Contacts of the helix formed by residues 120 - 145 (chain C) in PDB entry 3E6C
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 GLU 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116C PHE 3.4 12.3 + - - +
118C THR 4.2 0.2 - - - -
119C ASP* 1.3 72.8 + - - +
121C ASP* 1.3 66.4 + - - +
123C ILE* 3.1 42.3 + - + +
124C PHE* 3.7 14.7 - - + -
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Residues in contact with ASP 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ASP* 3.1 13.9 + - - +
120C GLU* 1.3 82.9 - - - +
122C MET* 1.3 69.8 + - + +
123C ILE 3.1 0.2 - - - -
124C PHE* 3.1 23.6 + - + +
125C GLU* 3.2 16.2 + - + +
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Residues in contact with MET 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 4.2 17.3 - - - -
24C LYS* 3.7 38.1 - - + -
25C LEU* 4.3 13.0 - - + -
28C TYR* 3.8 17.9 - - + -
115C VAL* 4.0 20.6 - - + -
116C PHE* 4.0 7.4 - - + -
119C ASP* 3.2 39.2 + - - +
121C ASP* 1.3 80.8 - - + +
123C ILE* 1.3 67.3 + - - +
125C GLU* 3.7 18.5 - - + +
126C ILE* 3.1 28.6 + - + +
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Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C PHE* 3.6 45.6 - - + +
120C GLU* 3.1 35.4 + - + +
122C MET* 1.3 80.2 - - - +
124C PHE* 1.3 68.3 + - + +
126C ILE* 3.3 4.0 + - - +
127C PHE* 3.1 55.1 + - + -
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Residues in contact with PHE 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C GLU* 3.7 32.1 - - + -
121C ASP* 3.1 15.6 + - + +
123C ILE* 1.3 85.4 - - + +
125C GLU* 1.3 62.1 + - - +
127C PHE* 3.5 31.2 + + + +
128C LYS* 3.0 43.6 + - - +
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Residues in contact with GLU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C PHE* 3.8 19.8 - - - -
22C ILE* 3.5 37.4 - - + +
24C LYS* 5.9 4.0 - - + -
121C ASP* 3.2 16.2 + - + +
122C MET* 3.7 27.1 - - + +
124C PHE* 1.3 78.4 - - - +
126C ILE* 1.3 61.9 + - - +
128C LYS* 3.0 35.8 + - - +
129C ASN* 3.1 17.0 + - - +
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Residues in contact with ILE 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 4.1 11.0 - - + -
25C LEU* 5.0 11.4 - - + -
53C MET* 3.9 20.9 - - + -
83C LEU* 3.9 21.8 - - + -
112C LEU* 4.1 16.4 - - + -
116C PHE* 3.9 26.5 - - + -
122C MET* 3.1 17.6 + - + +
123C ILE 3.7 7.4 - - - +
125C GLU* 1.3 73.7 - - - +
127C PHE* 1.3 67.4 + - + +
129C ASN* 3.1 2.9 + - - +
130C TYR* 2.9 46.2 + - + -
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Residues in contact with PHE 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C ILE* 3.1 39.9 + - + -
124C PHE* 3.6 37.2 - + - +
125C GLU 3.4 0.2 - - - -
126C ILE* 1.3 77.4 - - + +
128C LYS* 1.3 53.7 + - + +
130C TYR* 3.2 13.3 + + - +
131C LEU* 2.7 38.4 + - - +
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Residues in contact with LYS 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ASP 4.7 18.0 - - - +
11C CYS* 3.7 20.9 - - - -
20C PHE* 3.6 32.0 - - + -
124C PHE* 3.0 26.7 + - - +
125C GLU* 3.0 34.1 + - - +
126C ILE 3.2 0.2 - - - -
127C PHE* 1.3 76.4 - - + +
129C ASN* 1.3 55.2 - - - +
131C LEU* 3.5 2.2 + - + -
132C THR* 2.7 38.3 + - - -
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Residues in contact with ASN 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 3.4 14.6 + - - +
20C PHE* 3.0 35.6 + - - +
22C ILE* 4.0 8.2 - - + +
83C LEU* 3.8 34.5 + - + +
85C GLY* 5.7 0.3 - - - -
125C GLU 3.1 12.4 + - - +
126C ILE* 3.4 9.4 - - - +
128C LYS* 1.3 75.9 - - - +
130C TYR* 1.3 69.6 + - - +
132C THR* 3.5 3.1 + - - -
133C LYS* 3.1 47.8 + - - +
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Residues in contact with TYR 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C MET* 3.4 18.0 - - + +
85C GLY* 2.7 28.0 + - - -
87C LEU* 4.7 3.1 - - - +
88C TYR* 5.7 2.9 - - - -
126C ILE* 2.9 46.3 + - + -
127C PHE* 3.6 13.2 - + - +
129C ASN* 1.3 78.2 + - - +
131C LEU* 1.3 65.7 + - - +
133C LYS* 3.1 8.2 + - + +
134C VAL* 2.9 33.0 + - + +
604C 3C4 3.5 28.9 - - + -
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Residues in contact with LEU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C CYS* 4.1 22.2 - - + -
127C PHE 2.7 20.5 + - - +
128C LYS* 3.8 7.0 - - - +
130C TYR* 1.3 74.4 - - - +
132C THR* 1.3 56.3 + - - +
134C VAL* 3.3 11.3 + - + +
135C ALA* 2.8 40.1 + - + +
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Residues in contact with THR 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C CYS* 3.2 27.1 - - - +
12C GLY* 3.8 27.3 - - - +
13C ALA* 4.2 1.8 + - + +
19C PHE* 3.9 20.2 - - + -
20C PHE* 3.5 25.7 - - + +
128C LYS 2.7 21.3 + - - -
129C ASN 3.6 5.6 - - - -
130C TYR 3.2 0.2 - - - -
131C LEU* 1.3 77.6 - - - +
133C LYS* 1.3 62.4 + - - +
135C ALA* 4.0 1.7 - - - +
136C TYR* 3.1 22.7 + - - +
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Residues in contact with LYS 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 3.8 36.1 - - + -
76C TYR* 4.4 7.0 - - + -
83C LEU 2.7 29.0 + - - -
85C GLY* 3.8 4.0 - - - +
129C ASN* 3.1 33.0 + - - +
130C TYR* 3.1 12.1 + - + +
132C THR* 1.3 72.8 - - - +
134C VAL* 1.3 68.8 + - + +
136C TYR* 3.3 4.0 + - - +
137C TYR* 3.0 41.3 + - + -
604C 3C4 2.7 44.7 + - + +
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Residues in contact with VAL 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C TYR* 2.9 28.2 + - + +
131C LEU* 3.8 11.9 - - + +
133C LYS* 1.3 77.3 - - + +
135C ALA* 1.3 57.1 + - - +
137C TYR* 5.2 1.6 - - - -
138C ALA* 2.9 40.7 + - + +
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Residues in contact with ALA 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C CYS 3.9 18.6 - - - +
12C GLY* 5.8 0.9 - - - -
131C LEU* 2.8 29.4 + - + +
132C THR 4.0 1.1 - - - +
134C VAL* 1.3 71.8 - - - +
136C TYR* 1.4 62.2 + - - +
138C ALA* 4.6 2.9 - - - +
139C ARG* 3.2 27.5 + - - +
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Residues in contact with TYR 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ALA* 3.4 30.3 - - + +
14C ILE 3.5 23.5 + - - -
15C ILE* 4.2 3.1 - - - -
16C PRO* 3.4 28.0 - - + +
19C PHE* 3.7 20.6 - + + -
132C THR 3.1 18.7 + - - +
133C LYS 3.7 2.9 - - - +
134C VAL 3.2 0.2 - - - -
135C ALA* 1.4 77.9 - - - +
137C TYR* 1.3 91.8 + + - +
139C ARG* 3.5 6.7 + - - +
140C GLN* 3.0 53.1 + - + +
186C ILE* 3.9 14.4 + - - +
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Residues in contact with TYR 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 3.5 24.0 - + - -
75C LEU* 2.7 49.0 + - + -
76C TYR* 3.4 20.2 - + - +
133C LYS* 3.0 36.2 + - + +
134C VAL* 4.5 1.8 - - - +
136C TYR* 1.3 92.7 - + - +
138C ALA* 1.3 66.2 + - - +
140C GLN* 3.3 7.3 + - + +
141C VAL* 3.0 30.5 + - + +
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Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C VAL* 2.9 31.1 + - + +
135C ALA* 4.6 2.5 - - - +
137C TYR* 1.3 77.8 - - - +
139C ARG* 1.3 60.4 + - - +
141C VAL* 3.4 7.7 + - - +
142C ALA* 3.3 21.0 + - - +
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Residues in contact with ARG 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C ALA 3.2 22.4 + - - +
136C TYR* 3.7 4.7 - - - +
138C ALA* 1.3 75.7 - - - +
140C GLN* 1.3 53.7 + - - +
142C ALA* 3.2 7.1 + - + +
143C GLU* 2.8 41.3 + - + +
155C ARG* 3.8 23.6 - - - +
159C GLU* 4.4 17.2 + - - -
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Residues in contact with GLN 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C TYR* 3.0 46.6 + - + +
137C TYR* 3.3 13.0 + - + +
139C ARG* 1.3 72.1 - - - +
141C VAL* 1.3 67.1 + - + +
143C GLU* 3.3 20.8 + - - +
144C MET* 2.9 57.7 + - - +
152C ARG* 4.9 0.8 - - - +
186C ILE* 3.4 21.8 + - - +
187C THR* 4.3 9.9 + - - +
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Residues in contact with VAL 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C TYR* 3.0 21.1 + - + +
138C ALA* 3.7 9.9 - - - +
140C GLN* 1.3 79.0 - - + +
142C ALA* 1.3 63.0 + - + +
144C MET* 3.2 8.6 + - - +
145C ASN* 3.1 39.2 + - - +
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Residues in contact with ALA 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C ALA 3.3 9.7 + - - +
139C ARG* 3.2 11.5 + - + +
141C VAL* 1.3 80.5 - - + +
143C GLU* 1.3 56.6 + - - +
145C ASN* 3.3 11.0 + - - +
146C THR* 2.7 33.7 + - - +
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Residues in contact with GLU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C ARG* 2.8 31.2 + - + +
140C GLN* 3.5 22.9 + - - +
142C ALA* 1.3 70.9 - - - +
144C MET* 1.3 61.7 + - - +
146C THR* 4.4 0.2 - - - -
147C TYR* 2.9 50.2 + - + +
152C ARG* 3.7 32.8 - - - +
155C ARG* 2.7 47.9 + - - +
159C GLU* 4.3 4.5 - - - +
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Residues in contact with MET 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C GLN* 2.9 45.8 + - - +
141C VAL* 3.2 8.0 + - - +
143C GLU* 1.3 76.1 - - - +
145C ASN* 1.3 62.4 + - - +
146C THR 3.6 0.5 + - - -
147C TYR 3.8 3.5 + - - +
152C ARG* 3.6 49.0 + - - +
187C THR 4.7 4.3 - - - +
188C GLY* 4.9 9.0 - - - +
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Residues in contact with ASN 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C VAL* 3.1 31.4 + - - +
142C ALA* 3.6 12.3 - - - +
143C GLU 3.2 0.4 - - - -
144C MET* 1.3 78.4 - - - +
146C THR* 1.3 59.6 + - - +
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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