Contacts of the helix formed by residues 98 - 124 (chain O) in PDB entry 6QY3
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 LYS 98 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96O ALA 3.2 6.1 + - - +
97O TRP* 1.3 77.5 - - - +
99O GLU* 1.3 65.0 + - - +
100O ASN* 3.3 9.6 - - + +
101O VAL* 3.6 15.2 + - + +
102O LYS* 3.2 22.9 + - - +
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Residues in contact with GLU 99 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97O TRP 3.9 0.6 + - - -
98O LYS* 1.3 72.4 - - - +
100O ASN* 1.3 60.4 + - - +
102O LYS* 3.8 6.6 - - - +
103O CYS* 2.9 30.8 + - - +
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Residues in contact with ASN 100 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98O LYS* 3.3 6.3 - - + +
99O GLU* 1.3 79.7 - - - +
101O VAL* 1.3 56.0 + - - +
103O CYS* 3.4 5.0 + - - +
104O GLU* 2.9 29.5 + - - +
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Residues in contact with VAL 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97O TRP* 6.2 1.3 - - + -
98O LYS* 3.6 19.4 + - + +
99O GLU 3.4 0.4 - - - -
100O ASN* 1.3 75.8 - - - +
102O LYS* 1.3 60.7 + - - +
104O GLU* 3.7 5.4 - - - +
105O VAL* 2.9 31.9 + - - +
277O LEU* 5.1 12.3 - - + +
280O LEU* 4.8 20.4 - - + -
281O GLY* 5.1 5.2 - - - +
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Residues in contact with LYS 102 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97O TRP* 5.7 4.9 - - + -
98O LYS 3.2 18.9 + - - +
99O GLU* 3.8 7.2 - - - +
101O VAL* 1.3 77.2 - - - +
103O CYS* 1.3 56.8 + - - +
105O VAL* 4.1 3.7 - - - +
106O TRP* 2.9 32.1 + - - +
202O GLY 5.6 1.3 - - - +
203O LEU* 4.2 25.0 - - - +
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Residues in contact with CYS 103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99O GLU 2.9 18.9 + - - +
100O ASN* 3.8 6.3 - - - +
102O LYS* 1.3 74.6 - - - +
104O GLU* 1.3 60.4 + - - +
106O TRP* 3.9 4.6 - - - +
107O THR* 2.9 31.2 + - - -
142O ARG* 5.4 13.3 - - + +
143O PHE 5.8 3.1 - - - +
203O LEU 5.7 0.2 - - - -
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Residues in contact with GLU 104 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100O ASN 2.9 18.1 + - - +
101O VAL* 3.7 6.7 - - - +
103O CYS* 1.3 74.3 - - - +
105O VAL* 1.3 60.7 + - - +
107O THR* 3.4 5.0 + - - -
108O ALA* 2.9 29.9 + - - +
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Residues in contact with VAL 105 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101O VAL 2.9 17.4 + - - +
102O LYS* 4.1 4.3 - - - +
104O GLU* 1.3 76.5 - - - +
106O TRP* 1.3 57.9 + - - +
108O ALA* 3.4 6.2 + - - +
109O ILE* 2.9 29.6 + - - +
203O LEU* 5.9 3.1 - - + -
277O LEU* 6.5 0.9 - - + -
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Residues in contact with TRP 106 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102O LYS 2.9 20.4 + - - +
103O CYS* 3.9 5.2 - - - +
105O VAL* 1.3 78.1 - - - +
107O THR* 1.3 58.1 + - - +
109O ILE* 3.2 6.6 + - - +
110O ILE* 2.9 30.0 + - - +
203O LEU* 4.4 25.2 - - + +
204O LYS* 5.2 2.2 - - - +
217O ASP* 6.4 0.4 - - + -
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Residues in contact with THR 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103O CYS 2.9 20.6 + - - -
104O GLU* 3.8 5.4 - - - -
106O TRP* 1.3 76.3 - - - +
108O ALA* 1.3 56.6 + - - +
110O ILE* 3.5 6.0 + - - +
111O ALA* 2.9 29.8 + - - +
140O LEU* 5.9 2.4 - - - +
141O GLU 5.3 10.5 - - - -
142O ARG* 5.3 9.4 - - - -
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Residues in contact with ALA 108 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104O GLU 2.9 19.1 + - - +
105O VAL* 3.7 7.2 - - - +
106O TRP 3.3 0.2 - - - -
107O THR* 1.3 76.6 - - - +
109O ILE* 1.3 57.8 + - - +
111O ALA* 3.4 7.0 + - - +
112O GLN* 2.9 28.9 + - - +
284O ILE* 4.7 17.9 - - + -
285O PRO 6.2 0.4 - - - +
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Residues in contact with ILE 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105O VAL 2.9 18.7 + - - +
106O TRP* 3.2 7.4 + - - +
108O ALA* 1.3 74.6 - - - +
110O ILE* 1.3 60.5 + - - +
112O GLN* 3.2 8.2 + - - +
113O LYS* 2.9 28.6 + - - +
217O ASP* 4.1 20.0 - - + +
218O ILE* 5.8 2.0 - - - +
220O GLU* 5.0 5.6 - - + +
221O PRO* 4.6 8.4 - - + +
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Residues in contact with ILE 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106O TRP 2.9 16.9 + - - +
107O THR* 3.9 5.8 - - - +
109O ILE* 1.3 74.9 - - - +
111O ALA* 1.3 58.4 + - - +
113O LYS* 3.8 6.0 - - - +
114O ILE* 2.9 31.9 + - - +
149O GLU* 5.2 15.5 - - + +
220O GLU* 6.0 0.9 - - - -
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Residues in contact with ALA 111 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107O THR 2.9 18.5 + - - +
108O ALA* 3.7 7.6 - - - +
110O ILE* 1.3 77.7 - - - +
112O GLN* 1.3 56.8 + - - +
114O ILE* 4.2 3.9 - - - +
115O LEU* 2.9 31.7 + - - +
137O TYR* 5.0 15.2 - - + +
140O LEU* 5.6 8.9 - - + +
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Residues in contact with GLN 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108O ALA 2.9 17.8 + - - +
109O ILE* 3.2 6.9 + - - +
111O ALA* 1.3 77.5 - - - +
113O LYS* 1.3 56.8 + - - +
115O LEU* 3.8 4.6 - - - +
116O ASN* 2.9 30.3 + - - +
221O PRO* 4.0 18.8 - - + +
285O PRO 6.0 1.1 - - - +
286O GLU* 5.7 4.0 - - + -
287O PHE 4.4 19.2 - - - +
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Residues in contact with LYS 113 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109O ILE 2.9 16.5 + - - +
110O ILE* 3.8 6.3 - - - +
112O GLN* 1.3 74.8 - - - +
114O ILE* 1.3 60.5 + - - +
116O ASN* 3.2 5.7 + - - +
117O GLN* 2.9 28.1 + - - +
220O GLU* 3.5 32.1 - - + +
221O PRO* 4.1 8.0 - - - +
224O PRO* 5.4 1.9 - - - +
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Residues in contact with ILE 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110O ILE 2.9 18.1 + - - +
111O ALA* 4.2 3.4 - - - +
113O LYS* 1.3 74.8 - - - +
115O LEU* 1.3 58.0 + - - +
117O GLN* 3.2 8.0 + - - +
118O SER* 2.9 29.5 + - - -
133O ILE* 4.8 7.6 - - - +
136O LEU* 5.7 0.9 - - + -
137O TYR* 4.3 21.8 - - + +
149O GLU* 6.0 5.6 - - + -
152O SER* 5.1 14.4 - - - -
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Residues in contact with LEU 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111O ALA 2.9 21.0 + - - +
112O GLN* 3.8 5.4 - - - +
114O ILE* 1.3 77.2 - - - +
116O ASN* 1.3 55.7 + - - +
118O SER* 3.5 5.9 + - - +
119O TYR* 2.9 30.7 + - - +
137O TYR* 4.6 9.3 - - + +
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Residues in contact with ASN 116 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112O GLN 2.9 18.3 + - - +
113O LYS* 3.6 5.4 - - - +
115O LEU* 1.3 76.7 - - - +
117O GLN* 1.3 58.2 + - - +
119O TYR* 3.9 5.2 - - - +
120O TYR* 2.9 30.3 + - - +
221O PRO 4.2 17.7 - - - +
224O PRO* 4.5 11.6 - - + +
287O PHE 5.3 3.4 - - - +
288O ARG* 5.6 1.1 - - - +
289O ILE* 4.9 23.2 - - + +
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Residues in contact with GLN 117 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113O LYS 2.9 13.6 + - - +
114O ILE* 3.2 11.2 + - - +
116O ASN* 1.3 75.0 - - - +
118O SER* 1.3 58.9 + - - +
120O TYR* 3.3 6.2 + - - +
121O LEU* 2.9 28.8 + - - +
133O ILE* 5.2 5.6 - - + -
152O SER* 5.9 3.1 - - - +
156O TYR* 4.6 22.2 - - + +
224O PRO* 4.7 9.8 - - + +
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Residues in contact with SER 118 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114O ILE 2.9 15.7 + - - -
115O LEU* 4.0 6.1 - - - -
117O GLN* 1.3 75.6 - - - +
119O TYR* 1.3 57.6 + - - +
121O LEU* 3.3 0.8 + - - -
122O GLY* 2.9 23.6 + - - -
130O SER* 3.2 37.2 - - - +
133O ILE* 3.8 17.8 - - - +
134O MET* 3.8 14.1 - - - -
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Residues in contact with TYR 119 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115O LEU 2.9 19.0 + - - +
116O ASN* 3.9 7.4 - - - +
118O SER* 1.3 77.6 - - - +
120O TYR* 1.3 57.2 + - - +
122O GLY* 3.1 2.8 + - - +
123O GLU* 2.9 26.5 + - - +
289O ILE* 5.7 7.9 - - + +
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Residues in contact with TYR 120 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116O ASN 2.9 19.6 + - - +
117O GLN* 3.7 6.5 - - - +
119O TYR* 1.3 77.9 - - - +
121O LEU* 1.3 56.5 + - - +
123O GLU* 3.2 9.9 + - - +
124O CYS* 2.9 26.9 + - - +
224O PRO* 5.0 11.7 - - + +
228O ARG* 6.1 5.2 - - + -
289O ILE* 5.9 4.7 - - + +
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Residues in contact with LEU 121 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117O GLN 2.9 17.8 + - - +
118O SER* 3.6 5.2 - - - +
120O TYR* 1.3 75.9 - - - +
122O GLY* 1.3 60.1 + - - +
124O CYS* 3.3 9.1 + - - +
125O SER 3.2 4.7 + - - -
126O PHE* 3.1 33.9 + - + +
129O LYS* 4.8 5.8 - - + -
130O SER* 3.6 20.9 - - - +
156O TYR* 6.5 1.3 - - - -
159O THR* 5.6 7.2 - - - -
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Residues in contact with GLY 122 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118O SER 2.9 14.3 + - - -
119O TYR* 3.1 5.1 + - - -
121O LEU* 1.3 74.4 - - - +
123O GLU* 1.3 58.8 + - - +
125O SER* 3.1 17.6 + - - -
126O PHE 4.4 3.6 - - - -
127O PHE* 6.1 0.4 - - - -
130O SER* 3.7 8.4 - - - -
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Residues in contact with GLU 123 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119O TYR 2.9 12.9 + - - +
120O TYR* 3.2 12.3 + - - +
122O GLY* 1.3 76.0 - - - +
124O CYS* 1.3 60.2 + - - +
125O SER* 3.2 2.9 + - - -
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Residues in contact with CYS 124 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120O TYR 2.9 15.5 + - - +
121O LEU* 3.6 9.6 - - - +
122O GLY 3.2 0.4 - - - -
123O GLU* 1.3 74.3 - - - +
125O SER* 1.3 69.8 + - - +
126O PHE* 3.5 5.5 + - + +
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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) + - + + + + + -
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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