Contacts of the helix formed by residues 110 - 133 (chain C) in PDB entry 3H1J
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 110 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C SER 2.8 15.6 + - - +
108C TYR 3.6 2.2 - - - -
109C LEU* 1.3 79.6 - - - +
111C LYS* 1.3 62.0 + - - +
112C GLU* 3.5 3.4 - - - -
113C THR* 3.2 16.5 + - - +
114C TRP* 3.0 19.8 + - - +
201C LEU* 4.1 16.6 - - + -
204C SER* 3.5 29.9 + - - +
205C GLY 2.9 29.0 + - - -
206C SER 3.7 8.5 + - - -
207C ASN* 3.7 19.4 + - + -
314C ARG* 3.3 32.9 + - - -
502C HEM 4.1 9.9 - - + -
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Residues in contact with LYS 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C TYR 3.8 13.2 - - - +
109C LEU* 3.2 16.0 + - - +
110C TYR* 1.3 72.8 - - - +
112C GLU* 1.3 66.5 + - + +
114C TRP* 3.3 2.6 + - - +
115C ASN* 2.8 45.3 + - - +
306C PRO* 3.8 25.0 + - + +
307C PHE* 3.2 42.1 - - + -
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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
----------------------------------------------------------
110C TYR 3.5 1.3 - - - -
111C LYS* 1.3 80.6 + - + +
113C THR* 1.3 67.2 + - - +
115C ASN* 4.3 7.4 - - - +
116C THR* 2.9 32.6 + - + +
200C PHE* 3.3 48.1 - - + -
9P HIS* 6.4 0.2 - - - +
10P PRO* 5.4 5.0 - - - +
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Residues in contact with THR 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C TYR* 3.2 20.9 + - - +
112C GLU* 1.3 76.8 - - - +
114C TRP* 1.3 62.9 + - - +
116C THR* 2.9 11.0 + - - -
117C GLY 3.0 0.3 + - - -
197C HIS* 2.9 45.5 - - + +
200C PHE* 3.6 8.7 + - - +
201C LEU* 3.3 42.0 + - + -
204C SER* 5.1 0.2 + - - -
502C HEM 3.7 24.7 - - + -
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Residues in contact with TRP 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ILE* 4.1 20.4 - - + -
102C GLY* 3.9 24.5 - - - -
103C LEU* 4.2 13.0 - - + -
108C TYR* 3.4 33.0 - - + +
110C TYR 3.0 15.8 + - - +
111C LYS 3.7 2.9 - - - +
113C THR* 1.3 75.8 - - - +
115C ASN* 1.3 62.6 + - - +
117C GLY* 2.6 22.9 + - - -
118C VAL* 2.8 19.9 + - + +
302C LEU* 2.9 34.5 + - + -
303C PHE* 5.1 0.2 - - - -
305C ILE* 4.2 18.8 - - + -
306C PRO* 3.6 22.4 - - + +
502C HEM 3.6 58.2 - - + +
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Residues in contact with ASN 115 (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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111C LYS* 2.8 41.3 + - - +
112C GLU* 4.0 7.2 - - - +
114C TRP* 1.3 79.3 - - - +
116C THR* 1.3 65.4 + - + +
118C VAL* 3.0 18.7 + - - +
119C ILE* 3.1 16.8 + - + +
303C PHE* 3.4 32.5 - - + +
306C PRO* 5.1 2.8 - - - +
307C PHE* 5.9 3.5 - - - -
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Residues in contact with THR 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLU* 2.9 23.7 + - - +
113C THR 2.9 4.3 + - - -
115C ASN* 1.3 74.1 - - + +
117C GLY* 1.3 55.9 + - - +
119C ILE* 3.1 13.5 + - + +
120C LEU* 2.8 31.4 + - - +
193C ILE* 4.3 15.7 - - + +
196C ILE* 4.1 9.6 - - + -
197C HIS* 2.8 38.0 + - - -
200C PHE* 4.0 24.7 - - + -
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Residues in contact with GLY 117 (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 THR 3.0 6.5 + - - -
114C TRP 2.6 16.1 + - - -
116C THR* 1.3 73.1 + - - +
118C VAL* 1.3 54.7 + - - -
120C LEU* 3.0 5.7 + - - +
121C LEU 2.9 24.1 + - - -
197C HIS* 3.6 7.6 - - - -
502C HEM 2.9 41.7 - - - +
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Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C TRP* 3.3 21.8 - - + +
115C ASN* 3.0 10.5 + - - +
117C GLY* 1.3 76.5 - - - +
119C ILE* 1.3 58.6 + - - +
121C LEU* 3.4 5.0 + - + +
122C LEU* 2.9 36.1 + - + +
299C VAL* 4.6 7.4 - - + +
302C LEU* 4.0 30.7 - - + -
303C PHE* 3.6 39.9 - - + -
502C HEM 3.6 15.4 - - + +
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Residues in contact with ILE 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ASN 3.1 14.1 + - - +
116C THR* 3.1 14.3 + - + +
118C VAL* 1.3 74.0 - - - +
120C LEU* 1.3 62.0 + - - +
122C LEU* 3.3 10.6 + - + +
123C THR* 2.7 44.9 + - - +
193C ILE* 4.1 23.1 - - + -
303C PHE* 4.0 20.0 - - + -
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ILE* 4.8 0.9 - - - -
116C THR 2.8 18.8 + - - +
117C GLY 3.0 6.3 + - - +
119C ILE* 1.3 76.9 - - - +
121C LEU* 1.3 53.8 + - - +
123C THR* 3.0 5.3 + - - -
124C LEU* 2.6 38.1 + - - +
190C ILE* 3.7 25.2 - - + +
193C ILE* 4.1 12.1 - - + -
194C THR* 3.6 17.5 - - - +
197C HIS* 3.9 27.8 - - + +
502C HEM 3.5 57.0 - - + -
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Residues in contact with LEU 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C PHE* 5.2 4.0 - - + -
95C ILE* 3.5 34.0 - - + +
96C PHE* 4.7 5.8 - - + -
99C ILE* 3.7 16.4 - - + -
117C GLY 2.9 7.0 + - - +
118C VAL* 3.7 7.9 - - + +
120C LEU* 1.3 74.5 - - - +
122C LEU* 1.3 59.3 + - - +
124C LEU* 3.1 2.7 + - + +
125C MET* 2.9 66.2 + - + +
299C VAL* 4.1 11.7 - - + -
302C LEU* 3.7 28.7 - - + -
502C HEM 3.9 15.1 - - + +
2007C PEE 4.9 6.7 - - + -
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Residues in contact with LEU 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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118C VAL* 2.9 28.4 + - + +
119C ILE* 3.7 10.5 - - + +
121C LEU* 1.3 77.6 - - - +
123C THR* 1.3 61.6 + - - +
125C MET* 3.3 8.6 + - - +
126C ALA* 3.0 20.8 + - - +
299C VAL* 3.5 29.4 - - + -
300C LEU* 3.9 26.5 - - + -
303C PHE* 4.5 6.3 - - + -
2001C SMA 3.7 28.8 - - - +
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Residues in contact with THR 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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119C ILE* 2.7 35.4 + - - +
120C LEU* 3.6 4.0 - - - -
122C LEU* 1.3 71.2 - - - +
124C LEU* 1.3 67.5 + - - +
126C ALA* 3.2 4.9 + - - +
127C THR* 2.7 33.8 + - - +
186C LEU* 4.4 21.3 - - + +
189C ALA* 5.1 4.3 - - + -
190C ILE* 3.4 28.7 - - + +
193C ILE* 4.6 7.1 - - + +
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Residues in contact with LEU 124 (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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91C PHE* 3.5 37.7 - - + +
92C PHE* 3.9 25.6 - - + -
95C ILE* 3.7 27.6 - - + -
120C LEU 2.6 21.6 + - - +
121C LEU* 3.4 5.8 - - - +
123C THR* 1.3 75.0 - - - +
125C MET* 1.3 58.7 + - - +
127C THR* 3.4 0.3 - - - -
128C ALA* 2.8 28.4 + - - +
190C ILE* 3.8 11.2 - - + +
501C HEM 3.5 38.4 - - + -
502C HEM 6.0 2.2 - - + -
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Residues in contact with MET 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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92C PHE* 4.2 16.4 - - + -
96C PHE* 5.1 4.3 - - + -
121C LEU* 2.9 49.9 + - + +
122C LEU* 3.4 9.9 - - - +
124C LEU* 1.3 77.5 - - - +
126C ALA* 1.3 64.8 + - - +
128C ALA* 3.2 2.4 + - - +
129C PHE* 3.0 22.3 + - - +
274C TYR 5.6 0.7 - - - +
275C PHE* 3.8 17.9 - - + -
277C PHE* 4.4 18.6 - - + -
299C VAL* 3.9 21.3 - - + -
2001C SMA 3.7 48.2 - - + +
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Residues in contact with ALA 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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122C LEU 3.0 13.4 + - - +
123C THR* 3.8 7.4 - - - +
125C MET* 1.3 75.0 - - - +
127C THR* 1.3 64.0 + - - +
129C PHE* 3.1 4.8 + - - +
130C VAL* 3.1 27.2 + - - +
186C LEU* 4.5 11.7 - - + -
2001C SMA 3.7 38.7 + - + +
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Residues in contact with THR 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C THR 2.7 24.0 + - - -
124C LEU* 3.4 5.4 - - - -
126C ALA* 1.3 76.2 - - - +
128C ALA* 1.3 63.1 + - - +
130C VAL* 3.1 7.4 - - - +
131C GLY 3.0 19.6 + - - -
183C HIS* 3.0 28.3 + - + +
186C LEU* 3.2 24.2 - - + +
187C PRO* 4.1 15.7 - - + -
190C ILE* 3.6 8.1 - - - +
501C HEM 3.5 31.0 - - + -
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Residues in contact with ALA 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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92C PHE* 3.6 31.2 - - + -
124C LEU 2.8 20.0 + - - +
125C MET 3.8 2.5 - - - +
127C THR* 1.3 72.6 - - - +
129C PHE* 1.3 64.4 + - - +
131C GLY 3.9 0.4 - - - -
132C TYR* 3.2 20.6 + - - +
272C GLU* 4.7 1.1 - - - +
274C TYR* 4.2 15.0 + - + +
275C PHE* 4.9 0.9 - - + -
501C HEM 3.9 29.1 - - + +
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Residues in contact with PHE 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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125C MET 3.0 12.6 + - - +
126C ALA 3.3 6.1 - - - +
127C THR 3.1 0.2 - - - -
128C ALA* 1.3 74.1 - - - +
130C VAL* 1.3 77.1 + - + +
131C GLY 3.0 0.7 - - - -
132C TYR* 2.9 18.6 + + + +
133C VAL* 3.3 15.8 + - + +
143C GLY* 4.0 1.1 - - - -
144C ALA* 3.7 32.1 - - - -
147C ILE* 3.2 50.3 - - + -
148C THR* 4.3 2.5 - - + -
179C PHE* 3.9 20.2 - + - -
272C GLU* 4.9 3.8 - - - -
275C PHE* 4.4 8.0 - + + -
2001C SMA 3.7 52.0 - - + -
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Residues in contact with VAL 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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126C ALA 3.1 11.0 + - - +
127C THR* 3.1 15.7 - - - +
129C PHE* 1.3 89.7 - - + +
131C GLY* 1.3 66.7 + - - +
133C VAL* 3.1 16.7 + - - +
134C LEU* 3.5 13.3 - - - +
179C PHE* 4.0 35.5 - - + +
182C LEU* 4.5 10.3 - - + -
183C HIS* 3.5 29.2 - - + +
186C LEU* 4.8 3.6 - - + -
2001C SMA 4.0 20.0 - - + -
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Residues in contact with GLY 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C THR 3.0 10.0 + - - -
128C ALA 4.1 1.1 - - - -
129C PHE 3.0 1.4 - - - -
130C VAL* 1.3 77.7 - - - +
132C TYR* 1.3 61.4 + - - +
134C LEU* 3.0 22.8 + - - +
135C PRO* 3.7 0.2 - - - +
183C HIS* 3.1 37.5 - - - -
501C HEM 3.5 18.4 - - - +
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Residues in contact with TYR 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ALA 3.2 14.3 + - - +
129C PHE* 2.9 11.5 + + - +
131C GLY* 1.3 75.4 - - - +
133C VAL* 1.3 57.2 + - + +
134C LEU 3.1 0.7 - - - -
135C PRO* 3.0 10.3 - - - +
139C MET* 3.1 42.6 - - + +
140C SER* 2.8 24.0 + - - -
143C GLY* 6.0 2.5 - - - -
253C ASP* 4.2 12.4 + - - +
256C ASN* 3.7 22.0 - - + +
270C LYS 5.6 0.2 + - - -
272C GLU* 3.5 42.8 - - + +
274C TYR* 5.1 0.2 - - - +
501C HEM 3.5 33.7 - - + -
2001C SMA 4.3 7.3 - - - -
2010C UNL 4.5 11.2 - - - -
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Residues in contact with VAL 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C PHE* 3.4 37.5 - - + +
130C VAL 3.1 9.7 + - - +
132C TYR* 1.3 79.3 - - + +
134C LEU* 1.3 61.1 + - + +
135C PRO* 3.5 0.4 - - - -
136C TRP* 3.1 46.3 + - + -
140C SER* 3.6 18.2 - - - +
143C GLY* 5.3 0.4 - - - -
144C ALA* 3.7 22.7 - - + -
175C THR* 6.3 0.2 - - + -
176C LEU* 4.1 2.1 - - + +
179C PHE* 3.9 20.2 - - + -
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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