Contacts of the helix formed by residues 109 - 139 (chain C) in PDB entry 5X11
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 SER 109 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C LEU* 1.3 75.7 - - - +
110C ARG* 1.3 61.1 + - - +
111C GLN* 3.3 6.7 - - - -
112C GLU* 3.6 21.1 - - - +
113C ALA* 2.8 28.4 + - - +
81D HIS* 6.3 0.4 - - - -
147D PHE* 4.0 1.3 - - - -
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Residues in contact with ARG 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C SER* 1.3 74.4 - - - +
111C GLN* 1.3 57.5 + - - +
113C ALA* 3.7 1.7 - - - +
114C SER* 3.0 28.6 + - - -
178C MET 4.8 3.2 + - - -
179C ILE* 2.9 33.7 + - + +
180C ASP* 5.3 3.0 + - - +
146D SER* 6.0 1.6 - - - -
147D PHE* 3.6 55.1 - - + +
148D SER* 4.9 7.3 - - - +
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Residues in contact with GLN 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C SER* 3.3 5.9 - - - -
110C ARG* 1.3 77.6 - - - +
112C GLU* 1.3 58.1 + - - +
114C SER* 3.4 7.0 + - - -
115C ASP* 3.0 36.1 + - - -
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Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C LEU* 4.2 18.9 - - + +
109C SER* 3.3 29.7 + - - +
111C GLN* 1.3 75.1 - - - +
113C ALA* 1.3 64.9 + - - +
115C ASP* 3.4 6.9 + - - +
116C LEU* 3.1 24.1 + - - +
81D HIS* 5.6 4.0 - - + -
85D ILE* 4.5 13.1 - - + +
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Residues in contact with ALA 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ILE* 4.0 15.3 - - + -
108C LEU* 4.4 11.1 - - + +
109C SER 2.8 18.1 + - - +
110C ARG 3.7 4.0 - - - +
112C GLU* 1.3 72.1 - - - +
114C SER* 1.3 60.0 + - - +
116C LEU* 3.4 1.1 + - - -
117C PHE* 2.9 39.6 + - + +
179C ILE* 4.0 14.6 - - + -
147D PHE* 3.9 21.1 - - + -
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Residues in contact with SER 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ARG 3.0 18.3 + - - -
111C GLN* 3.6 9.0 - - - -
112C GLU 3.3 0.2 - - - -
113C ALA* 1.3 77.3 - - - +
115C ASP* 1.3 54.5 + - - +
118C THR* 2.7 47.6 + - - -
176C LEU* 3.8 18.0 - - - +
179C ILE* 4.3 8.0 - - - +
180C ASP* 5.0 9.1 - - - +
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Residues in contact with ASP 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C GLN* 3.0 23.6 + - - +
112C GLU* 3.9 6.1 - - - +
113C ALA 3.4 0.2 - - - -
114C SER* 1.3 76.2 - - - +
116C LEU* 1.3 62.1 + - - +
118C THR* 3.8 5.8 - - - -
119C ASP* 3.1 25.6 + - - +
87D HIS* 3.8 13.5 + - + +
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PHE* 4.0 15.5 - - + -
101C LYS* 3.9 33.7 - - + +
108C LEU* 4.2 17.5 - - + -
112C GLU 3.1 16.2 + - - +
113C ALA* 3.8 2.9 - - - +
115C ASP* 1.3 77.2 - - - +
117C PHE* 1.3 78.9 + - + +
119C ASP* 3.6 2.9 + - - +
120C GLN* 3.3 22.1 + - - +
84D LEU 3.3 27.8 - - - +
85D ILE* 4.9 4.5 - - - -
86D ARG 4.2 6.1 - - - +
87D HIS* 4.3 17.7 + - + -
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Residues in contact with PHE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PHE* 4.0 22.2 - + - -
101C LYS 5.8 0.2 - - - -
102C ALA* 4.2 21.1 - - + -
105C ILE* 4.1 27.6 - - + -
108C LEU* 5.9 0.4 - - + -
113C ALA* 2.9 29.0 + - + +
116C LEU* 1.3 91.7 - - + +
118C THR* 1.3 65.2 + - - +
119C ASP 3.3 0.2 - - - -
120C GLN* 3.4 6.4 + - - +
121C LEU* 3.1 22.5 + - - +
171C TRP* 4.2 13.0 - + - -
172C LEU* 4.0 22.1 - - + +
175C ILE* 3.6 32.5 - - + -
176C LEU* 3.8 21.6 - - + +
179C ILE* 4.2 4.5 - - + -
156D LEU* 4.3 3.6 - - + -
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Residues in contact with THR 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C SER* 2.7 33.9 + - - -
115C ASP* 3.8 6.3 - - - +
117C PHE* 1.3 73.2 - - - +
119C ASP* 1.3 61.6 + - - +
121C LEU* 3.3 7.3 + - + +
122C LEU* 3.2 33.0 + - + +
176C LEU* 3.8 20.7 - - + +
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Residues in contact with ASP 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ASP 3.1 17.1 + - - +
116C LEU 3.9 2.4 - - - +
118C THR* 1.3 76.2 - - - +
120C GLN* 1.3 67.9 + - - +
122C LEU* 3.7 9.8 + - - +
123C LYS* 3.3 34.4 + - - +
87D HIS* 3.1 52.9 + - + +
88D GLN 5.2 2.4 - - - +
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Residues in contact with GLN 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PHE* 3.4 51.0 - - + +
116C LEU* 3.3 16.3 + - - +
117C PHE 3.8 4.9 - - - +
118C THR 3.3 0.4 - - - -
119C ASP* 1.3 78.4 + - - +
121C LEU* 1.3 65.9 + - - +
123C LYS* 3.5 4.3 + - - +
124C ARG* 3.0 55.3 + - + +
168C TYR* 4.0 2.6 + - + -
172C LEU* 3.7 18.4 - - + -
88D GLN 4.4 11.3 + - - +
90D ILE* 3.3 21.5 - - - +
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Residues in contact with LEU 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C PHE 3.1 13.2 + - - +
118C THR* 3.3 11.2 - - + +
120C GLN* 1.3 78.1 - - - +
122C LEU* 1.3 57.9 + - + +
124C ARG* 3.3 1.9 + - - +
125C LYS* 2.9 53.6 + - + +
169C VAL* 3.7 43.5 - - + +
172C LEU* 3.8 18.1 - - + +
173C GLU* 4.0 15.0 - - + -
176C LEU* 3.9 20.9 - - + -
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C THR* 3.2 24.4 + - + +
119C ASP* 4.1 10.3 - - - +
121C LEU* 1.3 79.1 - - + +
123C LYS* 1.3 59.5 + - + +
125C LYS* 3.3 15.8 + - + +
126C ALA* 3.0 30.4 + - - +
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Residues in contact with LYS 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ASP* 3.3 29.2 + - - +
120C GLN* 3.8 5.4 - - - +
121C LEU 3.3 0.2 - - - -
122C LEU* 1.3 79.0 - - + +
124C ARG* 1.3 56.6 + - - +
126C ALA* 3.5 7.0 + - - +
127C LYS* 3.1 26.3 + - - +
88D GLN 5.6 1.6 - - - +
89D PRO* 5.4 7.0 - - + -
90D ILE* 4.3 29.0 - - + +
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Residues in contact with ARG 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ASP* 4.9 5.1 + - - -
120C GLN* 3.0 46.2 + - + +
121C LEU 3.6 4.3 - - - +
123C LYS* 1.3 73.9 - - - +
125C LYS* 1.3 54.9 + - - +
127C LYS* 3.2 5.8 + - - +
128C LEU* 2.7 35.0 + - - +
164C ARG* 5.9 0.6 - - - +
165C GLU* 3.4 34.4 + - - +
168C TYR* 3.4 46.8 + - - -
169C VAL* 3.8 18.1 - - + +
172C LEU* 3.9 13.7 - - + -
90D ILE* 3.5 32.1 - - + +
91D PRO* 4.8 8.9 + - - +
94D VAL* 6.2 3.0 - - - +
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Residues in contact with LYS 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LEU* 2.9 47.4 + - + +
122C LEU* 3.7 15.8 - - + +
124C ARG* 1.3 76.9 - - - +
126C ALA* 1.3 57.7 + - - +
128C LEU* 3.3 12.5 + - + +
129C SER* 3.0 28.6 + - - -
169C VAL* 4.1 17.5 - - + -
173C GLU* 4.0 20.5 + - - -
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Residues in contact with ALA 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LEU 3.0 16.3 + - - +
123C LYS* 3.6 8.1 - - - +
124C ARG 3.2 0.2 - - - -
125C LYS* 1.3 74.3 - - - +
127C LYS* 1.3 63.5 + - - +
129C SER* 3.3 7.2 + - - -
130C ASP* 3.1 22.7 + - - +
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Residues in contact with LYS 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C LYS 3.1 14.1 + - - +
124C ARG 3.5 7.4 - - - +
126C ALA* 1.3 75.6 - - - +
128C LEU* 1.3 61.6 + - - +
130C ASP* 3.4 7.1 + - - +
131C LEU* 3.1 31.3 + - + +
165C GLU* 3.9 18.4 - - + +
90D ILE* 4.1 14.4 - - + -
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Residues in contact with LEU 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ARG 2.7 19.0 + - - +
125C LYS* 3.5 10.5 - - + +
126C ALA 3.3 0.2 - - - -
127C LYS* 1.3 74.8 - - - +
129C SER* 1.3 57.7 - - - +
131C LEU* 3.4 2.9 + - + +
132C GLN* 2.8 43.6 + - - +
162C LEU* 3.9 31.0 - - + +
165C GLU* 4.1 22.8 - - + +
166C LYS* 4.0 21.5 - - + -
169C VAL* 4.4 22.0 - - + -
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Residues in contact with SER 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C LYS 3.0 17.2 + - - -
126C ALA* 3.3 8.0 + - - -
128C LEU* 1.3 73.9 - - - +
130C ASP* 1.3 59.4 + - - +
132C GLN* 4.2 5.2 - - - +
133C GLY* 3.0 24.6 + - - -
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Residues in contact with ASP 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ALA 3.1 12.6 + - - +
127C LYS* 3.6 11.4 - - - +
129C SER* 1.3 75.7 - - - +
131C LEU* 1.3 58.6 + - + +
133C GLY* 3.4 1.8 + - - -
134C SER* 2.9 29.0 + - - -
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Residues in contact with LEU 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLN* 4.0 30.1 - - + +
127C LYS* 3.1 18.3 + - + +
128C LEU* 3.8 3.8 - - - +
130C ASP* 1.3 77.4 - - + +
132C GLN* 1.3 59.5 + - - +
134C SER* 3.3 7.8 + - - -
135C TYR* 2.8 27.5 + - - +
158C LEU* 4.4 23.8 - - + +
161C ALA* 3.3 39.0 - - + +
162C LEU* 4.1 13.0 - - + +
165C GLU* 3.7 19.5 - - + -
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Residues in contact with GLN 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C LEU* 2.8 39.2 + - + +
129C SER* 4.2 5.2 - - - +
131C LEU* 1.3 72.3 - - - +
133C GLY* 1.3 57.3 + - - +
135C TYR* 3.1 14.4 + - + +
136C GLU* 3.0 48.3 + - + +
162C LEU* 4.3 21.5 - - + +
----------------------------------------------------------
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Residues in contact with GLY 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C SER 3.0 17.7 + - - -
130C ASP 3.8 1.3 - - - -
132C GLN* 1.3 74.8 - - - +
134C SER* 1.3 61.4 + - - +
136C GLU* 3.3 14.2 + - - +
137C LYS* 3.3 21.1 + - - +
----------------------------------------------------------
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Residues in contact with SER 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ASP 2.9 18.2 + - - -
131C LEU* 3.4 11.9 - - - -
133C GLY* 1.3 76.3 - - - +
135C TYR* 1.3 60.0 + - - +
137C LYS* 3.6 7.2 + - - +
138C LEU* 3.3 16.6 + - - +
158C LEU* 3.8 23.5 - - - +
----------------------------------------------------------
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Residues in contact with TYR 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C LEU 2.8 13.9 + - - +
132C GLN* 3.1 16.6 + - + +
134C SER* 1.3 73.4 - - - +
136C GLU* 1.3 68.5 + - + +
137C LYS 3.1 1.8 - - - -
138C LEU* 3.1 6.9 + - + +
139C MET* 3.0 40.8 + - + +
155C TYR* 4.1 34.8 + + - -
158C LEU* 4.1 23.3 - - + +
159C THR* 4.4 10.7 - - + +
162C LEU* 3.9 25.8 - - + -
----------------------------------------------------------
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Residues in contact with GLU 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C GLN* 3.0 44.8 + - - +
133C GLY* 3.3 10.0 + - - +
135C TYR* 1.3 85.9 - - + +
137C LYS* 1.3 60.0 + - - +
139C MET* 3.6 21.0 - - - +
140C ALA* 4.8 1.7 - - - +
----------------------------------------------------------
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Residues in contact with LYS 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C GLY 3.3 11.6 + - - +
134C SER* 3.8 11.4 - - - +
135C TYR 3.1 0.4 - - - -
136C GLU* 1.3 76.0 - - - +
138C LEU* 1.3 62.8 + - - +
140C ALA* 3.6 16.6 - - - +
----------------------------------------------------------
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Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C SER 3.3 11.1 + - - +
135C TYR* 3.1 10.1 + - + +
137C LYS* 1.3 75.4 - - - +
139C MET* 1.3 53.0 + - - +
140C ALA 2.6 27.1 + - - +
145C MET* 5.3 7.7 - - + +
151C ASP* 3.8 27.4 - - + +
154C HIS* 3.6 44.2 - - + +
155C TYR* 3.9 27.6 - - + +
158C LEU* 3.9 14.4 - - + -
----------------------------------------------------------
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Residues in contact with MET 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C TYR* 3.0 32.1 + - + +
136C GLU* 3.6 14.7 - - - +
137C LYS 3.3 0.6 - - - -
138C LEU* 1.3 73.8 - - - +
140C ALA* 1.3 59.6 + - - +
145C MET* 6.6 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
------------------------------------------------------------
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