Contacts of the helix formed by residues 106 - 135 (chain B) in PDB entry 2WLJ
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 GLY 106 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 3.8 23.3 - - - +
105B ILE* 1.3 89.3 - - - +
107B PRO* 1.3 70.0 - - - +
108B LEU* 2.9 11.7 - - - -
109B ALA* 3.7 3.2 - - - +
110B ASN* 2.9 21.7 + - - +
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Residues in contact with PRO 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE 4.2 2.7 - - - +
106B GLY* 1.3 81.3 - - - +
108B LEU* 1.3 67.1 + - + +
110B ASN* 4.0 7.1 - - + +
111B THR* 3.1 28.6 + - - -
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B CYS* 4.0 37.5 - - + +
74B VAL* 4.9 3.1 - - + -
106B GLY* 2.9 5.6 - - - -
107B PRO* 1.3 84.2 - - + +
109B ALA* 1.3 65.6 + - - +
111B THR* 3.1 16.6 + - + +
112B LEU* 3.1 20.6 + - + +
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 3.7 17.0 - - + -
74B VAL* 3.5 36.6 - - + +
89B PHE* 5.7 0.2 - - + -
104B PRO* 3.4 24.0 - - + -
105B ILE 3.8 5.4 - - - +
106B GLY* 3.6 4.5 + - - +
108B LEU* 1.3 78.3 - - - +
110B ASN* 1.3 56.7 + - - +
112B LEU* 3.1 5.0 + - - +
113B VAL* 2.8 31.2 + - - +
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Residues in contact with ASN 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PRO* 3.5 31.4 + - - +
105B ILE 4.0 2.3 - - - +
106B GLY 2.9 23.9 + - - +
107B PRO* 4.0 6.5 - - + +
108B LEU 3.4 0.2 - - - -
109B ALA* 1.3 73.3 - - - +
111B THR* 1.3 58.3 + - - +
113B VAL* 3.8 11.3 - - - +
114B THR* 3.1 26.3 + - - -
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Residues in contact with THR 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PRO 3.1 20.9 + - - -
108B LEU* 3.1 10.3 + - - +
110B ASN* 1.3 75.3 - - - +
112B LEU* 1.3 68.7 + - + +
114B THR* 3.1 7.7 + - - +
115B LEU* 3.0 29.9 + - + +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 3.9 15.7 - - + -
67B ALA* 4.0 27.6 - - + -
68B TYR* 3.5 39.3 - - + +
71B CYS* 3.9 25.6 - - - -
108B LEU 3.1 15.2 + - - +
109B ALA 3.6 1.3 - - - +
111B THR* 1.3 80.5 - - + +
113B VAL* 1.3 55.1 + - - +
115B LEU* 3.0 17.0 + - + +
116B GLU* 2.6 36.3 + - - +
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 3.2 15.4 + - - +
89B PHE* 4.1 9.2 - - + -
93B THR* 3.9 23.4 - - + +
104B PRO* 4.0 26.2 - - + -
109B ALA 2.8 19.4 + - - +
110B ASN* 3.8 11.4 - - + +
112B LEU* 1.3 76.7 - - - +
114B THR* 1.3 59.6 + - - +
116B GLU* 3.2 1.8 + - - +
117B ALA* 2.9 30.4 + - + +
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Residues in contact with THR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASN 3.1 14.2 + - - -
111B THR* 3.1 11.5 + - - +
113B VAL* 1.3 80.5 - - - +
115B LEU* 1.3 63.9 + - - +
117B ALA* 3.4 7.3 + - - +
118B LEU* 3.3 20.1 + - - +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 4.2 11.4 - - + -
111B THR* 3.0 16.4 + - + +
112B LEU* 3.0 23.5 + - + +
114B THR* 1.3 79.3 - - - +
116B GLU* 1.3 61.1 + - - +
118B LEU* 3.3 12.6 + - + +
119B CYS* 3.1 33.9 + - - -
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Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ASN* 3.2 5.4 - - - +
64B PHE* 3.5 35.4 - - + +
68B TYR* 3.0 28.1 + - - -
90B SER* 2.2 44.3 + - - +
93B THR* 3.5 14.6 - - + +
94B MET* 3.5 21.7 - - + +
112B LEU 2.6 18.6 + - - +
113B VAL 3.2 4.2 + - - +
115B LEU* 1.3 70.7 - - - +
117B ALA* 1.3 61.0 + - - +
119B CYS* 3.4 2.1 + - + +
120B GLY* 3.0 22.7 + - - -
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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
----------------------------------------------------------
93B THR* 5.0 10.5 - - + +
94B MET* 5.4 1.5 - - - +
96B THR* 5.9 4.7 - - + -
113B VAL* 2.9 18.7 + - + +
114B THR* 3.5 9.2 - - - +
116B GLU* 1.3 76.5 - - - +
118B LEU* 1.3 66.1 + - - +
120B GLY* 3.4 2.1 + - - -
121B MET* 3.1 34.8 + - - +
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR 3.3 8.7 + - - +
115B LEU* 3.3 16.0 + - + +
117B ALA* 1.3 80.2 - - - +
119B CYS* 1.3 59.2 + - - +
121B MET* 3.0 12.0 + - + +
122B LEU* 2.8 56.2 + - + +
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Residues in contact with CYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B THR* 5.3 5.8 - - + -
64B PHE* 4.1 17.9 - - + -
94B MET* 4.8 8.1 - - + -
115B LEU* 3.1 37.0 + - - -
116B GLU* 3.7 9.0 - - - +
117B ALA 3.2 0.2 - - - -
118B LEU* 1.3 77.4 - - - +
120B GLY* 1.3 57.1 + - - +
122B LEU* 4.0 9.8 - - - +
123B GLY* 2.7 30.0 + - - -
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Residues in contact with GLY 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A MET* 4.4 11.3 - - - +
94B MET* 3.6 35.4 - - - +
116B GLU 3.0 13.2 + - - -
117B ALA 3.4 1.8 + - - -
118B LEU 3.3 0.2 - - - -
119B CYS* 1.3 76.6 - - - +
121B MET* 1.3 57.1 + - - +
123B GLY* 3.8 1.1 - - - -
124B LEU* 3.0 30.3 + - - +
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Residues in contact with MET 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ALA* 3.1 21.5 + - - +
118B LEU* 3.0 16.2 + - + +
120B GLY* 1.3 75.2 - - - +
122B LEU* 1.3 67.0 + - + +
124B LEU* 3.7 6.9 - - + +
125B ALA* 3.0 23.7 + - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 2.8 51.2 + - + +
119B CYS* 4.0 8.5 - - - +
121B MET* 1.3 71.5 - - + +
123B GLY* 1.3 52.1 + - - +
125B ALA* 3.0 9.4 + - + +
126B VAL* 2.6 43.1 + - + +
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Residues in contact with GLY 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B CYS 2.7 22.3 + - - -
120B GLY* 3.8 1.1 - - - -
122B LEU* 1.3 73.3 - - - +
124B LEU* 1.3 51.7 + - - +
126B VAL* 3.4 7.0 + - - +
127B ALA* 2.7 36.2 + - - +
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A MET* 3.8 51.6 - - + +
124A LEU* 4.0 25.6 - - + -
125A ALA* 4.6 11.9 - - + -
120B GLY 3.0 18.2 + - - +
121B MET* 3.7 7.2 - - + +
123B GLY* 1.3 71.1 - - - +
125B ALA* 1.3 69.1 + - - +
127B ALA* 3.1 7.5 + - + +
128B ALA* 2.9 25.7 + - + +
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Residues in contact with ALA 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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121B MET 3.0 15.0 + - - +
122B LEU* 3.3 13.5 - - + +
124B LEU* 1.3 78.9 - - - +
126B VAL* 1.3 63.1 + - + +
128B ALA* 3.4 4.8 + - - +
129B SER* 3.1 24.4 + - - -
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ILE* 6.3 0.4 - - + -
122B LEU* 2.6 25.5 + - + +
123B GLY* 3.7 6.5 - - - +
125B ALA* 1.3 69.0 - - + +
127B ALA* 1.3 69.4 + - - +
128B ALA 3.0 2.1 + - - -
129B SER* 3.0 9.5 + - - -
130B LEU* 2.9 42.2 + - + +
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Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 5.1 6.7 - - + -
125A ALA* 5.6 1.8 - - + -
49B PHE* 4.7 1.5 - - + -
53B ILE* 4.8 23.6 - - + -
123B GLY 2.7 22.3 + - - +
124B LEU* 3.1 9.8 + - + +
126B VAL* 1.3 78.0 - - - +
128B ALA* 1.3 60.3 + - - +
130B LEU* 3.5 8.4 + - - +
131B ILE* 3.2 36.0 + - + +
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Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ALA* 3.5 32.7 - - + +
128A ALA* 6.1 2.2 - - + -
129A SER* 4.4 2.1 + - - +
124B LEU* 2.9 19.8 + - + +
125B ALA* 3.9 4.5 - - - +
127B ALA* 1.3 75.1 - - - +
129B SER* 1.3 61.8 + - - +
131B ILE* 3.4 2.0 + - - +
132B TYR* 2.8 32.9 + - - +
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Residues in contact with SER 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ALA 3.1 15.4 + - - -
126B VAL* 3.2 14.1 - - - -
128B ALA* 1.3 76.2 - - - +
130B LEU* 1.3 64.0 + - - -
132B TYR* 3.4 4.5 + - - +
133B ALA* 3.0 24.3 + - - +
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B HIS* 4.8 15.9 - - + +
41B LEU* 3.9 38.4 - - + +
42B LEU* 4.9 11.7 - - + +
49B PHE* 3.9 27.4 - - + -
53B ILE* 4.6 11.0 - - + -
126B VAL* 2.9 36.8 + - + +
127B ALA* 4.0 2.5 - - - +
129B SER* 1.3 77.8 - - - +
131B ILE* 1.3 59.1 + - - +
133B ALA* 3.4 4.8 + - - +
134B ARG* 2.9 35.8 + - + +
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Residues in contact with ILE 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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122A LEU* 4.5 18.8 - - + -
125A ALA* 4.0 18.8 - - + +
126A VAL* 4.3 20.6 - - + +
129A SER* 3.8 14.1 - - - +
46B TRP* 4.1 14.4 - - + -
49B PHE* 3.8 23.8 - - + -
127B ALA* 3.2 19.8 + - + +
128B ALA* 3.7 3.1 - - - +
130B LEU* 1.3 74.4 - - - +
132B TYR* 1.3 69.2 + - - +
134B ARG* 3.2 2.1 + - - +
135B PHE* 3.0 45.7 + - + -
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Residues in contact with TYR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A SER* 3.6 38.8 + - - +
132A TYR* 3.4 40.4 - + + -
133A ALA* 4.5 10.0 - - + +
136A THR* 4.4 7.1 + - - -
128B ALA 2.8 21.3 + - - +
129B SER* 4.0 4.9 - - - +
131B ILE* 1.3 74.5 - - - +
133B ALA* 1.3 68.6 + - - +
135B PHE* 3.2 20.1 - + + +
136B THR* 3.3 38.1 - - + +
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.8 23.1 - - + -
129B SER 3.0 17.3 + - - +
130B LEU* 3.6 5.8 - - - +
132B TYR* 1.3 80.8 - - - +
134B ARG* 1.3 54.8 + - - +
136B THR* 2.5 38.8 + - - -
137B ARG* 3.3 7.1 + - - +
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU 3.0 25.7 + - - -
42B LEU* 3.5 31.8 + - + +
44B VAL* 2.6 35.1 + - - +
45B SER* 3.4 0.6 - - - +
46B TRP* 3.2 70.3 + - + +
49B PHE* 3.7 24.5 - - - -
130B LEU* 2.9 21.4 + - - +
131B ILE 3.8 4.3 - - - +
133B ALA* 1.3 75.9 - - - +
135B PHE* 1.3 61.8 + - - +
136B THR 3.2 1.4 + - - -
137B ARG* 3.6 21.9 + - - +
138B PRO* 5.6 0.3 - - - +
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Residues in contact with PHE 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 3.5 52.6 + + - +
126A VAL* 4.4 18.6 - - + -
129A SER* 4.0 29.2 - - - -
130A LEU* 4.1 10.8 - - + -
46B TRP* 3.2 35.9 - + - -
131B ILE* 3.0 21.7 + - + -
132B TYR* 3.2 15.9 - + + +
133B ALA 2.9 0.2 - - - -
134B ARG* 1.3 75.7 - - - +
136B THR* 1.3 62.2 + - + +
137B ARG 3.6 0.7 - - - -
138B PRO* 4.3 8.7 - - - +
250B PHE* 5.1 2.1 - - - -
252B GLN* 3.8 5.4 - - - +
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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