Contacts of the helix formed by residues 103 - 127 (chain E) in PDB entry 5SV1
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 103 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A MLY 3.6 26.3 - - - -
225A ASP* 3.6 19.4 - - - +
229A SER* 4.0 2.4 + - - +
101E SER* 3.3 13.5 + - - +
102E ASP* 1.3 75.5 - - - +
104E ASN* 1.3 63.0 + - - +
105E GLU* 3.3 26.3 + - - +
106E GLY 3.7 10.2 + - - -
107E ILE* 3.7 16.1 + - - +
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Residues in contact with ASN 104 (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 SER 4.6 6.2 - - - +
102E ASP 3.5 6.7 + - - +
103E ASP* 1.3 70.9 + - - +
105E GLU* 1.3 68.6 + - - +
106E GLY 2.8 3.8 + - - -
107E ILE* 2.9 32.8 + - - +
108E MLY 3.3 27.1 + - - +
224E LEU* 3.7 33.6 + - + +
225E ASP* 5.5 1.3 + - - +
227E GLU* 6.1 0.2 - - - +
228E ALA* 3.6 28.9 - - - +
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Residues in contact with GLU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLU* 5.4 4.9 - - - +
103E ASP* 3.3 13.4 + - - +
104E ASN* 1.3 77.6 - - - +
106E GLY* 1.3 58.8 + - - +
108E MLY 4.1 22.5 - - - +
109E GLU* 3.5 30.8 + - - +
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Residues in contact with GLY 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A MLY 4.2 11.2 - - - -
221A SER* 5.6 0.2 - - - -
225A ASP* 4.1 16.4 - - - -
103E ASP* 3.6 8.2 + - - -
104E ASN 2.8 1.8 + - - -
105E GLU* 1.3 77.0 - - - +
107E ILE* 1.3 65.2 + - - +
109E GLU* 2.9 25.9 + - - +
110E ARG* 3.0 18.5 + - - +
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Residues in contact with ILE 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E GLU* 4.5 7.1 - - + +
95E LEU* 3.9 24.9 - - + +
98E SER* 3.9 23.3 - - - +
101E SER* 5.0 7.2 - - - +
103E ASP 3.7 12.0 + - - +
104E ASN* 2.9 31.5 + - - +
106E GLY* 1.3 68.1 - - - -
108E MLY 1.3 65.0 + - - +
110E ARG* 3.0 28.7 + - - +
111E THR* 3.0 24.0 + - - +
220E GLN* 4.2 9.6 - - - +
224E LEU* 3.6 21.8 - - + -
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Residues in contact with MLY 108 (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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103D ASP* 3.7 13.7 - - - -
105D GLU 5.5 0.2 - - - -
106D GLY* 4.0 18.6 - - - -
109D GLU* 3.7 22.9 - - - +
104E ASN* 3.7 15.5 - - - +
105E GLU* 4.1 31.0 - - - +
107E ILE* 1.3 73.8 + - - +
109E GLU* 1.3 66.7 + - + +
111E THR* 3.0 12.3 + - - -
112E SER* 3.1 13.4 + - - -
217E LEU* 5.1 1.0 - - - +
220E GLN* 4.4 10.5 - - - +
221E SER* 3.4 42.8 - - - +
224E LEU* 4.2 18.4 - - + -
225E ASP* 2.8 29.4 + - - -
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Residues in contact with GLU 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLU* 4.9 8.9 - - - +
108A MLY 3.9 22.5 - - - -
221A SER* 5.4 1.0 + - - -
105E GLU* 3.5 26.2 - - - +
106E GLY* 2.9 13.5 + - - +
108E MLY 1.3 76.3 + - + +
110E ARG* 1.3 66.7 + - + +
111E THR 3.0 0.2 + - - -
112E SER* 3.0 22.2 + - - -
113E PHE* 3.1 7.9 + - - +
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Residues in contact with ARG 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LEU* 3.9 25.0 - - + +
221A SER* 3.1 26.8 + - - +
222A ARG* 3.5 24.8 - - - +
225A ASP* 2.6 44.5 + - - +
94E GLU* 3.3 25.1 + - - +
98E SER* 2.9 25.9 + - - -
101E SER* 4.6 4.6 + - - -
103E ASP 4.8 0.4 + - - -
106E GLY* 3.0 4.8 + - - +
107E ILE* 3.0 44.1 + - - +
109E GLU* 1.3 80.1 - - + +
111E THR* 1.3 62.8 + - - +
113E PHE* 3.7 3.4 + - - +
114E ARG* 3.1 28.2 + - - +
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Residues in contact with THR 111 (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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90E GLU 5.6 0.4 - - - -
91E ALA* 4.2 20.2 - - + -
94E GLU* 3.7 14.8 - - + +
107E ILE 3.0 10.7 + - - -
108E MLY 3.0 8.0 + - - -
110E ARG* 1.3 76.1 - - - +
112E SER* 1.3 64.9 + - - +
114E ARG* 3.0 9.4 + - + +
115E LEU* 2.9 26.3 + - + +
216E VAL* 5.6 0.2 - - + -
217E LEU* 3.5 17.9 - - + -
220E GLN* 2.8 43.0 + - + +
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Residues in contact with SER 112 (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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108E MLY 3.1 8.8 + - - -
109E GLU* 3.0 16.2 + - - -
111E THR* 1.3 75.9 - - - +
113E PHE* 1.3 74.1 + - - +
115E LEU* 3.0 1.6 + - - -
116E GLU* 2.9 34.1 + - - +
217E LEU* 3.7 32.7 - - - +
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Residues in contact with PHE 113 (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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116A GLU* 5.2 11.2 - - - -
210A GLY 5.5 0.2 - - - -
214A ALA* 3.5 38.4 - - + -
217A LEU* 4.4 19.5 - - + -
218A LEU* 4.1 21.1 - - + -
109E GLU 3.1 7.0 + - - +
110E ARG* 3.9 8.3 - - - +
112E SER* 1.3 83.6 + - - +
114E ARG* 1.3 66.6 + - - +
116E GLU* 5.2 2.5 - - + -
117E ARG* 3.4 42.3 + - + +
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Residues in contact with ARG 114 (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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218A LEU* 3.7 25.9 - - + +
222A ARG* 4.4 4.5 - - - +
90E GLU* 2.6 64.2 + - + +
93E ASN* 3.3 27.7 + - - -
94E GLU* 3.2 34.4 + - - +
97E LEU* 4.7 1.2 - - - +
110E ARG 3.1 14.8 - - - +
111E THR* 3.0 7.9 + - + +
113E PHE* 1.3 75.8 - - - +
115E LEU* 1.3 67.8 + - + +
117E ARG* 3.0 15.3 + - - +
118E ARG* 3.0 12.6 + - - +
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Residues in contact with LEU 115 (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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87E LEU* 3.8 40.2 - - + +
90E GLU* 3.8 18.2 - - + -
91E ALA 4.8 1.1 - - - +
111E THR* 2.9 22.8 + - + +
112E SER* 3.8 2.0 - - - +
114E ARG* 1.3 76.9 - - + +
116E GLU* 1.3 66.0 + - + +
118E ARG* 2.9 17.4 + - + +
119E VAL* 3.0 15.9 + - - +
213E ALA* 4.1 21.1 - - + +
216E VAL* 3.8 26.5 - - + -
217E LEU* 3.7 31.4 - - + -
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Residues in contact with GLU 116 (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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113D PHE* 3.9 23.6 - - - -
117D ARG* 5.6 3.3 + - - -
112E SER* 2.9 29.1 + - - +
113E PHE* 4.7 3.1 - - + +
115E LEU* 1.3 72.9 - - - +
117E ARG* 1.3 65.5 + - + +
119E VAL* 3.0 19.6 + - - +
120E ALA* 2.8 20.9 + - - +
210E GLY* 5.2 9.1 - - - +
213E ALA* 5.0 9.6 - - - +
214E ALA 5.4 0.5 + - - -
217E LEU* 4.3 8.7 - - + +
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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
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206A LYS 5.0 0.2 + - - -
207A ALA* 3.4 21.2 + - - +
210A GLY* 3.6 21.9 + - - -
211A ASP* 2.5 32.6 + - - +
214A ALA* 3.9 13.2 - - - -
113E PHE* 3.4 44.4 + - + +
114E ARG* 3.0 5.1 + - - +
116E GLU* 1.3 79.7 - - + +
118E ARG* 1.3 52.3 + - - +
120E ALA* 3.0 11.6 + - + +
121E ALA* 2.7 36.0 + - - +
124E ARG* 4.5 14.0 + - - +
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Residues in contact with ARG 118 (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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83E LEU* 5.9 2.8 - - - +
86E HIS* 3.8 41.2 + - - +
87E LEU* 4.1 21.3 - - + -
90E GLU* 3.3 39.3 + - + +
114E ARG 3.0 10.1 + - - +
115E LEU* 2.9 13.6 + - + +
117E ARG* 1.3 74.1 - - - +
119E VAL* 1.3 63.8 + - - +
121E ALA* 3.0 11.2 + - - +
122E VAL* 2.9 33.0 + - + +
209E LEU* 5.7 0.2 - - - -
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Residues in contact with VAL 119 (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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87E LEU* 5.1 5.4 - - + -
115E LEU 3.0 11.4 + - - +
116E GLU* 3.0 16.9 + - - +
118E ARG* 1.3 74.5 - - - +
120E ALA* 1.3 65.2 + - - +
122E VAL* 2.9 5.0 + - - +
123E GLY* 2.8 19.9 + - - -
206E LYS* 4.1 34.5 - - + +
209E LEU* 4.0 34.1 - - + +
210E GLY* 4.5 5.6 - - - +
213E ALA* 4.2 22.2 - - + -
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Residues in contact with ALA 120 (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 GLU 2.8 15.0 + - - +
117E ARG* 3.0 16.1 + - + +
119E VAL* 1.3 73.6 - - - +
121E ALA* 1.3 65.2 + - - +
123E GLY* 3.0 12.8 + - - +
124E ARG* 3.0 33.8 + - - +
206E LYS* 5.7 7.9 - - - +
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Residues in contact with ALA 121 (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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211A ASP* 5.1 7.2 - - - +
117E ARG 2.7 16.6 + - - +
118E ARG* 3.4 15.5 - - - +
120E ALA* 1.3 71.0 - - - +
122E VAL* 1.3 64.5 + - + +
124E ARG* 3.0 25.6 + - - +
125E GLN* 2.9 24.8 + - - +
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Residues in contact with VAL 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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83E LEU* 4.5 21.5 - - + -
118E ARG* 2.9 24.9 + - + +
119E VAL 3.5 6.5 - - - +
121E ALA* 1.3 74.6 - - + +
123E GLY* 1.3 64.6 + - - +
125E GLN* 2.9 20.5 + - + +
126E MET* 2.8 42.5 + - + +
205E PHE* 4.6 8.1 - - + -
209E LEU* 3.9 26.7 - - + -
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Residues in contact with GLY 123 (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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119E VAL 2.8 16.6 + - - -
120E ALA* 3.0 6.0 + - - -
122E VAL* 1.3 72.7 - - - +
124E ARG* 1.3 57.6 + - - +
126E MET* 2.9 25.6 + - - +
127E GLY* 3.2 10.0 + - - -
202E ILE* 5.0 7.0 - - - +
206E LYS* 5.0 20.0 - - - -
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Residues in contact with ARG 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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203A GLY 5.0 2.9 - - - -
204A GLY* 4.9 9.4 - - - +
207A ALA* 3.4 36.2 - - - +
211A ASP* 4.6 9.3 + - - -
117E ARG* 4.5 16.0 + - - +
120E ALA* 3.0 28.7 + - - +
121E ALA* 3.0 33.9 + - - +
123E GLY* 1.3 74.9 - - - +
125E GLN* 1.3 61.6 + - - +
126E MET 3.5 0.5 + - - -
127E GLY* 3.6 9.0 + - - +
128E ARG* 3.7 27.8 + - - +
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Residues in contact with GLN 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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44E LYS* 4.6 6.4 + - - -
47E GLU* 5.7 1.0 - - - +
121E ALA* 2.9 14.4 + - - +
122E VAL* 2.9 22.5 + - + +
124E ARG* 1.3 76.0 - - - +
126E MET* 1.3 61.9 + - - +
128E ARG* 3.9 37.2 + - - +
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Residues in contact with MET 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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44E LYS* 3.6 24.0 - - - +
47E GLU* 6.1 1.1 - - - +
48E PHE* 3.9 25.4 - - + -
51E GLN* 6.5 0.4 - - - -
122E VAL* 2.8 29.4 + - + +
123E GLY* 2.9 10.9 + - - +
125E GLN* 1.3 76.8 - - - +
127E GLY* 1.3 56.3 + - - +
128E ARG 3.2 5.9 + - - -
130E ASN* 4.6 1.7 + - - -
202E ILE* 3.6 40.3 - - + +
205E PHE* 3.4 42.8 - - + -
206E LYS* 6.1 1.6 - - + +
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Residues in contact with GLY 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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200A ARG* 5.3 3.8 + - - -
123E GLY 3.2 8.5 + - - -
124E ARG* 3.6 5.9 + - - -
125E GLN 3.5 0.2 - - - -
126E MET* 1.3 77.6 - - - +
128E ARG* 1.3 62.8 + - - +
129E GLY 3.3 0.7 + - - -
130E ASN* 3.1 24.8 + - - +
131E GLY 4.1 3.6 + - - -
202E ILE* 3.7 14.3 - - - +
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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