Contacts of the helix formed by residues 105 - 132 (chain E) in PDB entry 2R6C
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 TYR 105 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ALA* 4.3 7.6 - - + +
19E ALA* 3.6 24.7 - - + -
20E VAL* 3.8 13.2 - - + -
96E VAL* 6.0 2.5 - - + -
98E THR 5.4 1.3 - - - -
101E ASN* 3.2 42.0 - - + -
102E VAL* 3.1 19.1 - - - +
104E TYR* 1.3 71.0 + + - -
106E ALA* 1.3 70.5 + - - +
108E ILE* 3.0 15.3 + - + +
109E VAL* 2.9 25.3 + - - +
66F ASP* 2.4 29.9 + - - -
68F VAL* 2.9 46.5 + - + +
69F THR* 3.6 8.7 - - - -
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Residues in contact with ALA 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E VAL* 3.5 8.9 - - + +
34E ALA* 4.5 8.7 - - - -
37E ILE* 3.7 25.6 - - + -
38E LEU* 3.9 17.6 - - + +
102E VAL 2.6 23.7 + - - +
103E GLU* 3.7 12.6 - - - -
104E TYR* 3.2 0.4 - - - +
105E TYR* 1.3 72.6 - - - +
107E ARG* 1.3 66.5 + - - +
109E VAL* 2.9 1.7 + - - +
110E GLU* 2.8 22.5 + - - +
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Residues in contact with ARG 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ILE* 4.0 14.3 - - + +
103E GLU* 3.5 37.5 + - - +
104E TYR* 3.1 18.3 - - - +
106E ALA* 1.3 79.0 - - - +
108E ILE* 1.3 57.3 + - + +
110E GLU* 3.8 19.5 - - - +
111E GLU* 3.0 40.2 + - + +
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Residues in contact with ILE 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ALA* 3.5 19.1 - - + -
104E TYR 3.6 6.7 + - - +
105E TYR* 3.0 35.1 + - + +
106E ALA 3.0 1.2 - - - -
107E ARG* 1.3 74.2 - - + +
109E VAL* 1.3 67.2 + - - +
111E GLU* 3.1 14.4 + - - +
112E LYS* 2.9 46.6 + - + +
63F GLU* 4.7 8.5 - - - +
69F THR* 4.6 14.4 - - - +
72F ALA* 3.9 28.9 - - + -
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Residues in contact with VAL 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ALA* 3.9 7.4 - - + +
17E GLU* 3.7 50.7 - - + +
20E VAL* 4.8 4.9 - - + -
38E LEU* 3.8 16.6 - - + -
42E ASP 3.4 23.0 - - - +
43E PHE* 4.2 6.3 - - + -
105E TYR 2.9 14.8 + - - +
106E ALA 3.7 4.0 - - - +
108E ILE* 1.3 75.1 - - - +
110E GLU* 1.3 53.5 + - - +
112E LYS* 3.4 7.2 + - + +
113E SER* 2.8 33.0 + - - -
116E ARG* 4.9 0.8 + - - +
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Residues in contact with GLU 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ILE* 3.7 31.3 - - + +
38E LEU* 3.8 10.0 - - + +
42E ASP* 4.7 7.0 - - - +
106E ALA 2.8 16.6 + - - +
107E ARG* 3.8 21.1 - - - +
109E VAL* 1.3 76.2 - - - +
111E GLU* 1.3 67.3 + - - +
113E SER* 3.4 7.7 - - - -
114E VAL* 3.2 42.3 + - + +
117E ARG* 6.2 0.7 - - - +
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Residues in contact with GLU 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLU 4.9 2.8 - - - +
134B ASP 5.8 0.3 + - - -
135B GLU 5.3 0.2 - - - +
136B ILE* 3.6 43.7 - - + +
137B ASP* 4.9 7.1 - - - +
107E ARG* 3.0 27.1 + - + +
108E ILE* 3.4 12.9 - - - +
110E GLU* 1.3 79.1 - - - +
112E LYS* 1.3 61.9 + - + +
113E SER 2.9 3.4 - - - -
114E VAL* 2.7 30.6 + - - +
115E LEU* 3.1 11.1 + - - +
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Residues in contact with LYS 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLU* 3.2 59.1 + - + +
108E ILE* 2.9 34.7 + - + +
109E VAL* 4.0 5.4 - - + +
111E GLU* 1.3 79.7 - - - +
113E SER* 1.3 59.9 + - - +
115E LEU* 4.0 10.6 - - + +
116E ARG* 2.8 38.0 + - - +
72F ALA* 4.5 8.7 + - - +
75F ALA* 5.8 1.4 - - - +
76F ALA* 4.3 15.6 - - - +
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Residues in contact with SER 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E GLU 4.8 0.9 + - - -
42E ASP* 3.0 41.4 + - - -
109E VAL 2.8 17.3 + - - -
110E GLU 3.4 8.1 - - - -
111E GLU 2.8 1.0 + - - -
112E LYS* 1.3 76.7 - - - +
114E VAL* 1.3 64.3 + - - -
116E ARG* 3.1 19.3 + - - +
117E ARG* 3.1 32.6 + - - +
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Residues in contact with VAL 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ILE* 4.0 12.1 - - + -
140B LEU* 3.5 38.6 - - + -
110E GLU* 3.2 30.1 - - + +
111E GLU* 2.7 14.3 + - - +
113E SER* 1.3 71.1 - - - +
115E LEU* 1.3 58.2 + - + +
117E ARG* 3.1 34.7 + - + +
118E LEU* 2.8 27.4 + - + +
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Residues in contact with LEU 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLY* 3.9 13.7 - - - +
133B GLU* 3.2 39.7 - - + +
136B ILE* 3.6 39.9 - - + +
139B LEU* 3.5 28.9 - - + -
140B LEU* 6.3 0.7 - - + -
111E GLU 3.1 6.3 + - - +
112E LYS* 4.0 14.4 - - + +
113E SER 3.3 0.2 - - - -
114E VAL* 1.3 76.4 - - + +
116E ARG* 1.3 60.1 + - + +
118E LEU* 3.4 11.9 + - + +
119E ILE* 2.9 35.9 + - + +
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Residues in contact with ARG 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E GLU* 5.3 0.8 + - - -
41E GLU 3.8 7.9 + - - -
42E ASP 3.0 31.7 + - - -
43E PHE 4.1 0.2 + - - -
44E TYR* 3.7 49.7 - - - +
109E VAL* 4.9 0.4 + - - +
112E LYS* 2.8 41.2 + - - +
113E SER* 3.1 17.3 + - - +
115E LEU* 1.3 77.4 - - + +
117E ARG* 1.3 55.7 + - - +
119E ILE* 3.4 11.2 + - + +
120E ARG* 2.9 30.0 + - - +
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Residues in contact with ARG 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ARG* 5.5 3.8 - - - +
42E ASP* 5.0 5.3 + - - -
110E GLU* 6.2 0.6 - - - +
113E SER* 3.1 26.0 + - - +
114E VAL* 3.1 36.0 + - + +
116E ARG* 1.3 71.4 - - - +
118E LEU* 1.3 61.0 + - - +
120E ARG* 3.2 8.8 + - - +
121E THR* 2.8 41.5 + - + +
149E GLU 4.4 20.8 + - - -
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Residues in contact with LEU 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ILE* 3.7 30.7 - - + +
129B GLY* 5.2 4.5 - - - -
139B LEU* 4.0 29.2 - - + +
140B LEU* 4.0 28.3 - - + +
143B ALA* 4.2 13.5 - - + -
114E VAL* 2.8 13.0 + - + +
115E LEU* 3.5 20.6 - - + +
117E ARG* 1.3 76.3 - - - +
119E ILE* 1.3 64.6 + - - +
121E THR* 3.5 5.1 + - - -
122E ALA* 2.8 27.1 + - - +
147E ILE* 4.3 15.3 - - + +
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Residues in contact with ILE 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ALA* 4.1 12.8 - - + +
129B GLY* 3.9 30.7 - - - +
130B TYR* 3.5 48.9 - - + +
115E LEU* 2.9 23.9 + - + +
116E ARG* 3.6 9.9 - - + +
118E LEU* 1.3 77.7 - - + +
120E ARG* 1.3 53.9 + - - +
122E ALA* 3.7 3.7 - - - +
123E THR* 2.7 51.3 + - - +
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Residues in contact with ARG 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E ARG 2.9 17.7 + - - +
117E ARG* 3.6 9.6 - - - +
119E ILE* 1.3 79.7 - - - +
121E THR* 1.3 59.9 + - + +
123E THR* 3.9 4.5 - - - -
124E SER* 2.9 31.0 + - - -
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Residues in contact with THR 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E ARG* 2.8 30.2 + - + +
118E LEU* 3.5 5.9 + - - -
120E ARG* 1.3 75.5 - - + +
122E ALA* 1.3 60.0 + - - +
124E SER* 3.8 8.4 + - - -
125E ILE* 3.2 29.8 + - - +
146E LYS* 3.8 38.3 + - + +
147E ILE* 4.0 12.9 - - - +
149E GLU* 6.2 2.5 - - + -
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Residues in contact with ALA 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ALA* 4.1 20.7 - - - +
125B ILE* 4.1 25.1 - - + -
126B ALA* 4.3 6.5 - - + +
118E LEU 2.8 19.8 + - - +
119E ILE 3.7 2.7 - - - +
121E THR* 1.3 76.9 + - - +
123E THR* 1.3 65.4 + - - +
125E ILE* 2.9 21.2 + - - +
126E ALA* 3.1 11.3 + - - +
147E ILE* 5.1 6.7 - - + -
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Residues in contact with THR 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ALA* 3.9 13.9 - - - +
119E ILE* 2.7 39.7 + - - +
120E ARG* 3.9 4.3 - - - -
122E ALA* 1.3 72.0 - - - +
124E SER* 1.3 53.2 + - - +
126E ALA* 3.0 10.5 + - + +
127E GLN* 2.8 38.5 + - + +
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Residues in contact with SER 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E ARG* 2.9 21.2 + - - -
121E THR* 3.8 10.1 - - - -
122E ALA 3.2 0.2 - - - -
123E THR* 1.3 75.3 - - - +
125E ILE* 1.3 56.5 + - - +
127E GLN* 4.3 8.1 - - - -
128E ASP* 3.0 36.8 + - - +
146E LYS* 4.4 17.3 + - - +
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Residues in contact with ILE 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 4.1 27.7 - - + +
119B ILE* 5.5 0.6 - - - +
122B ALA* 4.0 18.4 - - + -
147B ILE* 4.8 6.5 - - + -
121E THR 3.2 16.5 + - - +
122E ALA* 2.9 12.3 + - - +
124E SER* 1.3 76.3 - - - +
126E ALA* 1.3 60.1 + - - +
128E ASP* 3.3 6.4 + - - +
129E GLY* 2.9 24.9 + - - -
139E LEU* 4.6 5.1 - - + +
142E GLU 5.3 0.2 - - - +
143E ALA* 3.7 41.5 - - + +
146E LYS* 4.8 13.5 - - + +
147E ILE* 4.1 15.5 - - + -
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Residues in contact with ALA 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ILE* 4.6 12.1 - - + +
122B ALA* 4.6 8.0 - - + +
123B THR* 4.5 19.7 - - + +
122E ALA 3.1 9.7 + - - +
123E THR* 3.0 13.1 + - + +
125E ILE* 1.3 74.0 - - - +
127E GLN* 1.3 59.4 + - - +
129E GLY* 2.6 26.8 + - - -
130E TYR* 3.3 18.8 - - + -
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Residues in contact with GLN 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E THR* 2.8 24.3 + - + +
124E SER* 4.3 7.4 - - - +
126E ALA* 1.3 73.2 - - - +
128E ASP* 1.3 67.3 + - - +
129E GLY 3.3 0.5 + - - -
130E TYR* 3.7 15.3 + - - -
131E THR* 3.7 24.6 - - + +
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Residues in contact with ASP 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E SER* 3.0 31.4 + - - +
125E ILE* 3.5 7.2 - - - +
126E ALA 3.1 1.2 - - - -
127E GLN* 1.3 82.0 - - - +
129E GLY* 1.3 62.4 + - - +
130E TYR 3.2 2.4 + - - -
131E THR* 4.0 12.3 + - - -
132E ARG* 3.0 53.0 + - - +
139E LEU* 3.7 20.5 - - + +
146E LYS* 4.4 12.4 + - - +
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Residues in contact with GLY 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 4.5 12.2 - - - +
118B LEU* 5.4 2.5 - - - -
119B ILE* 4.4 16.9 - - - +
125E ILE 2.9 9.3 + - - -
126E ALA 2.6 21.0 + - - -
128E ASP* 1.3 72.7 - - - +
130E TYR* 1.3 59.9 + - - -
132E ARG 4.8 0.4 + - - -
133E GLU* 4.2 15.8 - - - +
139E LEU* 4.4 15.4 - - - +
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Residues in contact with TYR 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ILE* 3.3 38.4 - - + +
126E ALA* 3.3 26.9 - - + -
127E GLN* 3.7 9.6 + - - +
128E ASP 3.2 0.2 - - - -
129E GLY* 1.3 77.4 - - - +
131E THR* 1.3 65.5 + - + +
132E ARG 3.5 8.6 - - - +
133E GLU* 4.3 13.5 - - - +
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Residues in contact with THR 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E GLN* 3.7 30.3 - - + +
128E ASP* 3.7 17.5 + - - -
130E TYR* 1.3 78.5 - - + +
132E ARG* 1.3 71.3 + - - +
134E ASP* 4.2 6.1 - - - +
----------------------------------------------------------
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Residues in contact with ARG 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E ASP* 3.0 33.9 + - - +
129E GLY 5.2 0.2 - - - -
130E TYR 3.5 4.7 - - - +
131E THR* 1.3 89.6 - - - +
133E GLU* 1.3 75.8 + - - +
134E ASP* 3.3 13.1 - - - +
135E GLU* 2.6 46.9 + - + +
138E VAL* 5.4 0.2 - - - +
139E LEU* 3.5 36.0 - - + +
142E GLU* 3.2 29.6 + - - -
146E LYS* 5.1 0.4 - - - +
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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