Contacts of the helix formed by residues 111 - 136 (chain B) in PDB entry 3KCN
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 GLN 111 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B CYS* 1.3 75.9 - - - +
112B MSE 1.3 67.1 + - - +
113B SER* 3.0 14.4 + - - +
114B ASP* 3.0 32.3 + - - +
115B ILE* 3.2 8.5 + - - +
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Residues in contact with MSE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B THR* 4.5 7.6 - - + +
22B LEU* 3.5 32.3 - - + -
25B ASN* 4.0 34.3 - - + +
26B LEU* 3.9 26.7 - - - -
110B CYS 3.3 4.8 + - - +
111B GLN* 1.3 71.5 - - - +
113B SER* 1.3 57.1 + - - +
115B ILE* 3.2 14.0 + - + +
116B LYS* 2.9 48.1 + - - +
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Residues in contact with SER 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLN* 3.0 14.0 + - - +
112B MSE 1.3 76.9 - - - +
114B ASP* 1.3 62.5 + - - +
116B LYS* 4.0 11.2 - - - +
117B ALA* 3.0 29.1 + - - +
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Residues in contact with ASP 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASN* 5.9 5.2 - - + +
99A GLU* 5.6 2.1 - - - +
106B LEU* 3.8 8.9 - - + +
110B CYS* 3.6 18.1 - - - -
111B GLN* 3.0 30.9 + - - +
113B SER* 1.3 79.8 + - - +
115B ILE* 1.3 57.2 + - - +
117B ALA* 3.4 5.7 + - - +
118B ALA* 3.0 30.3 + - - +
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Residues in contact with ILE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU* 3.8 26.5 - - + -
26B LEU* 4.2 17.5 - - + -
55B MSE 4.6 12.8 - - + -
84B LEU* 5.6 5.8 - - + -
106B LEU* 4.5 12.8 - - + -
110B CYS* 3.7 39.0 - - + +
111B GLN 3.7 6.1 - - - +
112B MSE 3.2 17.6 + - + +
114B ASP* 1.3 73.9 - - - +
116B LYS* 1.3 65.4 + - - +
118B ALA* 3.3 4.2 + - - +
119B ILE* 3.0 41.8 + - + +
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Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ASN* 4.9 9.8 + - - +
26B LEU* 3.9 20.2 - - + -
29B ASP* 3.9 20.8 + - - +
30B PHE* 4.6 5.3 - - + -
112B MSE 2.9 43.7 + - - +
113B SER* 4.2 9.8 - - - +
115B ILE* 1.3 73.0 - - - +
117B ALA* 1.3 57.0 + - - +
119B ILE* 3.9 7.1 - - - +
120B ASN* 2.9 44.2 + - - +
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ASN 5.4 8.3 - - - +
104B ARG* 5.7 1.1 - - - -
113B SER 3.0 19.9 + - - +
114B ASP* 3.7 7.2 - - - +
115B ILE 3.2 0.2 - - - -
116B LYS* 1.3 74.6 - - - +
118B ALA* 1.3 65.1 + - - +
120B ASN* 4.0 6.4 - - - +
121B ALA* 3.0 24.8 + - - +
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ASN* 5.2 1.8 - - - +
82B LEU* 3.9 20.6 - - + +
103B PHE* 4.8 0.9 - - - -
104B ARG* 4.6 15.9 - - + +
106B LEU* 3.9 29.6 - - + -
114B ASP 3.0 17.3 + - - +
115B ILE 3.3 4.5 + - - +
117B ALA* 1.3 76.9 - - - +
119B ILE* 1.3 55.7 + - - +
121B ALA* 3.2 7.9 + - - +
122B GLY* 2.9 25.3 + - - -
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Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 3.9 20.9 - - + -
26B LEU* 3.6 33.4 - - + -
30B PHE* 3.6 30.1 - - + -
53B VAL* 3.9 8.3 - - + +
55B MSE 3.6 33.4 - - + -
82B LEU* 3.9 8.7 - - + -
115B ILE* 3.0 24.2 + - + +
116B LYS 3.9 3.1 - - - +
118B ALA* 1.3 71.3 - - - +
120B ASN* 1.3 66.7 + - - +
122B GLY* 3.1 2.4 + - - -
123B ILE* 2.9 29.5 + - + +
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Residues in contact with ASN 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLU* 5.6 0.5 - - - +
30B PHE* 3.5 25.4 - - - -
116B LYS* 2.9 35.4 + - - +
117B ALA* 4.0 6.1 - - - +
119B ILE* 1.3 76.1 - - - +
121B ALA* 1.3 60.4 + - - +
123B ILE* 3.3 10.1 + - - +
124B LYS* 3.1 23.9 + - - +
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B PHE* 3.9 6.9 - - + -
104B ARG* 3.6 30.5 - - - +
117B ALA 3.0 19.2 + - - +
118B ALA* 3.4 5.2 - - - +
119B ILE 3.2 0.2 - - - -
120B ASN* 1.3 76.5 - - - +
122B GLY* 1.3 56.9 + - - +
124B LYS* 3.6 9.3 + - - +
125B GLN* 3.0 28.1 + - - +
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Residues in contact with GLY 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B VAL* 3.6 17.5 - - - -
80B VAL* 3.5 21.8 - - - +
82B LEU* 5.4 0.7 - - - -
103B PHE* 3.9 5.1 - - - -
118B ALA 2.9 14.3 + - - -
119B ILE 3.1 4.4 + - - -
121B ALA* 1.3 73.9 - - - +
123B ILE* 1.3 52.5 + - - +
125B GLN* 3.0 3.1 + - - +
126B TYR* 2.7 35.5 + - - +
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 3.8 29.8 - - + +
6B ASN 3.6 13.5 - - - +
7B GLU* 4.2 16.2 - - + +
9B ILE* 4.7 2.9 - - + -
30B PHE* 3.4 38.8 - - + -
52B SER* 3.8 17.3 - - - +
53B VAL* 4.0 7.0 - - + -
119B ILE* 2.9 20.9 + - + +
120B ASN* 3.3 10.5 + - - +
122B GLY* 1.3 73.9 - - - +
124B LYS* 1.3 58.7 + - - +
126B TYR* 3.3 9.0 + - - +
127B ASP* 2.9 27.2 + - - +
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Residues in contact with LYS 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A VAL* 6.1 1.0 - - - +
5B LEU* 5.8 1.3 - - - -
120B ASN 3.1 16.1 + - - +
121B ALA* 3.8 8.3 - - - +
123B ILE* 1.3 73.1 - - - +
125B GLN* 1.3 64.7 + - - +
127B ASP* 3.4 8.6 + - + +
128B LEU* 3.1 43.6 + - + +
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Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A PHE* 5.1 1.8 - - - -
125A GLN* 3.0 40.1 + - - +
128A LEU* 4.1 5.1 - - - +
80B VAL* 3.9 14.8 - - + -
103B PHE* 3.7 34.6 - - + -
121B ALA 3.0 16.7 + - - +
122B GLY 3.0 8.3 + - - +
124B LYS* 1.3 75.4 - - - +
126B TYR* 1.3 65.0 + - - +
128B LEU* 3.1 15.8 + - - +
129B VAL* 3.1 39.4 + - + +
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Residues in contact with TYR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ASN* 3.6 32.9 + - + -
50B PRO* 3.7 24.3 - - + +
51B PHE 4.0 5.8 - - - -
52B SER* 3.5 40.2 - - - +
78B ASN* 3.4 40.8 + - + +
79B SER 4.1 0.7 - - - -
80B VAL* 3.7 5.5 - - + +
122B GLY 2.7 19.7 + - - +
123B ILE 3.5 5.6 - - - +
125B GLN* 1.3 71.8 - - - +
127B ASP* 1.3 65.3 + - + +
129B VAL* 3.6 3.8 + - - +
130B THR* 3.1 50.3 + - + +
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Residues in contact with ASP 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LYS* 3.1 37.0 + - - +
5B LEU* 4.4 22.4 - - + +
123B ILE 2.9 16.6 + - - +
124B LYS* 3.7 8.4 - - - +
125B GLN 3.2 0.2 - - - -
126B TYR* 1.3 80.3 - - + +
128B LEU* 1.3 58.6 + - - +
130B THR* 3.7 6.0 + - - -
131B SER* 3.0 34.7 + - - -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A GLN* 4.1 4.0 - - - +
128A LEU* 4.0 29.0 - - + +
129A VAL* 3.8 28.9 - - + +
132A LYS* 3.7 32.2 - - + +
124B LYS* 3.1 33.5 + - + +
125B GLN* 3.1 28.8 + - - +
127B ASP* 1.3 76.2 - - - +
129B VAL* 1.3 66.3 + - - +
131B SER* 3.7 4.6 - - - -
132B LYS* 3.1 23.7 + - - +
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 3.8 26.6 - - + +
78B ASN* 3.7 45.8 - - + +
80B VAL* 5.5 1.6 - - + -
125B GLN* 3.1 29.8 + - + +
126B TYR* 3.9 6.3 - - - +
128B LEU* 1.3 77.0 - - - +
130B THR* 1.3 58.6 + - - +
132B LYS* 3.3 3.8 + - - +
133B GLU* 3.1 25.1 + - + +
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Residues in contact with THR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ASN* 4.0 20.4 - - + +
126B TYR* 3.1 56.3 + - + +
127B ASP* 3.7 8.3 + - - -
129B VAL* 1.3 72.2 - - - +
131B SER* 1.3 65.7 + - - +
133B GLU* 3.5 14.1 + - - +
134B GLU* 3.1 31.7 + - - +
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LYS* 3.7 33.0 + - - +
135A LEU* 3.9 15.9 - - - +
127B ASP* 3.0 24.4 + - - -
128B LEU 3.7 3.6 - - - -
130B THR* 1.3 77.6 + - - +
132B LYS* 1.3 60.8 + - - +
134B GLU* 3.1 22.2 + - - +
135B LEU* 2.9 25.2 - - - +
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Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ASP* 3.0 29.8 + - - -
128A LEU* 3.6 29.8 - - + +
131A SER* 3.4 30.5 - - - +
128B LEU 3.1 8.7 + - - +
129B VAL 3.6 8.3 - - - +
131B SER* 1.3 76.1 - - - +
133B GLU* 1.3 62.4 + - - +
135B LEU* 3.2 24.5 + - + +
136B LEU* 3.2 39.8 + - + +
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Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ASN* 3.5 31.7 + - - +
129B VAL* 3.1 16.4 + - + +
130B THR* 3.8 13.2 - - - +
131B SER 3.3 0.2 - - - -
132B LYS* 1.3 77.8 - - - +
134B GLU* 1.3 60.7 + - - +
136B LEU* 3.4 9.7 + - + +
137B LYS* 3.3 31.9 + - + +
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B THR* 3.1 18.2 + - - +
131B SER* 3.1 28.2 + - - +
133B GLU* 1.3 73.2 + - - +
135B LEU* 1.3 62.6 + - + +
136B LEU 3.0 1.8 - - - -
137B LYS* 4.3 7.4 - - + +
138B LYS* 2.8 63.9 + - + +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A SER* 3.6 24.9 - - - +
134A GLU* 6.5 0.2 - - + -
135A LEU* 3.4 30.5 - - + -
131B SER* 2.9 27.5 + - - +
132B LYS* 3.2 18.1 + - + +
134B GLU* 1.3 80.2 - - + +
136B LEU* 1.3 65.9 + - + +
137B LYS 3.5 0.2 + - - -
138B LYS* 4.6 18.5 + - - +
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B LYS* 3.2 43.0 + - + +
133B GLU* 3.7 8.5 - - + +
134B GLU 3.0 1.2 - - - -
135B LEU* 1.3 86.2 - - + +
137B LYS* 1.3 58.9 + - + +
138B LYS 5.4 0.2 - - - -
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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