Contacts of the helix formed by residues 112 - 137 (chain E) in PDB entry 3EAB
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 GLU 112 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E MET* 1.3 88.8 - - + +
113E ALA* 1.3 57.5 + - - +
114E GLU 3.2 0.4 - - - -
115E ARG* 3.0 43.3 + - - +
116E VAL* 3.0 11.2 + - - +
162E VAL* 3.6 14.6 - - + +
163E ILE* 2.8 32.8 + - - +
164E VAL* 3.9 7.4 - - + +
165E THR* 3.4 30.2 + - - +
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Residues in contact with ALA 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E MET 3.7 9.5 - - - +
112E GLU* 1.3 77.2 - - - +
114E GLU* 1.3 65.5 + - - +
116E VAL* 3.1 12.4 + - - +
117E ARG* 3.0 40.5 + - - +
164E VAL* 4.3 11.7 - - + +
170E GLN 5.6 1.1 - - - +
171E CYS* 6.2 0.7 - - - -
174E ALA* 3.9 26.2 - - + +
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Residues in contact with GLU 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E MET* 3.6 20.6 - - + +
112E GLU 3.2 0.4 - - - -
113E ALA* 1.3 78.2 - - - +
115E ARG* 1.3 63.0 + - + +
117E ARG* 2.6 60.4 + - - +
118E VAL* 3.0 27.7 + - + +
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Residues in contact with ARG 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E MET* 4.4 18.4 - - + +
112E GLU* 3.0 32.6 + - - +
114E GLU* 1.3 77.7 - - + +
116E VAL* 1.3 61.3 - - - +
118E VAL* 2.5 36.0 - - + +
119E PHE* 3.1 19.6 - - + -
162E VAL* 3.7 43.3 - - + +
163E ILE 5.4 0.8 - - - +
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Residues in contact with VAL 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E GLU 3.0 13.1 + - - +
113E ALA* 3.1 10.7 + - - +
115E ARG* 1.3 77.2 - - - +
117E ARG* 1.3 57.3 + - - +
119E PHE* 3.3 8.7 + - - +
120E HIS* 3.0 24.9 + - - +
159E GLY* 3.7 9.6 - - - +
162E VAL* 3.7 27.1 - - + -
164E VAL* 4.1 11.9 - - + -
174E ALA* 5.0 3.6 - - + +
177E LEU* 3.7 27.8 - - + -
178E GLN* 3.9 15.9 - - + +
181E MET* 4.0 18.1 - - - +
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Residues in contact with ARG 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E MET* 6.0 0.6 - - - +
113E ALA* 3.0 26.1 + - - +
114E GLU* 2.6 48.5 + - - +
116E VAL* 1.3 73.9 - - - +
118E VAL* 1.3 63.8 + - - +
120E HIS* 3.2 11.0 + - + +
121E LYS* 2.9 22.5 + - - +
174E ALA* 5.7 0.2 - - - +
177E LEU* 4.4 16.8 - - + -
174K GLY* 3.3 29.2 + - - -
177K GLY* 3.5 34.2 - - - -
178K THR* 3.0 22.2 + - - +
181K ALA* 4.7 5.4 - - + -
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Residues in contact with VAL 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E GLU* 3.0 32.4 + - + +
115E ARG* 2.5 39.9 - - + +
117E ARG* 1.3 73.8 - - - +
119E PHE* 1.3 83.7 + - + +
121E LYS* 3.0 18.5 + - - +
122E GLN* 3.1 18.5 + - + +
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Residues in contact with PHE 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E ARG* 3.1 34.9 + - + -
116E VAL* 3.8 3.8 - - - +
118E VAL* 1.3 86.9 - - + +
120E HIS* 1.3 61.6 + - - +
122E GLN* 3.2 3.0 + - + +
123E ALA* 2.7 31.1 + - - +
155E GLU* 3.6 35.0 - - - +
158E LYS* 3.6 39.5 - - + -
159E GLY* 3.6 22.9 - - - -
162E VAL* 3.7 22.2 - - + -
181E MET* 4.3 2.5 - - + -
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Residues in contact with HIS 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E VAL 3.0 11.3 + - - +
117E ARG* 3.2 12.8 + - - +
119E PHE* 1.3 76.1 - - - +
121E LYS* 1.3 64.4 + - + +
123E ALA* 4.2 2.2 - - - -
124E PHE* 2.7 44.4 + + + +
177E LEU* 4.8 2.9 - - + +
181E MET* 3.4 21.4 - - + +
180K VAL* 5.7 1.1 - - + -
181K ALA* 3.4 42.7 + - + -
184K GLU* 2.8 38.7 + - + -
185K GLN* 3.1 31.8 + - - +
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Residues in contact with LYS 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E ARG 2.9 13.4 + - - +
118E VAL* 3.0 12.3 + - - +
120E HIS* 1.3 84.3 - - + +
122E GLN* 1.3 75.1 + - - +
124E PHE* 3.7 3.8 - - - +
125E GLU* 3.0 23.7 + - + +
154K GLN* 5.4 4.2 - - - +
158K ASP* 4.2 22.0 - - - +
163K ASP 5.3 10.5 - - - -
184K GLU* 5.7 0.4 - - - -
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Residues in contact with GLN 122 (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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118E VAL* 3.1 13.6 + - + +
119E PHE* 3.7 1.8 - - + +
121E LYS* 1.3 92.7 - - - +
123E ALA* 1.3 63.5 + - - +
124E PHE 3.1 0.5 + - - -
125E GLU* 3.3 6.6 + - - +
126E TYR* 3.0 50.7 + - + -
155E GLU* 3.2 32.1 - - + +
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Residues in contact with ALA 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E PHE 2.7 21.2 + - - +
120E HIS* 3.6 6.7 - - - +
122E GLN* 1.3 72.9 - - - +
124E PHE* 1.3 57.8 + - - +
126E TYR* 3.3 0.7 + - - +
127E ILE* 2.9 38.0 + - + +
152E GLY* 4.0 7.4 - - - +
155E GLU* 3.6 18.3 - - + +
156E LEU* 3.6 34.3 - - + +
185K GLN* 5.1 1.8 - - - +
188K LEU* 5.4 0.4 - - + -
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Residues in contact with PHE 124 (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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120E HIS* 2.7 33.0 + + + +
121E LYS* 3.7 3.1 - - - +
123E ALA* 1.3 71.5 - - - +
125E GLU* 1.3 64.9 + - - +
127E ILE* 4.0 0.3 - - - +
128E SER* 2.8 46.3 + - - -
155K GLU 5.3 0.2 - - - -
158K ASP* 3.7 12.1 - - + -
159K GLU* 3.7 44.9 - - + -
184K GLU* 3.7 52.9 - - + -
187K GLU* 3.5 20.0 - - + -
188K LEU* 3.9 24.2 - - + -
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Residues in contact with GLU 125 (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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121E LYS* 3.0 14.1 + - + +
122E GLN* 3.5 13.7 - - - +
124E PHE* 1.3 80.9 - - - +
126E TYR* 1.3 74.1 + - + +
128E SER* 3.0 5.1 + - - -
129E ILE* 2.9 43.9 + - - +
158K ASP 5.2 4.7 - - - +
159K GLU 5.4 0.5 - - - +
161K GLY* 3.6 27.1 + - - -
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Residues in contact with TYR 126 (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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122E GLN* 3.0 37.9 + - + +
125E GLU* 1.3 90.6 - - + +
127E ILE* 1.3 58.4 + - - +
129E ILE* 3.2 2.0 + - - +
130E ALA* 2.9 26.9 + - - +
148E TRP* 3.6 53.6 - + + +
151E LYS* 3.6 37.3 - - + +
152E GLY* 3.6 6.1 - - - +
155E GLU* 3.9 22.2 - - + -
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Residues in contact with ILE 127 (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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123E ALA 2.9 18.5 + - - +
124E PHE 4.4 0.2 - - - +
126E TYR* 1.3 76.7 - - - +
128E SER* 1.3 56.5 + - - +
130E ALA* 3.6 4.9 - - - +
131E LEU* 2.8 47.5 + - + +
148E TRP 4.9 1.3 - - - +
149E TYR* 4.5 18.4 - - + +
152E GLY* 3.7 22.0 - - - -
153E ILE 4.7 1.1 - - - +
156E LEU* 4.0 31.2 - - + -
184E ASN* 5.7 0.9 - - + +
188E ALA* 5.0 8.5 - - + -
188K LEU* 4.0 28.0 - - + -
192K LEU* 5.1 9.4 - - + -
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Residues in contact with SER 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E PHE* 2.8 41.5 + - - -
125E GLU* 3.0 7.8 + - - -
127E ILE* 1.3 76.1 - - - +
129E ILE* 1.3 61.0 + - - +
131E LEU* 3.2 10.7 + - - +
132E ARG* 2.9 27.5 + - - +
158K ASP 5.5 0.4 - - - -
159K GLU* 3.4 34.5 + - - -
188K LEU* 4.5 3.0 - - - +
191K ARG* 4.2 6.4 + - - +
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Residues in contact with ILE 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E GLU* 2.9 37.1 + - - +
126E TYR* 3.7 6.3 - - - +
128E SER* 1.3 76.7 - - - +
130E ALA* 1.3 65.8 + - - +
132E ARG* 2.8 23.9 + - + +
133E ILE* 2.9 29.6 + - + +
148E TRP* 4.3 30.7 - - + -
159K GLU 5.9 2.5 - - - +
160K ALA 6.4 1.3 - - - -
161K GLY 6.3 0.2 - - - +
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Residues in contact with ALA 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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126E TYR 2.9 17.5 + - - +
127E ILE* 3.6 6.5 - - - +
129E ILE* 1.3 75.4 - - - +
131E LEU* 1.3 58.5 + - - +
133E ILE* 3.4 0.4 + - - -
134E ASP* 2.9 33.1 + - - +
145E ALA* 3.7 8.8 - - - +
148E TRP* 3.6 9.1 - - + +
149E TYR* 3.6 49.6 - - + +
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Residues in contact with LEU 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E ILE* 2.8 41.1 + - + +
128E SER* 3.7 6.5 - - - +
130E ALA* 1.3 73.8 - - - +
132E ARG* 1.3 66.1 + - - +
134E ASP* 3.7 3.8 - - - +
135E GLU* 2.9 42.2 + - - +
149E TYR* 3.8 14.6 - - - +
188K LEU* 3.8 19.3 - - + -
191K ARG* 4.0 45.3 - - + +
192K LEU* 3.9 23.1 - - + -
194K ARG* 5.3 8.3 - - + -
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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
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128E SER 2.9 14.2 + - - +
129E ILE* 2.8 21.7 + - + +
131E LEU* 1.3 80.1 - - - +
133E ILE* 1.3 69.0 + - + +
135E GLU* 3.3 4.8 + - - +
136E ASP* 3.2 37.8 + - - +
159K GLU* 5.8 1.8 + - - -
160K ALA* 5.8 6.1 - - - +
191K ARG* 4.3 17.7 - - - +
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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
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129E ILE* 2.9 28.6 + - + +
130E ALA* 4.0 2.2 - - - +
132E ARG* 1.3 81.5 - - + +
134E ASP* 1.3 68.8 + - - +
136E ASP* 3.0 9.0 + - + +
137E GLU* 2.9 43.2 + - + +
142E LYS 5.3 0.2 - - - +
144E GLN* 4.1 24.0 - - + +
145E ALA* 4.1 11.4 - - + +
148E TRP* 5.1 8.1 - - + +
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Residues in contact with ASP 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 ALA 2.9 19.8 + - - +
131E LEU* 3.7 4.3 - - - +
133E ILE* 1.3 80.0 - - - +
135E GLU* 1.3 58.4 + - + +
136E ASP 3.2 0.3 + - - -
137E GLU 3.5 2.9 + - - -
142E LYS* 2.5 48.6 + - - +
145E ALA* 3.9 9.0 - - + +
149E TYR* 2.6 25.6 + - - +
191E ARG* 2.8 40.6 + - - -
195E LEU* 4.2 8.7 - - - -
194K ARG* 3.5 9.6 + - - +
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Residues in contact with GLU 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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131E LEU* 2.9 31.0 + - - +
132E ARG* 3.7 6.2 - - - +
134E ASP* 1.3 74.7 - - - +
136E ASP* 1.3 64.7 + - - +
137E GLU 4.2 2.3 - - - +
142E LYS* 4.6 1.2 + - - -
191K ARG* 3.4 48.5 + - - +
194K ARG* 3.2 42.2 + - - +
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Residues in contact with ASP 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E ARG* 3.2 29.7 + - - +
133E ILE* 3.0 13.4 + - + +
135E GLU* 1.3 81.2 - - - +
137E GLU* 1.3 74.8 + - + +
138E LYS* 3.7 3.8 + - - +
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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
----------------------------------------------------------
133E ILE* 2.9 33.6 + - + +
134E ASP 3.5 0.2 + - - -
135E GLU 4.2 1.4 - - - +
136E ASP* 1.3 86.7 - - + +
138E LYS* 1.3 71.8 + - - +
141E GLN* 3.3 43.2 - - - +
142E LYS* 3.1 21.5 + - + +
144E GLN* 2.6 24.0 - - - +
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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