Contacts of the helix formed by residues 103 - 127 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101D SER* 3.3 12.8 + - - +
102D ASP* 1.3 75.5 - - - +
104D ASN* 1.3 63.6 + - - +
105D GLU* 3.2 21.0 + - - +
106D GLY* 3.5 15.9 + - - -
107D ILE* 3.7 12.8 + - - +
108E MLY 3.7 25.3 - - - -
225E ASP* 3.5 19.2 - - - +
229E SER* 4.3 3.5 + - - +
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Residues in contact with ASN 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D SER 5.0 3.8 - - - +
102D ASP 3.5 8.9 + - - +
103D ASP* 1.3 71.6 + - - +
105D GLU* 1.3 66.7 + - - +
106D GLY 3.1 2.7 + - - -
107D ILE* 3.4 12.6 + - - +
108D MLY 3.3 36.4 + - - +
224D LEU* 2.8 58.7 + - + +
227D GLU* 5.3 3.3 + - - +
228D ALA* 3.1 22.4 - - + +
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Residues in contact with GLU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ASP* 4.7 4.8 - - - +
105C GLU* 3.5 28.2 - - - +
109C GLU* 3.8 13.0 - - - +
103D ASP* 3.2 12.6 + - - +
104D ASN* 1.3 78.3 - - - +
106D GLY* 1.3 63.2 + - - +
108D MLY 3.9 29.0 - - + +
109D GLU* 3.5 32.1 + - + +
108E MLY 5.5 0.4 - - - -
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Residues in contact with GLY 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ASP* 3.5 9.8 + - - -
104D ASN 3.1 0.6 - - - -
105D GLU* 1.3 76.3 - - - +
107D ILE* 1.3 69.3 + - - +
109D GLU* 2.9 15.1 + - - +
110D ARG* 3.1 30.3 + - - +
108E MLY 4.0 17.5 - - - -
225E ASP* 3.9 8.7 - - - -
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Residues in contact with ILE 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D GLU* 4.7 5.6 - - + +
95D LEU* 3.9 22.9 - - + +
98D SER* 3.6 35.4 - - - +
101D SER* 5.2 6.5 - - - +
103D ASP 3.7 10.5 + - - +
104D ASN* 3.4 17.8 + - - +
106D GLY* 1.3 73.4 - - - +
108D MLY 1.3 65.6 + - - +
110D ARG* 3.0 16.4 + - - +
111D THR* 2.8 26.3 + - - +
220D GLN* 3.4 25.6 - - - +
224D LEU* 3.7 16.2 - - + -
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Residues in contact with MLY 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ASP* 3.5 14.4 - - - -
106C GLY* 4.0 17.3 - - - -
109C GLU* 3.7 24.2 - - - +
104D ASN* 3.3 17.7 - - - +
105D GLU* 3.9 39.9 - - + +
106D GLY 3.2 0.4 - - - -
107D ILE* 1.3 77.1 + - - +
109D GLU* 1.3 64.7 + - + +
111D THR* 3.0 2.3 + - - -
112D SER* 2.9 27.2 + - - +
217D LEU* 5.1 0.3 - - - +
220D GLN* 4.3 11.7 - - - +
221D SER* 3.8 38.4 - - - +
224D LEU* 4.2 18.6 - - + -
225D ASP* 2.7 28.1 + - - -
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Residues in contact with GLU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D GLU* 3.5 25.9 + - + +
106D GLY 2.9 10.0 + - - +
108D MLY 1.3 75.6 - - + +
110D ARG* 1.3 66.4 + - + +
112D SER* 2.9 6.2 + - - -
113D PHE* 2.9 22.5 + - - +
108E MLY 3.7 25.6 - - - +
221E SER* 5.1 0.7 + - - -
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Residues in contact with ARG 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D GLU* 3.2 25.4 + - - +
98D SER* 3.1 26.4 + - - -
101D SER* 4.7 3.6 + - - -
106D GLY* 3.1 16.4 + - - +
107D ILE* 3.0 33.1 + - - +
109D GLU* 1.3 77.6 - - + +
111D THR* 1.3 64.2 + - - +
113D PHE* 3.1 4.9 + - - +
114D ARG* 2.8 27.9 + - - +
218E LEU* 3.6 36.3 - - + -
221E SER* 3.3 24.2 + - - +
222E ARG* 3.6 20.6 - - - +
225E ASP* 2.8 40.2 + - - +
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Residues in contact with THR 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D GLU 5.4 0.4 - - - +
91D ALA* 4.0 23.6 - - + +
94D GLU* 3.5 17.6 - - - +
107D ILE* 2.8 11.2 + - - +
108D MLY 3.4 4.9 - - - -
110D ARG* 1.3 75.4 - - - +
112D SER* 1.3 63.7 + - - +
114D ARG* 3.0 7.9 + - + +
115D LEU* 2.8 27.2 + - + +
217D LEU* 3.6 14.8 - - + -
220D GLN* 2.9 44.9 + - - +
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Residues in contact with SER 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D MLY 2.9 15.4 + - - +
109D GLU* 3.5 9.1 - - - -
111D THR* 1.3 75.4 - - - +
113D PHE* 1.3 53.9 + - - +
115D LEU* 3.0 2.9 + - - +
116D GLU* 2.7 47.0 + - - +
217D LEU* 3.4 32.8 - - - +
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Residues in contact with PHE 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D GLU 2.9 12.2 + - - +
110D ARG* 3.4 12.1 - - - +
112D SER* 1.3 75.3 - - - +
114D ARG* 1.3 66.8 + - - +
116D GLU* 3.0 16.3 + - + +
117D ARG* 3.1 27.9 + - + +
116E GLU* 3.9 21.1 - - - -
214E ALA* 3.3 39.5 - - + -
217E LEU* 4.4 15.5 - - + -
218E LEU* 4.1 20.2 - - + -
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Residues in contact with ARG 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D GLU* 3.0 65.6 + - + +
93D ASN* 3.1 29.1 + - - +
94D GLU* 3.2 36.7 + - - +
97D LEU* 4.8 2.2 - - - +
110D ARG 2.8 21.0 + - - +
111D THR* 3.4 7.2 - - + +
113D PHE* 1.3 71.4 - - - +
115D LEU* 1.3 65.1 + - + +
117D ARG* 3.0 18.4 + - - +
118D ARG* 3.2 12.3 + - - +
218E LEU* 3.6 26.2 - - + +
222E ARG* 4.8 0.8 - - - +
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Residues in contact with LEU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D LEU* 3.8 43.1 - - + +
90D GLU* 4.2 13.7 - - + +
91D ALA* 4.9 1.6 - - + +
111D THR* 2.8 25.2 + - + +
112D SER* 3.7 4.5 - - - +
114D ARG* 1.3 73.7 - - + +
116D GLU* 1.3 64.1 + - + +
118D ARG* 3.0 15.8 + - + +
119D VAL* 3.2 17.4 + - - +
213D ALA* 3.8 26.2 - - + +
216D VAL* 4.1 17.0 - - + -
217D LEU* 3.7 33.2 - - + -
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Residues in contact with GLU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C PHE* 5.9 2.3 - - - -
112D SER* 2.7 41.8 + - - +
113D PHE* 3.0 11.4 + - + +
115D LEU* 1.3 74.4 - - - +
117D ARG* 1.3 66.8 + - - +
119D VAL* 4.6 7.0 - - - +
120D ALA* 3.7 18.4 + - - +
217D LEU* 5.0 8.6 - - - +
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Residues in contact with ARG 117 (chain D).
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* 3.1 27.2 + - + +
114D ARG* 3.0 9.6 + - - +
116D GLU* 1.3 81.1 - - - +
118D ARG* 1.3 73.1 + - - +
120D ALA* 3.0 11.3 + - - +
121D ALA* 2.8 24.6 + - + +
124D ARG* 5.0 8.3 + - - +
116E GLU* 5.6 3.8 + - - -
207E ALA* 3.9 9.5 + - - +
210E GLY* 3.0 39.3 + - - -
211E ASP* 2.7 31.9 + - - +
214E ALA* 4.3 20.5 - - + +
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Residues in contact with ARG 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D HIS* 5.1 21.1 - - + +
87D LEU* 3.6 28.9 - - + -
90D GLU* 3.2 37.5 + - + +
114D ARG 3.2 8.4 + - - +
115D LEU* 3.0 11.8 + - + +
117D ARG* 1.3 83.5 - - - +
119D VAL* 1.3 66.1 + - - +
121D ALA* 2.9 8.4 + - - +
122D VAL* 2.9 32.5 + - + +
209D LEU* 5.1 0.2 - - - -
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Residues in contact with VAL 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D LEU* 4.9 3.8 - - + -
115D LEU 3.2 11.0 + - - +
116D GLU* 4.6 7.9 - - - +
118D ARG* 1.3 78.1 - - + +
120D ALA* 1.3 67.0 + - - +
122D VAL* 3.0 3.8 + - - +
123D GLY* 2.8 20.8 + - - -
206D LYS* 4.8 12.3 - - + +
209D LEU* 3.6 34.6 - - + +
210D GLY* 4.6 13.2 - - - +
213D ALA* 3.9 28.0 - - + -
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Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D GLU 3.7 12.7 + - - +
117D ARG* 3.0 18.0 + - - +
119D VAL* 1.3 79.0 - - - +
121D ALA* 1.3 64.9 + - - +
123D GLY* 3.0 3.8 + - - -
124D ARG* 2.8 34.8 + - + +
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Residues in contact with ALA 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ARG* 2.8 17.1 + - + +
118D ARG* 3.4 15.5 - - - +
120D ALA* 1.3 70.9 - - - +
122D VAL* 1.3 65.0 + - + +
124D ARG* 3.0 32.6 + - - +
125D GLN* 2.9 23.5 + - - +
211E ASP* 5.3 4.7 - - - +
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Residues in contact with VAL 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D GLN* 6.1 0.2 - - - +
83D LEU* 4.5 22.4 - - + -
118D ARG* 2.9 25.9 + - - +
119D VAL 3.6 5.8 - - - +
121D ALA* 1.3 76.3 - - + +
123D GLY* 1.3 65.1 + - - +
125D GLN* 3.0 16.4 + - + +
126D MET* 3.0 18.4 + - + +
205D PHE* 3.8 29.2 - - + -
209D LEU* 4.0 18.4 - - + -
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Residues in contact with GLY 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D VAL 2.8 17.3 + - - -
120D ALA* 3.4 4.7 - - - -
122D VAL* 1.3 73.9 - - - +
124D ARG* 1.3 61.6 + - - +
126D MET* 3.0 18.4 + - - +
127D GLY* 3.3 9.5 + - - -
202D ILE* 5.1 0.5 - - - +
205D PHE* 6.0 0.4 - - - -
206D LYS* 3.9 38.3 - - - -
209D LEU* 5.5 0.2 - - - +
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Residues in contact with ARG 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ARG* 5.0 4.8 - - - +
120D ALA* 2.8 22.8 + - - +
121D ALA* 3.5 33.1 + - - +
123D GLY* 1.3 71.2 - - - +
125D GLN* 1.3 62.5 + - - +
127D GLY* 3.9 2.7 + - - -
128D ARG* 3.8 17.2 + - - +
203E GLY 5.5 1.1 - - - -
204E GLY* 4.7 14.8 + - - -
207E ALA* 3.5 35.2 - - - +
208E MET* 5.2 6.7 - - - +
211E ASP* 4.3 17.0 + - - -
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Residues in contact with GLN 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LYS* 5.1 3.8 + - - -
47D GLU* 5.0 3.8 - - - +
121D ALA 2.9 12.8 + - - +
122D VAL* 3.6 11.0 - - + +
124D ARG* 1.3 79.9 + - - +
126D MET* 1.3 64.7 + - + +
128D ARG* 3.8 19.7 - - - +
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Residues in contact with MET 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LYS* 4.0 12.1 - - - -
47D GLU* 3.8 11.0 - - - +
48D PHE* 3.4 44.5 - - + -
51D GLN* 3.6 26.9 - - + +
122D VAL* 3.0 19.2 + - + +
123D GLY* 3.0 7.3 + - - +
125D GLN* 1.3 78.8 - - + +
127D GLY* 1.3 57.4 - - - +
128D ARG 3.2 5.4 + - - -
129D GLY 4.5 0.7 + - - -
130D ASN* 5.4 1.4 + - - +
202D ILE* 3.4 24.1 - - + +
205D PHE* 3.5 50.7 - - + -
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Residues in contact with GLY 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D GLY 3.3 10.4 + - - -
124D ARG* 3.9 5.4 + - - -
125D GLN 3.4 0.4 - - - -
126D MET* 1.3 77.0 - - - +
128D ARG* 1.3 62.8 + - - +
129D GLY 3.2 3.3 + - - -
130D ASN* 3.7 18.9 + - - +
131D GLY 4.5 2.1 + - - -
202D ILE* 3.4 15.7 - - - +
200E ARG* 4.8 7.6 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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