Contacts of the helix formed by residues 106 - 133 (chain G) in PDB entry 6XAV
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 THR 106 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G ALA 6.1 0.2 - - - -
31G LEU* 4.7 15.6 - - + +
34G ALA* 4.2 24.6 - - + +
103G ASP* 2.5 41.4 + - + +
105G ILE* 1.3 82.5 - - + +
107G THR* 1.3 60.2 + - - +
108G GLN 3.2 0.4 - - - -
109G THR* 3.4 12.9 - - - +
110G ALA* 3.2 21.3 + - - +
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Residues in contact with THR 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G ASP 4.3 2.3 + - - -
104G ARG* 2.9 22.1 + - - -
105G ILE 3.1 1.0 - - - -
106G THR* 1.3 75.1 + - - +
108G GLN* 1.3 59.1 + - - +
110G ALA* 3.6 12.1 - - + -
111G LYS* 2.9 35.1 + - + +
911I SER 4.2 14.0 + - - +
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Residues in contact with GLN 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G ARG 4.7 0.4 + - - -
105G ILE* 3.3 28.3 + - - +
106G THR 3.2 1.0 - - - -
107G THR* 1.3 80.0 - - - +
109G THR* 1.3 63.8 + - - +
111G LYS* 3.5 10.2 + - - +
112G GLN* 3.5 11.3 + - - +
911I SER 4.5 14.1 + - - +
912I ASP* 3.9 28.8 + - + +
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Residues in contact with THR 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G ALA* 4.7 3.9 + - - +
33G THR* 4.8 12.9 - - - +
34G ALA* 4.2 25.4 - - + -
105G ILE 5.3 0.7 - - - +
106G THR* 3.4 15.7 - - - +
108G GLN* 1.3 77.5 - - - +
110G ALA* 1.3 66.9 + - - +
111G LYS 3.4 0.2 - - - -
112G GLN* 3.4 10.4 + - - +
113G VAL* 3.2 29.6 + - - +
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Residues in contact with ALA 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G LEU* 6.4 2.0 - - + -
30G ALA* 3.6 24.4 - - + +
31G LEU* 5.4 8.3 - - + -
106G THR 3.2 19.8 + - - +
107G THR* 3.7 14.4 - - + +
108G GLN 3.2 0.4 - - - -
109G THR* 1.3 76.5 - - + +
111G LYS* 1.3 64.5 + - - +
113G VAL* 3.3 3.8 + - - +
114G ILE* 3.1 30.6 + - + +
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Residues in contact with LYS 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G THR* 2.9 23.4 + - + +
108G GLN* 3.9 5.2 - - - +
109G THR 3.4 0.2 - - - -
110G ALA* 1.3 76.7 - - - +
112G GLN* 1.3 62.4 + - - +
114G ILE* 3.3 7.6 + - + +
115G VAL* 3.0 40.6 + - + +
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Residues in contact with GLN 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G GLN 3.5 9.8 + - - +
109G THR* 3.4 12.8 + - - +
110G ALA 3.2 0.8 - - - -
111G LYS* 1.3 80.5 - - - +
113G VAL* 1.3 72.5 + - - +
115G VAL* 3.3 12.3 - - + +
116G GLN* 3.0 41.7 + - - +
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Residues in contact with VAL 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G ALA* 3.6 28.7 - - + +
29G SER* 4.9 6.1 - - - +
30G ALA* 3.8 22.0 - - + +
33G THR* 5.4 6.3 - - + +
109G THR* 3.2 19.3 - - - +
110G ALA 3.3 6.8 + - - +
112G GLN* 1.3 84.1 - - - +
114G ILE* 1.3 66.1 + - - +
116G GLN* 3.6 5.4 - - + +
117G LYS* 3.1 36.5 + - + +
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Residues in contact with ILE 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G ALA* 3.8 26.2 - - + -
27G LEU* 4.2 21.8 - - + +
30G ALA* 5.9 0.4 - - + -
110G ALA* 3.1 20.0 + - + +
111G LYS* 3.7 8.1 - - + +
112G GLN 3.3 0.2 - - - -
113G VAL* 1.3 77.0 - - - +
115G VAL* 1.3 67.7 + - + +
117G LYS* 3.3 4.3 + - - +
118G VAL* 3.1 33.0 + - + +
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Residues in contact with VAL 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G LYS* 3.0 39.6 + - + +
112G GLN* 3.3 18.6 - - + +
114G ILE* 1.3 80.5 - - + +
116G GLN* 1.3 62.3 + - - +
118G VAL* 3.5 10.3 + - + +
119G ARG* 3.3 37.8 + - - +
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Residues in contact with GLN 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G GLN* 3.0 32.5 + - - +
113G VAL* 3.6 8.0 - - - +
114G ILE 3.1 0.6 - - - -
115G VAL* 1.3 77.8 - - + +
117G LYS* 1.3 81.9 + - - +
119G ARG* 3.2 13.7 + - + +
120G GLU* 3.0 52.8 + - - +
191G ARG* 5.6 1.0 + - - +
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Residues in contact with LYS 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G GLU* 4.8 2.8 + - - +
26G ALA* 3.6 36.6 - - + +
29G SER* 4.8 9.5 + - - -
113G VAL* 3.1 27.4 + - - +
114G ILE 3.8 4.0 - - - +
116G GLN* 1.3 87.7 - - - +
118G VAL* 1.3 55.3 + - + +
120G GLU* 3.5 10.8 - - + +
121G ALA* 2.6 36.8 + - - +
191G ARG* 6.2 6.7 - - - +
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Residues in contact with VAL 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G ILE* 3.1 25.6 + - + +
115G VAL* 3.7 12.1 - - + +
116G GLN 3.2 0.2 - - - -
117G LYS* 1.3 77.4 - - + +
119G ARG* 1.3 53.3 + - + +
121G ALA* 3.6 7.3 - - + +
122G GLU* 2.7 36.8 + - + +
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Residues in contact with ARG 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G VAL* 3.3 24.1 + - - +
116G GLN* 3.2 15.3 + - + +
118G VAL* 1.3 78.0 - - + +
120G GLU* 1.3 60.4 + - + +
122G GLU* 3.7 11.0 - - - +
123G ARG* 2.8 28.2 + - - +
157G ASN* 6.0 2.2 - - - +
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Residues in contact with GLU 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116G GLN* 3.0 48.1 + - - +
117G LYS* 3.2 16.8 + - + +
119G ARG* 1.3 75.3 - - - +
121G ALA* 1.3 59.8 + - - +
123G ARG* 3.2 13.8 + - - +
124G ALA* 2.9 27.0 + - - +
191G ARG 3.8 21.2 - - - +
192G GLY* 4.2 11.5 - - - -
193G ALA 5.5 1.2 - - - +
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Residues in contact with ALA 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G LYS 2.6 20.9 + - - +
118G VAL* 3.6 8.5 - - + +
120G GLU* 1.3 70.0 - - - +
122G GLU* 1.3 65.0 + - - +
124G ALA* 3.3 9.7 + - - +
125G MET* 3.1 20.8 + - - +
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Residues in contact with GLU 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118G VAL* 2.7 24.3 + - + +
119G ARG* 3.7 10.5 - - - +
121G ALA* 1.3 69.8 - - - +
123G ARG* 1.3 67.8 + - - +
125G MET* 3.2 27.5 + - + +
126G VAL* 3.1 33.8 + - - +
156G ASN 4.6 0.3 - - - +
157G ASN* 3.5 39.4 + - - +
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Residues in contact with ARG 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119G ARG 2.8 19.1 + - - +
120G GLU* 3.2 17.0 + - - +
122G GLU* 1.3 81.5 + - - +
124G ALA* 1.3 61.8 + - - +
126G VAL* 3.2 19.6 + - - +
127G VAL* 3.1 26.3 + - + +
130G PHE* 6.1 0.6 - - - -
157G ASN 3.4 18.2 - - - +
158G ALA* 3.5 10.8 - - - +
159G GLU* 2.4 52.3 + - - +
193G ALA 5.4 7.4 - - - +
194G GLN* 4.7 8.3 + - - +
195G LEU* 3.6 24.5 - - - +
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Residues in contact with ALA 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G GLU 2.9 13.5 + - - +
121G ALA* 3.6 11.4 - - - +
122G GLU 3.3 0.2 - - - -
123G ARG* 1.3 76.1 - - - +
125G MET* 1.3 58.1 + - - +
127G VAL* 3.2 12.1 + - - +
128G ASP* 3.0 36.0 + - - +
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Residues in contact with MET 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G ALA 3.1 12.9 + - - +
122G GLU* 3.2 38.1 + - + +
124G ALA* 1.3 77.7 - - - +
126G VAL* 1.3 58.9 + - + +
128G ASP* 3.3 9.1 + - - +
129G GLN* 2.9 48.4 + - - +
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Residues in contact with VAL 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G GLU* 3.1 32.6 + - - +
123G ARG* 3.2 12.3 + - - +
125G MET* 1.3 77.7 - - + +
127G VAL* 1.3 56.1 + - - +
129G GLN* 3.6 7.1 - - + -
130G PHE* 2.7 39.2 + - + +
156G ASN* 3.6 22.7 - - + +
157G ASN 4.1 7.2 - - - +
158G ALA* 3.7 26.5 - - + -
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Residues in contact with VAL 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G ARG* 3.1 40.1 + - + +
124G ALA* 3.2 13.7 + - + +
126G VAL* 1.3 76.6 - - - +
128G ASP* 1.3 66.6 + - - +
130G PHE* 3.3 5.8 + - - +
131G ARG* 3.0 32.1 + - - +
186G VAL* 5.1 9.2 - - + -
193G ALA 5.6 6.3 - - - +
195G LEU* 3.7 30.5 - - + +
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Residues in contact with ASP 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F ASP 5.9 3.4 - - - +
124G ALA* 3.0 19.4 + - - +
125G MET* 3.3 10.4 + - - +
127G VAL* 1.3 79.8 - - - +
129G GLN* 1.3 67.5 + - - +
131G ARG* 3.3 6.9 + - - +
132G GLU* 3.2 27.9 + - + +
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Residues in contact with GLN 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A PHE* 4.7 22.6 - - + -
125G MET* 2.9 42.4 + - - +
126G VAL* 3.8 8.1 - - + +
128G ASP* 1.3 81.4 - - - +
130G PHE* 1.3 61.3 + - - +
132G GLU* 3.4 10.0 + - + +
133G HIS* 3.4 32.7 + - + +
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Residues in contact with PHE 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G ARG* 5.9 0.4 - - - -
126G VAL* 2.7 26.6 + - + +
127G VAL* 3.6 7.2 - - - +
128G ASP 3.2 0.2 - - - -
129G GLN* 1.3 72.0 - - - +
131G ARG* 1.3 64.2 + - - +
133G HIS* 3.1 16.2 + - + +
134G GLU* 3.0 35.7 + - + +
136G GLU* 5.5 4.9 - - + -
138G ILE* 3.6 46.9 - - + -
154G LEU* 4.5 16.2 - - + -
158G ALA* 5.9 4.3 - - + -
183G LEU* 4.5 16.2 - - + -
195G LEU* 3.9 23.3 - - + -
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Residues in contact with ARG 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F SER* 6.4 0.4 - - - -
83F PRO* 4.5 35.8 - - + +
84F SER* 5.2 11.8 + - - +
87F ARG* 4.3 10.9 - - - -
127G VAL* 3.0 27.8 + - - +
128G ASP* 3.3 7.6 + - - +
130G PHE* 1.3 79.4 - - - +
132G GLU* 1.3 64.0 + - + +
133G HIS 3.4 0.5 + - - -
134G GLU* 3.6 33.7 + - + +
183G LEU* 3.4 37.8 + - - +
184G TYR 4.3 3.8 + - - -
185G SER* 3.9 22.2 - - - +
186G VAL* 3.8 25.5 - - - +
195G LEU* 3.9 11.1 - - - +
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Residues in contact with GLU 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F GLN 5.3 0.3 - - - +
60F ASP 3.4 22.3 - - - +
61F GLY* 4.1 10.3 - - - -
83F PRO* 5.5 5.0 - - - +
87F ARG* 3.3 32.9 + - - +
128G ASP* 3.2 17.2 + - + +
129G GLN* 3.6 11.0 - - + +
130G PHE 3.2 0.6 - - - -
131G ARG* 1.3 80.0 - - + +
133G HIS* 1.3 78.8 + - + +
134G GLU 3.6 0.2 - - - -
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Residues in contact with HIS 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ARG* 4.3 15.9 + - + +
213A PRO* 5.0 2.9 - - + -
214A GLU* 3.2 33.4 + - - -
232A PHE* 4.1 28.5 - + - -
87F ARG* 5.2 3.8 - - - +
129G GLN* 3.4 20.0 + - + +
130G PHE* 3.1 19.6 + - + +
132G GLU* 1.3 92.8 - - + +
134G GLU* 1.3 59.7 + - - +
135G GLY 4.2 0.2 + - - -
136G GLU* 4.4 15.0 - - - +
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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