Contacts of the helix formed by residues 129 - 151 (chain E) in PDB entry 6NR8
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 HIS 129 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E GLY 3.5 4.8 + - - +
128E ILE* 1.3 74.9 - - - +
130E PRO* 1.3 78.5 - - + +
131E ILE* 3.2 43.7 + - + +
132E ARG* 3.3 43.2 - - + +
133E ILE* 3.4 8.5 - - - +
451G ASP* 3.6 33.4 + - + +
452G ASN* 4.8 1.8 - - - -
474L ILE* 4.2 31.5 - - + +
478L THR* 5.4 0.2 - - - +
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Residues in contact with PRO 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E GLY* 6.3 1.3 - - - -
34E LEU* 5.1 4.3 - - + -
124E LEU* 3.8 32.3 - - + -
128E ILE 4.1 0.7 - - - +
129E HIS* 1.3 101.4 - - + +
131E ILE* 1.3 66.6 + - + +
133E ILE* 3.3 24.6 - - + +
134E ALA* 3.4 4.5 + - - +
528E LEU* 3.3 24.0 - - + +
44G GLY 6.2 0.2 - - - -
45G MET* 4.4 19.3 - - + -
474L ILE* 6.0 1.6 - - + -
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Residues in contact with ILE 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E HIS* 3.1 28.6 - - + +
130E PRO* 1.3 80.6 - - + +
132E ARG* 1.3 54.0 + - - +
133E ILE 3.2 2.2 - - - -
134E ALA* 3.0 4.2 + - - +
135E ASP* 2.8 41.9 + - - +
528E LEU* 3.8 14.8 - - + -
38G THR* 6.2 0.2 - - + -
43G ARG* 3.6 27.4 - - + -
44G GLY* 3.4 35.9 - - - +
452G ASN* 3.3 41.5 - - + +
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Residues in contact with ARG 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E ILE* 3.7 23.6 - - + -
129E HIS* 3.3 36.1 + - + +
131E ILE* 1.3 77.7 - - - +
133E ILE* 1.3 61.4 + - + +
135E ASP* 3.6 14.2 - - - +
136E GLY* 3.2 18.5 + - - -
443E LEU* 3.4 44.2 - - + +
444E GLU* 4.7 8.1 + - - +
447E ALA* 4.5 1.6 - - - +
451G ASP* 4.3 7.6 + - - +
452G ASN 4.4 4.9 + - - +
453G ALA 5.2 1.8 - - - +
454G GLY* 3.3 35.2 - - - -
455G PHE 3.9 10.9 + - - +
474L ILE 5.8 1.4 + - - -
475L SER* 5.2 8.7 + - - +
478L THR* 4.4 14.4 - - - +
479L GLU* 3.5 10.3 + - - -
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Residues in contact with ILE 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E ALA* 3.8 38.8 - - + +
123E LEU* 3.8 21.8 - - + -
128E ILE* 3.7 26.9 - - + +
129E HIS 3.4 11.9 - - - +
130E PRO* 3.3 22.2 - - + +
132E ARG* 1.3 79.4 - - + +
134E ALA* 1.3 55.9 + - + +
135E ASP 3.2 0.2 - - - -
136E GLY 3.4 0.3 - - - -
137E TYR* 2.6 57.5 + - + +
443E LEU 5.6 1.8 - - - +
446E TYR* 4.7 1.1 - - + -
447E ALA* 3.7 18.2 - - + +
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Residues in contact with ALA 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E PRO 3.4 15.9 - - - +
131E ILE* 3.0 5.5 + - - +
133E ILE* 1.3 78.7 - - + +
135E ASP* 1.3 64.9 + - - +
137E TYR* 3.8 17.9 + - + +
138E GLU* 3.7 14.0 + - - +
524E VAL* 5.1 3.6 - - + +
525E ARG* 5.6 1.5 - - - +
528E LEU* 3.7 20.0 - - + -
43G ARG* 3.4 35.1 + - - +
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Residues in contact with ASP 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131E ILE* 2.8 22.6 + - - +
132E ARG* 3.6 11.4 - - - +
134E ALA* 1.3 77.4 - - - +
136E GLY* 1.3 60.8 + - - +
137E TYR 3.6 0.2 + - - -
138E GLU* 3.6 11.4 + - - +
139E GLN* 3.8 9.0 + - - +
444E GLU* 5.0 0.6 - - - +
43G ARG* 3.4 25.1 + - - +
452G ASN 3.0 25.3 - - - +
453G ALA* 4.6 5.7 - - - +
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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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132E ARG 3.2 5.0 + - - -
133E ILE 3.0 7.5 + - - -
135E ASP* 1.3 75.2 - - - +
137E TYR* 1.3 55.6 + - - +
138E GLU 3.2 2.0 - - - -
139E GLN* 3.7 2.1 - - - +
140E ALA* 2.8 35.0 + - - +
444E GLU* 3.6 32.1 - - - +
447E ALA* 3.7 11.1 - - - +
448E MET* 4.5 2.8 - - - +
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Residues in contact with TYR 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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116E LEU* 3.6 29.0 + - + -
120E ALA* 3.3 29.5 - - + +
123E LEU* 4.0 1.4 - - - +
133E ILE* 2.6 45.2 + - + +
134E ALA* 3.8 10.8 - - + +
135E ASP 3.4 0.4 - - - -
136E GLY* 1.3 72.2 - - - +
138E GLU* 1.3 60.1 + - - +
140E ALA* 3.5 4.9 + - - +
141E ALA* 2.9 22.3 + - - +
447E ALA* 3.3 37.7 - - + -
450E ALA* 3.5 21.3 - - + +
451E PHE* 4.6 4.0 - - + -
521E THR* 3.4 18.7 + - - +
524E VAL* 3.5 33.4 - - + -
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Residues in contact with GLU 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 ALA 3.7 16.3 - - - +
135E ASP 3.6 7.2 + - - +
136E GLY 3.2 0.6 - - - -
137E TYR* 1.3 78.7 - - - +
139E GLN* 1.3 58.4 + - - +
141E ALA* 3.1 7.1 + - - +
142E ARG* 3.0 38.6 + - - +
521E THR* 2.9 32.1 + - - +
525E ARG* 3.0 44.5 + - - +
43G ARG* 4.4 10.5 - - - +
384G GLU* 3.5 14.1 - - - +
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Residues in contact with GLN 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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135E ASP 3.8 6.1 + - - +
136E GLY 3.3 5.1 + - - +
138E GLU* 1.3 74.1 - - - +
140E ALA* 1.3 65.5 + - - +
142E ARG* 3.1 32.4 + - - +
143E VAL* 3.3 20.3 + - - +
444E GLU* 3.3 31.6 - - - +
448E MET* 3.7 12.8 - - + -
167G LEU* 5.0 15.6 - - - +
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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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136E GLY 2.8 17.9 + - - +
137E TYR* 3.6 7.2 - - - +
139E GLN* 1.3 77.1 - - - +
141E ALA* 1.3 60.7 + - - +
143E VAL* 3.4 21.1 - - - +
144E ALA 3.5 5.7 + - - -
433E VAL* 4.0 0.9 - - + -
447E ALA 4.4 0.2 - - - +
448E MET* 3.7 21.7 - - + +
451E PHE* 3.5 44.7 - - + -
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Residues in contact with ALA 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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137E TYR 2.9 14.7 + - - +
138E GLU* 3.1 12.5 + - - +
140E ALA* 1.3 76.0 - - - +
142E ARG* 1.3 64.1 + - - +
144E ALA 3.6 0.2 + - - -
145E ILE* 3.2 32.2 + - + +
451E PHE* 4.1 6.0 - - + -
517E ILE* 3.7 18.5 - - + +
521E THR* 3.8 27.8 - - + -
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Residues in contact with ARG 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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138E GLU* 3.0 26.4 + - - +
139E GLN* 3.1 32.7 + - - +
141E ALA* 1.3 79.0 - - - +
143E VAL* 1.3 58.2 + - + +
145E ILE* 3.3 11.2 + - - +
146E GLU* 2.8 28.3 + - - +
166G LYS* 5.9 0.4 - - - +
167G LEU* 4.0 37.9 + - - +
381G PHE* 3.9 19.8 - - - -
384G GLU* 3.7 24.0 + - - -
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Residues in contact with VAL 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E GLN* 3.6 22.4 - - - +
140E ALA* 3.4 20.6 - - - +
142E ARG* 1.3 74.8 - - + +
144E ALA* 1.3 59.8 + - - +
146E GLU* 3.4 23.5 - - - +
147E HIS* 3.0 24.6 + - - +
150E LYS* 5.5 0.2 + - - -
432E ALA* 5.2 3.5 - - - +
433E VAL* 3.8 18.1 - - + +
436E GLU* 3.8 42.8 - - + +
440E CYS* 6.1 1.3 - - - -
448E MET* 4.7 6.5 - - + -
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Residues in contact with ALA 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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140E ALA 3.5 3.7 + - - +
141E ALA 3.9 4.3 - - - +
142E ARG 3.2 0.8 - - - -
143E VAL* 1.3 80.0 - - - +
145E ILE* 1.3 60.4 + - - +
147E HIS* 2.9 21.4 + - - +
148E LEU* 3.1 21.0 + - - +
429E CYS* 3.9 11.4 - - + -
433E VAL* 4.1 9.2 - - + -
451E PHE* 3.7 32.5 - - + -
455E LEU* 6.1 0.4 - - + -
517E ILE* 4.1 12.6 - - + -
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Residues in contact with ILE 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 ALA* 3.2 22.7 + - + +
142E ARG* 3.7 9.9 - - - +
144E ALA* 1.3 74.7 - - - +
146E GLU* 1.3 61.7 + - - +
148E LEU* 3.3 14.3 + - - +
149E ASP* 3.5 19.2 + - - +
514E LYS* 3.7 38.1 - - + +
517E ILE* 3.7 30.7 - - + -
518E SER* 5.0 9.0 - - - +
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Residues in contact with GLU 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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142E ARG 2.8 17.0 + - - +
143E VAL* 3.4 29.2 - - - +
144E ALA 3.2 0.2 - - - -
145E ILE* 1.3 76.5 - - - +
147E HIS* 1.3 59.5 + - - +
149E ASP* 3.5 22.8 + - - +
150E LYS* 2.9 25.3 + - - +
436E GLU* 5.3 5.6 - - - +
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Residues in contact with HIS 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E VAL 3.0 12.5 + - - +
144E ALA* 2.9 11.4 + - - +
146E GLU* 1.3 74.2 - - - +
148E LEU* 1.3 60.7 + - - +
149E ASP 3.1 0.4 - - - -
150E LYS* 2.9 42.3 + - - +
151E ILE* 3.0 18.0 + - + +
428E SER* 3.0 42.0 + - - -
429E CYS* 3.3 20.2 - - - -
431E LEU* 6.0 1.8 - - + -
432E ALA* 3.4 24.3 - - + +
486E ASN* 3.6 14.9 + - - -
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Residues in contact with LEU 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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144E ALA 3.1 24.0 + - - +
145E ILE* 3.3 10.5 + - + +
147E HIS* 1.3 76.2 - - - +
149E ASP* 1.3 59.3 + - - +
151E ILE* 2.9 34.3 - - + +
417E ARG* 3.7 0.9 + - - -
419E VAL* 4.9 3.6 - - + -
425E ALA* 5.6 2.9 - - + -
429E CYS* 3.7 20.0 - - - -
510E LEU* 3.3 41.4 - - + +
513E LYS* 3.8 18.4 - - + -
514E LYS* 3.6 37.2 - - + +
517E ILE* 3.8 15.0 - - + -
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Residues in contact with ASP 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E ILE* 3.6 19.6 - - - +
146E GLU* 3.6 15.1 - - - +
147E HIS 3.1 0.8 - - - -
148E LEU* 1.3 78.4 - - - +
150E LYS* 1.3 62.7 + - + +
151E ILE 4.3 1.9 - - - +
153E ASP* 6.2 0.3 - - - -
154E SER* 5.6 0.5 + - - -
417E ARG* 3.2 28.5 + - - +
510E LEU* 4.7 2.9 - - - +
514E LYS* 5.4 5.0 + - - +
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Residues in contact with LYS 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E GLU* 2.9 42.7 + - - +
147E HIS* 2.9 31.0 + - - +
149E ASP* 1.3 77.9 - - + +
151E ILE* 1.3 63.1 + - - +
152E SER 3.6 1.7 + - - -
153E ASP* 5.1 1.7 + - - -
486E ASN* 3.7 27.4 + - - +
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Residues in contact with ILE 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E HIS* 3.0 43.6 + - + +
148E LEU* 2.9 27.0 + - + +
149E ASP 4.3 2.1 - - - +
150E LYS* 1.3 78.5 - - - +
152E SER* 1.3 82.0 + - - +
153E ASP* 5.0 0.2 - - - -
154E SER* 5.3 0.2 + - - -
417E ARG* 5.2 0.9 + - - -
419E VAL* 4.4 15.5 - - + -
420E TYR 5.2 1.3 - - - +
425E ALA* 4.5 12.6 - - + -
428E SER* 3.9 11.9 - - - +
429E CYS* 3.7 15.9 - - - -
486E ASN* 3.3 26.5 - - + +
487E PRO* 5.1 11.7 - - + +
510E LEU* 3.8 4.0 - - + +
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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