Contacts of the helix formed by residues 111 - 139 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A PRO 4.0 1.7 + - - +
110A CYS* 1.3 72.8 - - - +
112A MSE 1.3 67.9 + - - +
113A SER* 4.2 11.4 + - - +
114A ASP* 3.0 36.4 + - - +
115A ILE* 3.1 12.3 + - - +
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Residues in contact with MSE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A THR* 5.6 0.9 - - - +
22A LEU* 4.3 19.3 - - - -
25A ASN* 3.5 40.2 - - - +
26A LEU* 3.3 31.4 - - + -
110A CYS 3.7 2.6 + - - -
111A GLN* 1.3 72.6 + - - +
113A SER* 1.3 56.8 + - - +
115A ILE* 3.1 23.4 + - + +
116A LYS* 2.9 46.6 + - - +
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Residues in contact with SER 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN* 4.2 10.5 - - - +
112A MSE 1.3 78.1 - - - +
114A ASP* 1.3 60.8 + - - +
116A LYS* 3.5 8.4 + - - +
117A ALA* 3.0 30.9 + - - +
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Residues in contact with ASP 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 3.7 18.0 - - + +
110A CYS* 5.3 1.3 - - + -
111A GLN* 3.0 32.0 + - - +
113A SER* 1.3 81.9 - - - +
115A ILE* 1.3 56.8 + - - +
117A ALA* 3.4 6.1 + - - +
118A ALA* 3.0 28.1 + - - +
99B GLU* 6.2 0.2 - - - +
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Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.9 27.8 - - + -
26A LEU* 4.6 4.5 - - + -
55A MSE 4.2 15.2 - - + +
84A LEU* 5.0 9.6 - - + -
106A LEU* 4.0 12.1 - - + -
110A CYS* 3.9 32.8 - - + +
111A GLN 3.5 13.9 - - - +
112A MSE 3.1 22.1 + - + +
114A ASP* 1.3 73.3 - - - +
116A LYS* 1.3 61.0 + - - +
118A ALA* 3.2 4.3 + - - +
119A ILE* 3.0 45.9 + - + +
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Residues in contact with LYS 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN* 3.6 23.5 + - - +
26A LEU* 4.2 15.5 - - + -
29A ASP* 4.0 21.7 + - - +
30A PHE* 4.4 9.0 - - + -
112A MSE 2.9 32.6 + - + +
113A SER* 3.8 7.2 - - - +
115A ILE* 1.3 74.5 - - - +
117A ALA* 1.3 65.3 + - - +
119A ILE* 4.0 7.2 - - - +
120A ASN* 3.0 42.4 + - - +
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A SER 3.0 17.5 + - - +
114A ASP* 3.7 7.4 - - - +
116A LYS* 1.3 78.5 - - - +
118A ALA* 1.3 56.3 + - - +
120A ASN* 3.6 6.5 + - - +
121A ALA* 2.9 30.5 + - - +
99B GLU* 4.0 25.9 - - + +
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Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A MSE 6.4 0.2 - - - -
82A LEU* 3.7 25.9 - - + +
103A PHE* 5.2 1.0 - - - -
104A ARG* 4.7 15.7 - - + +
106A LEU* 3.8 22.2 - - + -
114A ASP 3.0 14.7 + - - +
115A ILE 3.2 8.5 + - - +
117A ALA* 1.3 75.0 - - - +
119A ILE* 1.3 57.0 + - - +
121A ALA* 3.3 6.7 + - - +
122A GLY* 2.8 26.3 + - - -
99B GLU* 5.3 1.7 - - + +
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 4.1 20.6 - - + -
26A LEU* 3.5 36.6 - - + -
30A PHE* 3.6 29.2 - - + -
53A VAL* 3.8 9.2 - - + +
55A MSE 4.5 11.2 - - + -
82A LEU* 4.1 16.2 - - + -
115A ILE* 3.0 35.8 + - + +
116A LYS* 4.0 4.0 - - - +
118A ALA* 1.3 73.8 - - - +
120A ASN* 1.3 59.5 + - - +
122A GLY* 3.1 2.3 + - - -
123A ILE* 2.9 41.0 + - + +
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Residues in contact with ASN 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU* 5.5 1.0 - - - +
30A PHE* 3.5 22.5 - - - -
116A LYS* 3.0 38.7 + - - +
117A ALA* 3.8 6.3 - - - +
119A ILE* 1.3 76.1 - - - +
121A ALA* 1.3 61.0 + - - +
123A ILE* 3.4 8.7 + - - +
124A LYS* 3.3 24.0 + - - +
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Residues in contact with ALA 121 (chain A).
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* 4.0 4.8 - - + -
104A ARG* 3.5 32.1 - - - +
117A ALA 2.9 18.1 + - - +
118A ALA 3.6 4.9 - - - +
119A ILE 3.2 0.4 - - - -
120A ASN* 1.3 74.4 - - - +
122A GLY* 1.3 58.0 + - - +
124A LYS* 3.4 12.8 + - - +
125A GLN* 3.0 27.5 + - - +
99B GLU* 3.9 11.4 - - - +
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Residues in contact with GLY 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A VAL* 3.5 14.6 - - - -
80A VAL* 3.5 29.3 - - - +
82A LEU* 5.0 1.3 - - - -
103A PHE* 4.2 3.3 - - - -
118A ALA 2.8 14.8 + - - -
119A ILE 3.1 4.0 + - - -
121A ALA* 1.3 76.0 - - - +
123A ILE* 1.3 57.5 + - - +
125A GLN* 3.3 2.3 + - - -
126A TYR* 2.9 25.6 + - - +
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 4.1 27.0 - - + +
6A ASN 3.6 18.6 - - - +
7A GLU* 4.4 9.4 - - + +
9A ILE* 4.6 2.5 - - + -
30A PHE* 3.5 37.7 - - + -
52A SER* 3.7 18.4 - - - +
53A VAL* 3.9 7.0 - - + -
119A ILE* 2.9 24.5 + - + +
120A ASN* 3.8 7.9 - - - +
121A ALA 3.4 0.4 - - - -
122A GLY* 1.3 75.4 - - - +
124A LYS* 1.3 61.3 + - - +
126A TYR* 3.4 8.4 + - - +
127A ASP* 3.2 20.4 + - - +
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Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 6.0 0.9 - - - -
120A ASN 3.3 14.6 + - - +
121A ALA* 3.5 9.9 - - - +
123A ILE* 1.3 75.8 - - - +
125A GLN* 1.3 65.9 + - - +
127A ASP* 3.5 8.4 + - + +
128A LEU* 3.2 38.7 + - + +
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Residues in contact with GLN 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A VAL* 3.7 16.8 - - + -
103A PHE* 3.6 35.2 - - + -
121A ALA 3.0 15.0 + - - +
122A GLY 3.5 9.4 - - - +
124A LYS* 1.3 76.1 - - - +
126A TYR* 1.3 61.5 + - - +
128A LEU* 3.3 14.8 + - - +
129A VAL* 3.2 36.6 + - + +
103B PHE* 5.8 0.2 - - - -
125B GLN* 3.0 39.7 + - - +
128B LEU* 4.1 4.4 - - - +
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Residues in contact with TYR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ASN* 3.6 32.1 + - + -
50A PRO* 3.6 24.2 - - + +
51A PHE 3.8 13.0 - - - -
52A SER* 3.5 32.1 - - - +
78A ASN* 3.5 41.5 + - + +
79A SER 4.0 0.4 - - - -
80A VAL* 4.0 5.2 - - + -
122A GLY 2.9 17.0 + - - +
123A ILE 3.6 6.5 - - - +
124A LYS 3.3 0.2 - - - -
125A GLN* 1.3 75.5 - - - +
127A ASP* 1.3 59.9 + - + +
129A VAL* 3.3 5.0 + - - +
130A THR* 2.9 56.5 + - + +
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Residues in contact with ASP 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.5 22.1 + - + +
123A ILE 3.2 9.7 + - - +
124A LYS* 3.6 11.8 - - - +
125A GLN 3.2 0.6 - - - -
126A TYR* 1.3 80.1 - - + +
128A LEU* 1.3 63.4 + - - +
130A THR* 3.9 7.1 + - - -
131A SER* 2.8 35.0 + - - -
132B LYS* 3.0 36.7 + - - +
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LYS* 3.2 31.0 + - + +
125A GLN* 3.4 27.4 - - - +
127A ASP* 1.3 76.8 - - - +
129A VAL* 1.3 63.3 + - - +
131A SER* 3.8 3.5 - - - -
132A LYS* 3.0 25.8 + - - +
125B GLN* 4.1 4.5 - - - +
128B LEU* 4.0 27.1 - - + +
129B VAL* 3.8 30.7 - - + +
132B LYS* 3.6 32.1 - - + +
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Residues in contact with VAL 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASN* 3.7 43.3 - - + +
80A VAL* 5.6 0.9 - - + -
125A GLN* 3.2 25.5 + - + +
126A TYR* 3.6 9.6 - - - +
128A LEU* 1.3 77.6 - - - +
130A THR* 1.3 58.3 + - + +
132A LYS* 3.7 2.8 - - - +
133A GLU* 3.0 26.2 + - + +
124B LYS* 6.1 1.1 - - - +
128B LEU* 3.8 27.8 - - + +
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Residues in contact with THR 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASN* 3.9 22.7 - - + +
126A TYR* 2.9 58.8 + - + +
127A ASP* 3.9 8.0 + - - -
129A VAL* 1.3 74.4 - - - +
131A SER* 1.3 58.7 + - - +
133A GLU* 3.7 9.6 - - - +
134A GLU* 2.7 40.4 + - - +
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Residues in contact with SER 131 (chain A).
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* 2.8 23.5 + - - -
128A LEU 3.8 2.9 - - - -
130A THR* 1.3 76.2 + - - +
132A LYS* 1.3 66.1 + - - +
134A GLU* 3.4 20.7 + - - +
135A LEU* 3.2 23.2 + - - +
132B LYS* 3.4 33.8 - - - +
135B LEU* 3.6 15.6 - - - +
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Residues in contact with LYS 132 (chain A).
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 3.0 17.9 + - - +
129A VAL 3.7 4.0 - - - +
130A THR 3.3 0.2 - - - -
131A SER* 1.3 76.1 + - - +
133A GLU* 1.3 64.6 + - - +
135A LEU* 3.2 16.9 + - + +
136A LEU* 3.0 50.9 + - + +
127B ASP* 3.1 31.4 + - - +
128B LEU* 3.7 23.3 - - + +
131B SER* 3.7 25.9 + - - +
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Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ASN* 3.6 31.9 + - - +
129A VAL* 3.0 17.8 + - + +
130A THR* 3.8 8.3 - - - +
132A LYS* 1.3 79.2 - - - +
134A GLU* 1.3 58.7 + - - +
135A LEU 3.0 0.4 + - - -
136A LEU* 3.1 9.7 + - - +
137A LYS* 2.9 42.7 + - + +
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Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A THR* 2.7 24.8 + - - +
131A SER* 3.4 23.2 + - - +
132A LYS 3.3 0.2 - - - -
133A GLU* 1.3 75.1 - - - +
135A LEU* 1.3 60.7 + - + +
137A LYS* 3.9 8.5 + - - +
138A LYS* 2.9 34.0 + - + +
135B LEU* 6.5 0.4 - - + -
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Residues in contact with LEU 135 (chain A).
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* 3.2 13.7 + - - +
132A LYS* 3.2 19.8 + - + +
133A GLU 3.0 1.0 - - - -
134A GLU* 1.3 80.9 - - + +
136A LEU* 1.3 74.3 + - + +
137A LYS 3.4 0.2 - - - -
138A LYS* 4.1 4.0 - - - +
139A THR* 3.3 26.4 + - - -
131B SER* 3.9 14.1 - - - +
135B LEU* 3.4 39.3 - - + -
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Residues in contact with LEU 136 (chain A).
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* 3.0 47.5 + - + +
133A GLU* 3.7 10.5 - - + +
135A LEU* 1.3 85.2 - - + +
137A LYS* 1.3 64.2 + - - +
138A LYS 3.2 1.1 + - - -
139A THR 3.3 17.7 + - - -
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Residues in contact with LYS 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU* 2.9 30.8 + - + +
134A GLU* 3.9 9.7 - - - +
135A LEU 3.4 0.2 - - - -
136A LEU* 1.3 78.3 - - - +
138A LYS* 1.3 70.4 + - + +
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Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLU* 2.9 25.0 + - + +
135A LEU* 4.8 2.7 - - - +
137A LYS* 1.3 93.6 - - + +
139A THR* 1.3 63.7 + - - +
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Residues in contact with THR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 3.3 24.7 + - - -
136A LEU* 3.3 17.6 + - - -
138A LYS* 1.3 84.8 - - - +
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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