Contacts of the helix formed by residues 134 - 157 (chain O) in PDB entry 1H2I
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 134 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103O PHE* 3.8 1.3 - - - -
132O LEU* 3.4 2.7 - - - +
133O LYS* 1.3 80.0 - - - +
135O LYS* 1.3 64.3 + - - +
136O ALA 3.7 0.2 + - - -
137O LEU* 3.1 39.2 + - - +
138O SER* 3.0 27.4 + - - -
130P GLU* 2.8 27.2 + - - -
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Residues in contact with LYS 135 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96O VAL* 4.3 15.5 - - + -
103O PHE* 3.5 47.0 - - + -
133O LYS 3.6 0.2 + - - -
134O SER* 1.3 72.1 + - - +
136O ALA* 1.3 60.3 + - - +
138O SER* 3.0 4.5 + - - -
139O LEU* 2.8 40.6 + - + +
95P PHE* 3.5 37.2 - - + +
97P ASP* 2.8 36.3 + - - +
130P GLU* 5.0 1.0 + - - -
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Residues in contact with ALA 136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134O SER* 3.3 6.5 + - - +
135O LYS* 1.3 81.2 - - - +
137O LEU* 1.3 59.3 + - - +
139O LEU* 3.7 0.2 - - - +
140O GLU* 2.9 31.3 + - - +
95P PHE* 3.3 25.8 - - + -
105P VAL 4.3 3.6 - - - +
106P GLY* 4.4 2.0 - - - -
126P TYR* 3.7 7.7 - - + -
128P VAL* 3.6 35.4 - - + -
130P GLU* 4.1 7.2 + - + +
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Residues in contact with LEU 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132O LEU* 4.1 17.0 - - + +
134O SER* 3.1 30.3 + - - +
136O ALA* 1.3 79.9 - - + +
138O SER* 1.3 56.7 + - - +
140O GLU* 3.7 22.7 - - - +
141O LYS* 3.1 27.9 + - - +
128P VAL* 4.7 9.6 - - + -
130P GLU* 3.8 15.5 - - - +
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Residues in contact with SER 138 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103O PHE* 3.8 16.8 + - - +
105O VAL* 3.8 21.1 - - - -
129O SER* 3.3 29.7 + - - -
132O LEU* 3.4 15.0 - - - +
134O SER 3.0 21.1 + - - -
135O LYS* 3.0 6.1 + - - -
137O LEU* 1.3 75.0 - - - +
139O LEU* 1.3 65.4 + - - +
141O LYS 3.2 0.9 + - - -
142O ALA* 3.0 21.8 + - - +
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Residues in contact with LEU 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93O VAL* 4.5 17.3 - - + -
96O VAL* 4.0 22.7 - - + -
105O VAL* 3.6 25.6 - - + -
107O VAL* 4.7 2.5 - - + -
135O LYS* 2.8 30.9 + - + +
136O ALA 3.7 0.4 - - - +
138O SER* 1.3 71.7 - - - +
140O GLU* 1.3 64.8 + - - +
141O LYS 3.2 0.2 + - - -
142O ALA* 3.2 0.9 + - - +
143O ARG* 2.8 32.7 + - + +
94P ASP* 3.5 20.6 - - + +
95P PHE* 4.0 24.7 - - + -
126P TYR* 3.3 16.6 - - + +
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Residues in contact with GLU 140 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136O ALA 2.9 17.0 + - - +
137O LEU* 3.7 25.9 - - - +
139O LEU* 1.3 75.9 - - - +
141O LYS* 1.3 65.5 + - - +
143O ARG* 4.3 0.4 - - - +
144O LYS* 2.9 56.0 + - + +
126P TYR* 3.5 41.9 - - + +
128P VAL* 4.8 7.1 - - + +
149P ASP* 4.4 0.7 - - - +
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Residues in contact with LYS 141 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128O VAL 2.6 27.4 + - - +
129O SER* 3.9 14.9 - - - +
132O LEU* 5.0 7.2 - - + -
137O LEU 3.1 16.8 + - - +
138O SER 3.7 3.8 - - - +
139O LEU 3.2 0.2 - - - -
140O GLU* 1.3 82.1 - - - +
142O ALA* 1.3 64.3 + - - +
144O LYS* 3.9 2.5 - - - +
145O GLU* 3.0 57.5 + - + +
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Residues in contact with ALA 142 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105O VAL* 3.8 17.0 - - + +
107O VAL* 3.8 19.1 - - + -
127O GLY* 3.3 33.7 - - - +
128O VAL* 4.1 5.2 - - - +
129O SER* 4.5 0.2 - - - -
138O SER 3.0 17.4 + - - +
139O LEU 3.9 0.9 - - - +
141O LYS* 1.3 75.9 - - - +
143O ARG* 1.3 66.8 + - - +
146O ALA* 3.0 22.5 + - - +
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Residues in contact with ARG 143 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91O GLN* 2.8 61.5 + - - +
93O VAL* 3.5 27.1 - - - +
107O VAL* 4.1 12.1 - - + -
139O LEU* 2.8 27.5 + - + +
140O GLU* 4.3 3.1 - - - +
142O ALA* 1.3 73.6 - - - +
144O LYS* 1.3 64.9 + - + +
147O VAL* 3.4 11.4 + - - +
92P ASN* 4.9 4.8 + - - +
94P ASP* 2.5 52.9 + - - -
108P CYS* 3.4 25.3 - - - -
110P PHE* 4.6 5.9 - - - -
124P VAL* 4.1 9.4 - - + -
126P TYR* 3.8 15.9 - - + -
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Residues in contact with LYS 144 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140O GLU* 2.9 48.6 + - + +
141O LYS* 4.1 2.5 - - - +
143O ARG* 1.3 75.9 - - + +
145O GLU* 1.3 67.0 + - + +
147O VAL* 3.4 4.7 + - - +
148O THR* 3.2 24.0 + - - -
124P VAL* 4.0 14.8 - - + +
126P TYR* 3.9 10.8 - - + +
149P ASP* 2.7 36.1 + - - -
153P ARG* 3.5 41.5 + - - +
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Residues in contact with GLU 145 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126O TYR 4.1 4.0 - - - +
127O GLY* 4.2 7.8 - - - -
128O VAL* 3.7 11.1 + - - +
141O LYS* 3.0 62.8 + - + +
144O LYS* 1.3 78.8 - - + +
146O ALA* 1.3 53.6 + - - +
148O THR* 3.2 5.8 + - - +
149O ASP* 2.6 38.9 + - + +
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Residues in contact with ALA 146 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91O GLN* 3.7 11.9 - - - +
107O VAL* 3.4 26.2 - - + +
109O ALA* 3.6 16.6 - - + +
125O GLY* 3.5 9.0 - - - -
126O TYR 3.6 13.5 - - - -
127O GLY* 3.5 1.4 - - - +
142O ALA 3.0 18.4 + - - +
143O ARG 3.6 5.8 - - - +
144O LYS 3.3 0.2 - - - -
145O GLU* 1.3 76.5 - - - +
147O VAL* 1.3 56.5 + - - +
150O GLY 2.9 23.0 + - - -
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Residues in contact with VAL 147 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86O HIS* 5.1 6.5 - - + +
88O ILE* 3.9 31.0 - - + -
91O GLN* 3.5 17.5 - - - +
109O ALA* 3.9 10.8 - - + -
111O VAL* 3.7 5.7 - - + +
143O ARG 3.4 0.4 + - - +
144O LYS 3.4 6.0 + - - +
145O GLU 3.2 0.4 - - - -
146O ALA* 1.3 74.5 - - - +
148O THR* 1.3 62.2 + - - +
150O GLY* 3.1 1.4 + - - -
151O LEU* 2.8 28.5 + - + +
110P PHE* 5.1 0.4 - - + -
122P GLU 4.6 4.0 - - - +
123P ASP* 3.6 25.8 - - - +
124P VAL* 3.3 27.4 - - + -
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Residues in contact with THR 148 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68O GLY* 4.0 27.6 - - - +
72O ILE* 6.6 0.2 - - + -
144O LYS 3.2 15.3 + - - -
145O GLU* 3.9 5.4 - - - -
147O VAL* 1.3 77.9 - - - +
149O ASP* 1.3 65.0 + - - +
151O LEU* 3.2 10.8 + - + +
152O LYS* 2.9 34.2 + - + +
123P ASP* 5.1 3.1 + - - -
153P ARG* 3.8 17.0 + - - -
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Residues in contact with ASP 149 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140N GLU* 5.3 0.2 - - - -
144N LYS* 2.7 33.6 + - - -
125O GLY* 3.5 1.8 - - - -
126O TYR 2.9 28.6 + - - +
145O GLU* 2.6 23.8 + - + +
146O ALA 3.7 2.7 - - - +
148O THR* 1.3 73.7 - - - +
150O GLY* 1.3 57.2 + - - +
152O LYS* 3.3 19.6 + - - +
153O ARG* 2.9 39.0 + - - +
156O ARG* 5.2 4.3 + - - -
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Residues in contact with GLY 150 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111O VAL* 3.8 16.3 - - - +
123O ASP* 4.5 3.0 - - - +
124O VAL 4.0 5.6 - - - -
125O GLY* 3.3 21.9 - - - -
146O ALA 2.9 13.1 + - - -
147O VAL 3.6 2.9 - - - -
149O ASP* 1.3 74.3 - - - +
151O LEU* 1.3 65.7 + - - +
153O ARG* 3.2 1.7 + - - +
154O ALA* 2.9 25.5 + - - +
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Residues in contact with LEU 151 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71O VAL* 5.4 1.8 - - + -
72O ILE* 4.4 26.2 - - + -
84O TRP* 3.9 12.1 - - + -
86O HIS* 3.8 47.1 - - + +
111O VAL* 3.7 14.4 - - + +
113O VAL* 4.7 3.6 - - + -
147O VAL* 2.8 21.1 + - + +
148O THR* 3.6 11.0 - - + +
150O GLY* 1.3 71.2 - - - +
152O LYS* 1.3 65.6 + - + +
154O ALA* 3.3 1.4 + - - +
155O LEU* 3.0 50.2 + - + +
157P SER* 5.3 0.2 - - - +
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Residues in contact with LYS 152 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65O TYR* 4.2 16.2 - - - +
66O ILE* 3.0 33.1 + - + +
67O GLU* 5.0 0.2 - - - +
68O GLY* 4.1 9.6 - - - +
71O VAL* 3.9 35.0 - - + -
148O THR* 2.9 32.7 + - + +
149O ASP* 3.6 20.9 + - - +
151O LEU* 1.3 79.8 - - + +
153O ARG* 1.3 61.9 + - - +
155O LEU* 3.4 2.6 + - - +
156O ARG* 3.1 44.1 + - - +
162O LEU 4.7 1.7 - - - +
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Residues in contact with ARG 153 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144N LYS* 3.6 49.4 + - - +
148N THR* 3.8 17.0 + - - -
123O ASP* 2.4 58.7 + - + +
124O VAL* 2.8 27.9 + - - +
149O ASP* 2.9 25.3 + - - +
150O GLY 3.9 2.7 - - - +
152O LYS* 1.3 74.0 - - - +
154O ALA* 1.3 68.5 + - - +
156O ARG* 3.3 41.2 + - - +
157O SER* 3.8 4.0 + - - -
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Residues in contact with ALA 154 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111O VAL* 3.8 14.8 - - + +
113O VAL* 3.3 27.3 - - + +
121O HIS* 3.7 15.2 - - - +
122O GLU 4.8 1.1 - - - -
123O ASP* 3.7 12.5 - - - +
150O GLY 2.9 17.6 + - - +
151O LEU* 3.7 5.4 - - - +
153O ARG* 1.3 75.3 - - - +
155O LEU* 1.3 64.1 + - - +
157O SER* 3.0 27.4 + - - -
158O PHE* 4.4 1.0 + - - -
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Residues in contact with LEU 155 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71O VAL* 3.8 20.6 - - + -
75O ALA* 4.7 8.5 - - + -
79O PHE* 5.0 5.4 - - + -
84O TRP* 4.3 16.4 - - + -
113O VAL* 3.5 29.8 - - + -
151O LEU* 3.0 45.6 + - + +
152O LYS 3.7 4.7 - - - +
154O ALA* 1.3 77.0 - - - +
156O ARG* 1.3 63.4 + - - +
158O PHE* 3.0 32.6 + - + -
162O LEU* 3.5 35.6 - - + +
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Residues in contact with ARG 156 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72N ILE* 4.2 3.1 - - + +
65O TYR* 6.2 2.8 - - - +
66O ILE* 5.0 8.7 - - - +
71O VAL* 6.1 1.0 - - - +
149O ASP* 5.2 4.4 + - - -
152O LYS* 3.1 40.1 + - - +
153O ARG* 3.5 33.6 - - - +
154O ALA 3.2 0.4 - - - -
155O LEU* 1.3 74.9 - - - +
157O SER* 1.3 63.9 + - - +
159O GLY 3.0 13.2 + - - +
162O LEU 3.9 12.2 + - - +
163O GLY* 3.9 22.3 + - - -
164O ASN* 3.3 30.2 - - - +
166O ILE* 3.9 25.7 - - - +
167O LEU* 4.3 15.9 - - - +
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Residues in contact with SER 157 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72N ILE* 3.5 22.3 - - - +
76N ASN* 2.9 25.0 + - - +
84N TRP* 3.9 9.2 - - - -
86N HIS* 3.5 18.7 - - - -
151N LEU* 5.4 0.2 - - - +
121O HIS* 3.3 28.9 - - - +
123O ASP* 5.0 2.6 + - - -
153O ARG 3.9 5.4 + - - -
154O ALA* 3.0 18.1 + - - -
156O ARG* 1.3 78.4 - - - +
158O PHE* 1.3 56.6 + - - +
159O GLY 3.3 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