Contacts of the helix formed by residues 111 - 141 (chain D) in PDB entry 4O9U
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 111 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D PHE* 3.1 11.7 + - - +
110D GLU* 1.3 80.7 + - - +
112D THR* 1.3 79.0 + - - +
113D GLY* 3.1 14.4 + - - -
114D LEU* 3.6 32.1 + - + +
115D MET* 3.6 18.4 + - - +
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Residues in contact with THR 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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111D ASN* 1.3 79.8 + - - +
113D GLY* 1.3 61.8 + - - -
115D MET* 3.7 9.0 + - - +
116D ALA* 3.3 19.6 + - - +
172D LEU* 4.0 31.3 - - + +
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Residues in contact with GLY 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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111D ASN* 3.1 10.3 + - - -
112D THR* 1.3 76.4 - - - +
114D LEU* 1.3 60.5 + - - +
116D ALA* 3.3 10.1 + - - +
117D LEU* 3.0 36.4 + - - +
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Residues in contact with LEU 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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109D PHE* 3.6 24.5 - - + -
110D GLU 5.4 2.2 - - - +
111D ASN* 3.6 32.9 + - + +
112D THR 3.3 0.6 - - - -
113D GLY* 1.3 75.5 - - - +
115D MET* 1.3 55.4 + - - +
117D LEU* 3.1 15.3 + - + +
118D ALA* 2.8 34.3 + - - +
223D PHE 4.2 18.6 - - - +
224D ALA* 3.9 12.3 - - - +
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Residues in contact with MET 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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104D LEU* 3.8 22.4 - - + -
109D PHE* 3.4 38.1 - - + +
111D ASN 3.6 6.1 + - - +
112D THR* 3.8 11.2 - - - +
113D GLY 3.4 0.2 - - - -
114D LEU* 1.3 76.7 - - - +
116D ALA* 1.3 56.2 + - - +
118D ALA* 3.0 7.2 + - - -
119D ILE* 2.7 50.4 + - + +
171D LEU* 3.2 35.2 - - + +
172D LEU* 4.3 16.4 - - + +
175D ASP* 4.3 16.4 - - + +
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Residues in contact with ALA 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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112D THR 3.3 11.4 + - - +
113D GLY* 3.3 14.6 + - - +
114D LEU 3.2 0.6 - - - -
115D MET* 1.3 77.3 - - - +
117D LEU* 1.3 61.2 + - + +
119D ILE* 5.0 3.4 - - - -
120D LEU* 3.3 33.6 + - + +
172D LEU* 4.6 15.4 - - + +
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Residues in contact with LEU 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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5C PHE* 6.6 0.4 - - + -
113D GLY 3.0 22.0 + - - +
114D LEU* 3.7 17.9 - - + +
115D MET 3.1 0.4 - - - -
116D ALA* 1.3 81.7 - - + +
118D ALA* 1.3 62.9 + - - +
119D ILE 3.6 0.4 - - - -
120D LEU* 4.2 8.7 - - + -
121D GLY* 3.5 6.2 + - - -
220D PHE* 3.4 56.7 - - + +
221D GLU 4.2 0.2 + - - -
223D PHE* 4.3 20.9 - - + +
224D ALA* 4.2 4.0 - - + -
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Residues in contact with ALA 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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100D ALA* 3.3 16.6 - - - +
104D LEU* 5.3 2.9 - - + -
109D PHE* 3.5 32.8 - - + -
114D LEU 2.8 15.4 + - - +
115D MET* 3.0 4.9 + - - +
117D LEU* 1.3 78.1 - - - +
119D ILE* 1.3 66.4 + - + +
122D GLY 3.3 0.3 + - - -
221D GLU* 2.7 30.2 - - - +
224D ALA* 3.8 10.3 - - + -
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Residues in contact with ILE 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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100D ALA* 5.0 1.6 - - - -
104D LEU* 3.8 25.6 - - + -
115D MET* 2.7 44.7 + - + +
116D ALA* 5.0 2.7 - - - -
118D ALA* 1.3 71.2 - - - +
120D LEU* 1.3 58.7 + - - +
122D GLY* 3.1 3.5 + - - -
123D LEU* 2.9 24.8 + - + -
168D GLY* 4.1 18.6 - - - +
171D LEU* 3.7 28.5 - - + -
172D LEU* 4.4 9.2 - - + -
183D PHE* 3.5 34.6 - - + -
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Residues in contact with LEU 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 ALA* 3.3 24.6 + - + +
117D LEU* 4.5 8.5 - - + +
118D ALA 3.4 0.4 - - - -
119D ILE* 1.3 79.9 - - - +
121D GLY* 1.3 59.6 + - - +
123D LEU* 3.2 26.4 - - + +
124D ILE* 3.1 44.8 + - + +
220D PHE* 5.1 11.4 - - + -
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Residues in contact with GLY 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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96D ALA 4.9 1.1 - - - +
117D LEU 3.5 12.7 + - - -
119D ILE 3.2 0.6 - - - -
120D LEU* 1.3 79.6 - - - +
122D GLY* 1.3 50.8 + - - +
124D ILE* 3.3 2.2 + - - -
125D GLY* 2.7 30.0 + - - -
217D ALA* 3.3 30.5 - - - +
220D PHE* 4.2 6.8 - - - +
221D GLU* 3.3 15.7 - - - +
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Residues in contact with GLY 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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97D ALA* 4.1 11.0 - - - -
100D ALA* 3.7 22.0 - - - -
118D ALA 3.3 0.8 + - - -
119D ILE 3.1 7.2 + - - -
121D GLY* 1.3 72.3 - - - +
123D LEU* 1.3 60.7 + - - +
125D GLY 4.1 0.7 - - - -
126D SER* 2.9 35.9 + - - -
183D PHE* 4.6 6.3 - - - -
184D PHE* 4.7 3.6 - - - -
187D ALA* 4.9 0.3 - - - +
221D GLU* 3.0 7.8 + - - -
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Residues in contact with LEU 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 ILE* 2.9 12.5 + - + +
120D LEU* 3.2 29.8 - - + +
122D GLY* 1.3 78.6 - - - +
124D ILE* 1.3 74.9 + - + +
127D VAL* 3.2 37.5 + - + +
161D LEU* 5.5 9.0 - - + -
164D THR* 5.0 7.2 - - - +
165D VAL* 4.8 19.5 - - + -
183D PHE* 4.0 23.9 - - + -
187D ALA* 4.3 8.9 - - + +
190D PHE* 6.4 1.6 - - + -
213D PHE* 5.7 4.5 - - + -
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Residues in contact with ILE 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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120D LEU* 3.1 26.8 + - + +
121D GLY* 3.6 4.7 - - - +
123D LEU* 1.3 86.3 - - + +
125D GLY* 1.3 59.8 + - - +
127D VAL* 3.9 1.4 - - - +
128D ALA* 2.9 34.8 + - - +
213D PHE* 2.9 60.3 - - + +
216D MET* 4.1 12.3 - - + -
217D ALA* 3.8 4.9 - - + +
220D PHE* 3.7 34.1 - - + -
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Residues in contact with GLY 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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93D GLY* 2.9 31.9 - - - +
97D ALA* 3.8 7.6 - - - -
121D GLY 2.7 19.9 + - - -
122D GLY 3.3 2.4 + - - -
124D ILE* 1.3 73.0 - - - +
126D SER* 1.3 55.7 + - - +
128D ALA* 4.8 0.2 - - - -
129D PHE* 2.9 24.8 + - - +
217D ALA* 3.7 10.7 - - - +
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Residues in contact with SER 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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97D ALA* 3.3 12.0 - - - +
122D GLY 2.9 17.1 + - - -
125D GLY* 1.3 71.0 - - - +
127D VAL* 1.3 61.9 + - - +
129D PHE* 3.7 2.8 - - - +
130D THR* 3.1 27.5 + - - +
184D PHE* 3.2 29.0 - - - -
187D ALA* 3.7 23.1 - - - -
188D LEU* 3.4 25.6 - - - +
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Residues in contact with VAL 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 LEU* 3.2 27.5 + - + +
124D ILE* 3.9 4.3 - - - +
125D GLY 3.3 0.6 - - - -
126D SER* 1.3 76.9 - - - +
128D ALA* 1.3 57.9 + - - +
130D THR* 3.6 1.4 - - - +
131D GLY* 2.9 30.7 + - - -
187D ALA* 3.2 26.2 - - + +
190D PHE* 4.0 13.7 - - + -
191D GLY* 3.7 19.9 - - - +
194D MET* 3.8 24.7 - - + -
210D TYR* 3.9 9.6 - - + -
213D PHE* 4.6 10.8 - - + -
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Residues in contact with ALA 128 (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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89D ASN 3.8 7.5 - - - +
93D GLY* 4.8 1.6 - - - -
124D ILE 2.9 20.2 + - - +
125D GLY 4.1 1.8 - - - +
127D VAL* 1.3 73.2 - - - +
129D PHE* 1.3 62.8 + - - +
131D GLY 4.4 0.4 - - - -
132D SER* 3.2 26.3 + - - -
210D TYR* 3.7 23.0 - - + +
213D PHE* 3.9 14.4 - - + -
214D THR* 3.5 26.0 - - - +
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Residues in contact with PHE 129 (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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67C LEU* 6.5 0.4 - - + -
71C LEU* 3.9 27.6 - - + -
90D GLY* 2.9 30.7 - - - -
91D MET* 4.6 2.0 - - - -
93D GLY* 3.6 0.4 - - - -
94D GLY* 3.2 25.1 - - - +
125D GLY 2.9 19.0 + - - +
126D SER* 3.7 3.4 - - - +
128D ALA* 1.3 79.7 - - - +
130D THR* 1.3 74.2 + - - +
132D SER* 3.4 4.7 + - - -
133D LEU* 3.2 58.3 + - + +
188D LEU* 3.8 22.4 - - + -
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Residues in contact with THR 130 (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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126D SER 3.1 19.3 + - - +
127D VAL 3.6 0.2 - - - +
129D PHE* 1.3 83.4 - - - +
131D GLY* 1.3 65.8 + - - +
133D LEU* 3.2 11.5 + - - +
134D ILE* 3.2 24.4 + - - +
188D LEU* 3.3 39.2 + - - +
191D GLY* 3.6 20.6 - - - -
192D VAL* 3.0 17.9 - - - +
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Residues in contact with GLY 131 (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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127D VAL 2.9 14.9 + - - -
130D THR* 1.3 76.7 - - - +
132D SER* 1.3 56.2 + - - +
133D LEU 3.1 1.8 - - - -
134D ILE 3.2 0.9 + - - -
135D ALA* 2.8 28.9 + - - +
191D GLY 3.4 21.3 - - - -
195D THR* 3.6 13.3 - - - +
210D TYR* 3.7 15.3 - - - -
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Residues in contact with SER 132 (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 ALA* 2.9 40.9 + - - +
87D ILE 4.4 0.2 + - - -
89D ASN* 3.3 18.4 + - - -
90D GLY* 3.9 3.1 - - - -
128D ALA 3.2 21.4 + - - -
129D PHE 3.4 5.5 + - - -
130D THR 3.3 0.4 - - - -
131D GLY* 1.3 74.9 - - - +
133D LEU* 1.3 59.5 - - - +
134D ILE 3.4 0.2 - - - -
135D ALA* 4.0 8.1 - - - -
136D PHE* 3.2 24.4 + - - +
207D ILE* 5.3 0.2 - - - -
210D TYR* 3.5 11.5 - - - +
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Residues in contact with LEU 133 (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 ILE* 3.6 27.1 - - + -
90D GLY* 4.4 6.7 - - - -
91D MET* 5.2 1.1 - - - +
129D PHE* 3.2 59.3 + - + +
130D THR* 3.2 14.1 + - - +
131D GLY 3.1 0.6 - - - -
132D SER* 1.3 78.3 - - - +
134D ILE* 1.3 64.5 + - + +
136D PHE* 3.5 12.2 - - + +
137D ALA* 3.2 21.3 + - - +
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Residues in contact with ILE 134 (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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130D THR* 3.2 14.3 + - - +
131D GLY 3.2 1.4 + - - -
133D LEU* 1.3 81.0 - - + +
135D ALA* 1.3 63.6 + - - +
136D PHE 3.2 0.2 - - - -
137D ALA* 3.1 16.9 + - + +
138D LYS* 3.1 27.6 + - + +
192D VAL* 3.7 36.1 - - + -
195D THR* 3.5 36.1 - - + +
196D LEU* 5.0 4.5 - - + -
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Residues in contact with ALA 135 (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 ALA* 4.8 1.8 - - + -
131D GLY 2.8 17.0 + - - +
132D SER* 4.0 10.1 - - - +
134D ILE* 1.3 77.3 - - - +
136D PHE* 1.3 61.6 + - - +
138D LYS* 3.0 11.8 + - - +
139D LEU* 3.1 26.4 + - + +
195D THR* 4.1 3.5 + - - +
203D MET* 3.7 28.7 - - - -
206D ALA* 5.8 0.4 - - + -
207D ILE* 4.8 14.1 - - + -
210D TYR* 5.0 7.2 - - + -
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Residues in contact with PHE 136 (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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83D GLN* 4.2 29.7 - - + +
84D MET* 5.8 4.7 - - - -
86D ALA* 5.0 1.9 - - - +
87D ILE* 4.0 39.7 - - + -
132D SER 3.2 18.7 + - - +
133D LEU* 3.5 13.2 - - + +
135D ALA* 1.3 78.6 - - - +
137D ALA* 1.3 65.2 + - + +
139D LEU* 3.5 1.0 + - - +
140D GLN* 3.2 50.6 + - + +
142D ILE* 5.9 5.8 - - + -
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Residues in contact with ALA 137 (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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133D LEU 3.2 11.3 + - - +
134D ILE* 3.1 18.9 + - + +
136D PHE* 1.3 84.6 - - + +
138D LYS* 1.3 61.9 + - + +
139D LEU 3.6 0.2 - - - -
140D GLN* 4.3 3.1 - - - +
141D GLY 4.1 7.7 + - - -
142D ILE* 4.8 1.1 + - - -
143D MET* 3.4 34.1 + - + +
144D LYS* 3.6 2.3 + - - -
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Residues in contact with LYS 138 (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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134D ILE* 3.3 29.5 - - + +
135D ALA 3.0 5.6 + - - +
137D ALA* 1.3 81.8 - - + +
139D LEU* 1.3 62.7 + - - +
140D GLN 3.6 0.4 - - - -
143D MET 4.6 3.6 - - - +
144D LYS* 3.4 29.0 + - - +
145D SER* 3.6 39.6 - - - +
146D ARG 3.9 9.8 + - - -
148D ILE* 5.4 3.4 - - - +
195D THR 2.9 23.4 + - - +
196D LEU* 3.4 21.4 + - - +
198D ILE 3.6 13.8 + - - -
200D GLY* 4.6 9.3 - - - +
203D MET* 3.7 18.6 - - + +
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Residues in contact with LEU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D PRO* 3.8 20.0 - - + -
83D GLN* 3.2 41.7 + - + +
86D ALA* 5.7 0.2 - - + -
135D ALA* 3.1 31.9 + - + +
136D PHE 4.3 0.2 - - - +
138D LYS* 1.3 80.2 - - - +
140D GLN* 1.3 62.9 + - - +
141D GLY 3.8 0.2 - - - -
144D LYS* 4.9 7.8 + - - +
200D GLY 4.9 5.8 - - - +
203D MET* 3.8 33.7 - - + -
204D PRO* 5.3 0.7 - - + -
207D ILE* 4.3 14.4 - - + -
336D ARG* 4.0 17.5 - - + +
337D MET* 5.2 0.2 - - + -
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Residues in contact with GLN 140 (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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80D ASP* 4.7 13.7 + - - +
83D GLN* 4.1 14.3 - - + +
136D PHE* 3.2 42.0 + - + +
137D ALA* 4.9 2.7 - - - +
138D LYS 4.3 0.2 - - - +
139D LEU* 1.3 81.1 - - - +
141D GLY* 1.3 59.2 + - - +
142D ILE* 3.5 30.3 + - + +
144D LYS* 5.9 0.4 - - - -
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Residues in contact with GLY 141 (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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137D ALA 4.1 5.9 + - - -
139D LEU 3.8 0.6 - - - -
140D GLN* 1.3 80.0 - - - +
142D ILE* 1.3 64.7 + - - +
143D MET 3.3 3.2 + - - -
144D LYS* 3.8 28.1 + - - +
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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).
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