.3 104.6 + + + -
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Residues in contact with LEU 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E ILE* 3.8 29.4 - - + -
18E ARG* 2.6 70.5 + - + +
19E LEU* 4.2 7.4 - - + -
22E ALA* 4.3 2.0 - - + -
147E VAL* 2.7 40.6 + - + +
150E TYR* 1.3 74.5 - - + +
152E ALA* 1.3 58.5 + - - +
154E ASN 3.4 7.1 - - - +
155E PRO* 4.0 1.4 - - - +
157E VAL* 4.0 16.6 - - + +
158E PHE* 4.1 5.2 - - + -
203E 2AN 3.5 24.2 - - + -
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Residues in contact with ALA 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E PRO* 5.9 4.7 - - + -
14E ILE* 3.8 13.4 - - + +
18E ARG* 4.9 0.4 - - - +
148E GLU* 3.0 21.5 + - + +
149E GLU* 3.6 6.5 - - - +
151E LEU* 1.3 79.2 - - - +
153E ALA* 1.3 57.2 + - - +
154E ASN 3.8 0.5 + - - -
155E PRO* 4.2 10.9 - - - +
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Residues in contact with ALA 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E GLU* 3.2 25.0 + - - +
150E TYR* 3.0 6.6 + - + +
152E ALA* 1.3 75.0 - - - +
154E ASN* 1.3 70.7 + - - +
155E PRO* 3.7 5.9 - - - +
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Residues in contact with ASN 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ARG* 2.8 17.0 + - - -
150E TYR* 3.2 38.2 + - + +
151E LEU* 3.4 3.6 - - - +
153E ALA* 1.3 89.4 + - - +
155E PRO* 1.3 62.2 - - - +
156E GLU* 3.2 25.2 + - - +
157E VAL* 3.4 24.9 - - + +
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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