Contacts of the helix formed by residues 129 - 153 (chain C) in PDB entry 2HYE
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 VAL 129 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ASP* 2.2 35.9 + - + +
128C SER* 1.3 72.4 - - - +
130C LEU* 1.3 72.6 + - + +
131C PHE 3.8 2.0 - - - +
132C LEU* 3.6 11.8 - - - +
133C LYS* 3.2 38.5 + - - +
199C LEU* 5.0 17.0 - - + -
213C LEU* 5.0 4.9 - - + -
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Residues in contact with LEU 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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125C SER* 4.5 11.2 - - - +
127C ASP* 2.6 38.4 + - + +
129C VAL* 1.3 82.8 - - + +
131C PHE* 1.3 66.6 + - - +
132C LEU 2.8 1.9 + - - -
133C LYS* 3.0 10.0 + - + +
134C LYS* 2.7 41.3 + - + +
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Residues in contact with PHE 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PHE* 4.1 24.5 - + + -
125C SER 5.8 1.1 + - - +
127C ASP 3.4 10.6 + - - +
128C SER* 4.3 11.7 - - - +
130C LEU* 1.3 79.5 - - - +
132C LEU* 1.3 64.1 + - + +
134C LYS* 3.2 10.5 - - - +
135C ILE* 3.1 36.0 + - + +
188C VAL* 3.6 24.0 - - + -
191C LYS* 3.4 62.8 - - + -
192C THR* 3.2 23.6 - - - -
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Residues in contact with LEU 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C SER* 3.8 17.3 - - - +
129C VAL* 3.6 13.2 - - - +
130C LEU 2.8 1.6 + - - -
131C PHE* 1.3 82.2 - - + +
133C LYS* 1.3 65.8 + - - +
134C LYS 2.7 5.3 + - - -
135C ILE* 2.8 16.0 + - - +
136C ASN* 2.8 11.3 + - - +
191C LYS 4.6 2.5 - - - +
192C THR* 4.0 33.0 - - + +
195C GLY* 3.7 22.4 - - - +
196C ILE* 4.7 4.7 - - + +
199C LEU* 4.0 15.9 - - + -
213C LEU* 3.7 22.4 - - + -
214C LEU* 6.3 1.1 - - + -
217C LEU* 4.2 21.3 - - + +
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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
----------------------------------------------------------
129C VAL* 3.2 25.7 + - - +
130C LEU* 3.0 11.7 + - + +
132C LEU* 1.3 75.3 - - - +
134C LYS* 1.3 65.1 + - - +
136C ASN* 3.6 3.7 + - - +
137C THR* 2.9 25.2 + - - +
210C ASP* 4.9 15.5 - - - +
213C LEU* 3.8 26.4 - - + +
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Residues in contact with LYS 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PHE* 3.5 21.3 - - + -
130C LEU* 2.7 38.9 + - + +
131C PHE* 3.2 14.6 - - - +
132C LEU 2.7 0.2 + - - -
133C LYS* 1.3 76.7 - - - +
135C ILE* 1.3 57.7 + - - +
137C THR* 3.0 3.8 + - - -
138C CYS* 2.8 27.0 + - - +
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Residues in contact with ILE 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PHE* 3.6 27.6 - - + -
131C PHE* 3.4 30.5 - - + +
132C LEU* 2.8 5.6 + - - +
134C LYS* 1.3 78.0 - - - +
136C ASN* 1.3 61.6 + - - +
138C CYS* 3.6 4.1 + - + +
139C TRP* 3.2 20.8 + - - +
178C PHE* 4.7 3.5 - - + -
182C ILE* 4.9 8.5 - - + +
183C ILE* 5.3 5.4 - - + -
188C VAL* 3.2 35.9 - - + -
192C THR* 3.6 7.9 - - + +
217C LEU* 3.5 28.9 - - + -
220C MET* 4.1 12.3 - - + -
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Residues in contact with ASN 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU 2.8 11.2 + - - +
133C LYS* 3.6 9.8 + - - +
135C ILE* 1.3 78.4 - - - +
137C THR* 1.3 56.2 + - - +
139C TRP* 2.8 8.7 + - - +
140C GLN* 2.6 69.5 + - - +
213C LEU* 4.1 22.6 - - + +
216C SER* 2.7 32.6 + - - -
217C LEU* 4.4 10.8 + - + +
220C MET* 5.8 0.9 - - - -
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Residues in contact with THR 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C LYS* 2.9 18.7 + - - +
134C LYS* 3.7 2.7 - - - -
136C ASN* 1.3 72.0 + - - +
138C CYS* 1.3 63.2 + - - +
139C TRP 2.9 6.8 + - - -
140C GLN* 3.6 18.1 + - - +
141C ASP* 3.1 41.0 + - - +
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Residues in contact with CYS 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C GLN* 4.1 22.4 - - - +
121C PHE* 3.4 42.8 - - + -
134C LYS 2.8 9.3 + - - +
135C ILE* 3.7 5.4 - - - +
136C ASN 3.1 0.2 - - - -
137C THR* 1.3 77.4 - - - +
139C TRP* 1.3 57.8 + - - +
141C ASP* 4.4 2.6 - - - +
142C HIS* 3.7 12.4 + - - +
178C PHE* 3.4 14.7 - - - -
182C ILE* 3.9 19.7 - - - -
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Residues in contact with TRP 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 ILE 3.2 12.2 + - - +
136C ASN* 2.8 11.0 + - - +
138C CYS* 1.3 78.8 - - - +
140C GLN* 1.3 66.5 + - + +
141C ASP 2.7 15.2 + - - -
142C HIS* 3.2 6.6 + - - +
143C CYS* 2.9 52.1 + - - +
171C TRP* 5.3 7.6 - + - -
175C LEU* 5.4 4.8 - - + +
178C PHE* 3.1 43.4 - + + +
216C SER* 4.7 13.5 - - - -
220C MET* 3.5 42.2 - - + +
223C ASP* 3.5 33.0 - - + -
224C LEU* 4.8 7.4 - - + +
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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 ASN* 2.6 53.6 + - - +
137C THR* 3.6 17.5 + - - +
139C TRP* 1.3 82.0 - - + +
141C ASP* 1.3 65.9 + - - +
143C CYS* 3.5 6.1 - - - +
144C ARG* 3.5 21.6 + - - +
216C SER* 4.2 8.8 + - - +
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Residues in contact with ASP 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C SER* 4.5 4.5 + - - -
137C THR* 3.1 33.8 + - - +
138C CYS* 4.9 2.2 - - - -
139C TRP 2.7 5.5 + - - -
140C GLN* 1.3 75.8 - - - +
142C HIS* 1.3 54.9 + - - +
143C CYS 2.5 15.7 + - - -
144C ARG* 2.5 61.5 + - - +
145C GLN* 2.8 24.0 + - - +
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Residues in contact with HIS 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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113C HIS* 6.3 0.7 - - - -
114C VAL* 4.4 18.8 - - + +
138C CYS 3.7 18.2 + - - +
139C TRP* 3.2 7.9 + - - +
141C ASP* 1.3 76.5 - - - +
143C CYS* 1.3 73.6 + - - +
145C GLN* 3.4 20.0 - - - +
146C MET* 3.1 44.4 + - + +
174C GLY* 3.4 34.4 + - - -
175C LEU* 4.4 11.9 - - + -
178C PHE* 3.6 32.4 + + + +
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Residues in contact with CYS 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 TRP* 2.9 66.2 + - - +
140C GLN* 3.5 8.5 - - - +
141C ASP 2.5 4.8 + - - -
142C HIS* 1.3 79.1 - - - +
144C ARG* 1.3 57.6 + - - +
146C MET* 2.8 23.8 + - - +
147C ILE* 3.0 22.8 + - + +
171C TRP* 4.8 15.7 + - + -
175C LEU* 6.2 1.3 - - - -
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Residues in contact with ARG 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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76C SER* 3.9 17.4 + - - -
140C GLN* 3.5 9.0 + - - +
141C ASP* 2.5 65.1 + - - +
143C CYS* 1.3 76.1 - - - +
145C GLN* 1.3 63.0 + - - +
147C ILE* 3.4 16.8 + - + +
148C MET* 3.1 23.4 + - - +
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Residues in contact with GLN 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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73C VAL* 3.6 35.2 - - + +
74C GLN* 3.7 19.5 - - - +
75C SER 4.5 0.7 + - - -
76C SER* 4.7 8.1 + - - -
113C HIS* 3.3 32.6 + - - -
141C ASP* 2.8 31.2 + - - +
142C HIS* 3.4 22.7 - - - +
144C ARG* 1.3 79.1 + - + +
146C MET* 1.3 68.5 + - + +
147C ILE 3.3 0.9 - - - -
148C MET* 3.9 2.2 - - - -
149C ILE* 3.4 25.3 - - - +
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Residues in contact with MET 146 (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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74C GLN* 4.8 6.5 - - + +
110C CYS* 3.6 28.0 - - + -
142C HIS* 3.1 47.6 - - + +
143C CYS* 2.8 5.1 + - - +
145C GLN* 1.3 87.4 - - + +
147C ILE* 1.3 61.8 - - - +
148C MET 3.3 0.7 - - - -
149C ILE* 3.4 36.4 - - + +
150C ARG* 3.2 24.8 + - - +
170C ILE* 4.8 10.6 - - + +
171C TRP* 4.4 20.0 - - + +
173C MET* 4.2 16.2 - - - -
174C GLY* 4.4 8.5 - - - -
175C LEU* 6.1 0.4 - - + -
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Residues in contact with ILE 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A GLU* 3.0 38.2 - - + +
143C CYS* 3.0 25.8 - - + +
144C ARG* 3.4 19.1 - - + +
146C MET* 1.3 80.2 - - - +
148C MET* 1.3 67.0 + - - +
150C ARG* 3.7 4.0 + - - +
151C SER* 3.3 19.4 + - - -
171C TRP* 3.9 16.6 - - + +
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Residues in contact with MET 148 (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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561A TRP* 5.8 0.2 - - - -
562A THR* 5.7 2.9 - - - +
73C VAL* 3.6 40.4 - - + -
79C ILE* 5.8 6.3 - - + -
83C LEU* 3.9 35.4 - - + -
144C ARG 3.1 15.2 + - - +
145C GLN* 4.1 0.9 - - - +
147C ILE* 1.3 75.1 - - - +
149C ILE* 1.3 67.3 + - - +
151C SER* 2.2 32.9 + - - -
152C ILE* 3.2 7.4 + - + +
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Residues in contact with ILE 149 (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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70C VAL* 4.2 30.7 - - + -
73C VAL* 4.4 13.0 - - + -
74C GLN* 4.9 3.8 - - + +
106C LEU* 3.9 20.9 - - + -
110C CYS* 4.5 7.6 - - - -
145C GLN 3.4 12.3 + - - +
146C MET* 3.4 35.7 - - + +
147C ILE 3.4 0.2 - - - -
148C MET* 1.3 79.6 - - - +
150C ARG* 1.3 68.1 + - - +
152C ILE* 2.6 24.8 + - + +
153C PHE* 2.9 28.5 + - + -
170C ILE* 4.1 10.8 - - + -
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Residues in contact with ARG 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A GLU* 3.1 42.1 + - - +
586A ILE* 4.6 15.2 - - - +
608A ASP* 5.1 0.6 + - - -
146C MET 3.2 17.7 + - - +
147C ILE 3.8 3.6 - - - +
149C ILE* 1.3 78.7 - - - +
151C SER* 1.3 54.1 + - - +
153C PHE 3.1 1.6 + - - -
154C LEU* 2.6 51.3 + - + +
157C ASP* 3.6 29.2 + - + +
158C ARG* 4.5 22.6 - - - +
169C SER* 4.4 7.3 + - - -
170C ILE* 4.0 19.2 - - + +
171C TRP* 4.1 24.6 - - + +
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Residues in contact with SER 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A TRP* 3.5 32.3 - - - -
585A GLU* 5.0 11.7 - - - -
587A ILE* 5.4 8.7 - - - +
87C TYR* 4.1 3.1 - - - -
147C ILE 3.3 8.5 + - - -
148C MET* 2.2 40.8 + - - -
149C ILE 2.9 1.0 + - - -
150C ARG* 1.3 79.2 - - - +
152C ILE* 1.3 61.4 + - - +
154C LEU* 3.6 18.8 + - - +
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Residues in contact with ILE 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A TRP* 4.4 5.6 - - + -
66C LEU* 4.6 3.6 - - + -
69C ALA* 4.4 11.2 - - + -
70C VAL* 6.0 1.3 - - + -
73C VAL* 5.0 13.7 - - + -
79C ILE* 6.1 1.6 - - + -
83C LEU* 3.7 29.4 - - + +
86C LEU* 3.8 39.9 - - + +
87C TYR* 3.5 19.1 - - - +
90C VAL* 3.6 19.6 - - + +
148C MET* 4.1 8.5 - - + +
149C ILE* 2.6 18.5 + - + +
151C SER* 1.3 77.8 + - - +
153C PHE* 1.3 80.1 + - + +
154C LEU 3.2 3.4 + - - -
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Residues in contact with PHE 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 4.4 27.6 - - + -
69C ALA* 6.4 0.2 - - + -
70C VAL* 4.1 17.0 - - + -
90C VAL* 4.0 19.3 - - + -
102C LEU* 3.9 22.9 - - + -
106C LEU* 3.6 36.6 - - + -
149C ILE* 2.9 26.2 + - + +
150C ARG 3.1 2.9 - - - -
152C ILE* 1.3 93.0 - - + +
154C LEU* 1.3 65.1 + - - +
155C PHE 3.0 3.6 - - - +
156C LEU* 2.7 29.7 + - + +
157C ASP* 3.1 9.2 + - - +
170C ILE* 3.6 18.8 - - + -
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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