Contacts of the helix formed by residues 134 - 157 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PHE* 3.8 1.6 - - - -
132A LEU* 3.4 2.6 - - - +
133A LYS* 1.3 79.4 - - - +
135A LYS* 1.3 57.4 + - - +
136A ALA 3.6 0.2 + - - -
137A LEU* 3.1 38.4 + - - +
138A SER* 2.8 31.7 + - - -
130B GLU* 3.0 26.4 + - - -
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Residues in contact with LYS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A VAL* 4.4 13.9 - - + -
103A PHE* 3.6 47.1 - - + -
133A LYS 3.7 0.2 + - - -
134A SER* 1.3 67.7 + - - +
136A ALA* 1.3 67.7 + - - +
138A SER* 3.0 4.8 + - - -
139A LEU* 2.8 34.6 + - + +
95B PHE* 3.7 38.0 - - + +
97B ASP* 2.8 32.9 + - - +
130B GLU* 5.0 1.2 + - - -
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A SER* 3.6 0.6 + - - +
135A LYS* 1.3 80.2 - - - +
137A LEU* 1.3 64.3 + - + +
139A LEU 3.3 0.2 + - - -
140A GLU* 2.9 25.3 + - - +
95B PHE* 3.6 24.7 - - + -
105B VAL 4.7 1.1 - - - +
126B TYR* 3.8 10.4 - - + -
128B VAL* 3.7 35.9 - - + -
130B GLU* 3.8 14.5 + - + +
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 4.1 16.0 - - + +
134A SER* 3.1 28.9 + - - +
136A ALA* 1.3 85.4 - - + +
138A SER* 1.3 61.8 + - - +
140A GLU* 3.6 21.9 - - - +
141A LYS* 3.1 24.4 + - - +
128B VAL* 4.9 8.1 - - + -
130B GLU* 4.1 13.5 - - - +
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Residues in contact with SER 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PHE* 3.8 15.2 + - - +
105A VAL* 3.8 21.5 - - - -
129A SER* 3.4 26.4 + - - -
132A LEU* 3.3 20.0 - - - +
134A SER 2.8 21.2 + - - -
135A LYS 3.0 5.8 + - - -
137A LEU* 1.3 75.4 - - - +
139A LEU* 1.3 65.7 + - - +
141A LYS 3.3 1.0 + - - -
142A ALA* 3.0 21.0 + - - +
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A VAL* 4.4 20.0 - - + -
96A VAL* 4.1 22.9 - - + -
105A VAL* 3.6 25.5 - - + +
107A VAL* 4.6 2.5 - - + -
135A LYS* 2.8 30.5 + - + +
136A ALA 3.8 1.1 - - - +
138A SER* 1.3 72.5 - - - +
140A GLU* 1.3 65.5 + - - +
142A ALA* 3.2 1.0 + - - +
143A ARG* 2.8 33.5 + - + +
94B ASP* 3.5 20.6 - - + +
95B PHE* 4.2 23.3 - - + -
126B TYR* 3.5 14.8 - - + +
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Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA 2.9 16.4 + - - +
137A LEU* 3.6 25.4 - - - +
139A LEU* 1.3 77.4 - - - +
141A LYS* 1.3 64.2 - - - +
143A ARG* 4.0 1.1 - - - +
144A LYS* 3.0 61.1 + - + +
126B TYR* 3.6 36.6 - - + +
128B VAL* 4.9 7.3 - - - +
149B ASP* 4.4 1.0 - - - +
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A VAL 2.7 28.3 + - - +
129A SER* 4.0 13.6 - - - +
132A LEU* 5.0 7.9 - - + -
137A LEU 3.1 16.1 + - - +
138A SER 3.7 3.4 - - - +
140A GLU* 1.3 80.9 - - - +
142A ALA* 1.3 64.8 + - - +
144A LYS* 3.4 2.7 + - - +
145A GLU* 3.0 56.5 + - - +
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A VAL* 4.0 16.2 - - + +
107A VAL* 3.8 17.6 - - + +
127A GLY* 3.3 33.5 - - - +
128A VAL 4.1 7.0 - - - +
129A SER* 4.5 0.2 - - - -
138A SER 3.0 17.4 + - - +
139A LEU 3.9 1.8 - - - +
141A LYS* 1.3 80.1 - - - +
143A ARG* 1.3 62.0 + - - +
146A ALA* 3.1 21.1 + - - +
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Residues in contact with ARG 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLN* 2.9 62.0 + - - +
93A VAL* 3.5 28.2 - - - +
107A VAL* 4.1 12.3 - - + -
139A LEU* 2.8 26.4 + - + +
140A GLU* 4.2 2.9 - - - +
142A ALA* 1.3 72.1 - - - +
144A LYS* 1.3 65.7 + - + +
146A ALA 3.3 0.9 + - - -
147A VAL* 3.3 13.0 + - - +
92B ASN* 4.9 3.4 + - - +
94B ASP* 2.6 44.7 + - - -
108B CYS* 3.4 25.8 - - - -
110B PHE* 4.5 4.9 - - - -
124B VAL* 4.1 8.7 - - + -
126B TYR* 3.9 22.4 - - + -
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Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLU* 3.0 47.4 + - + +
141A LYS* 4.0 3.6 - - - +
143A ARG* 1.3 77.9 - - + +
145A GLU* 1.3 64.7 + - + +
147A VAL* 3.2 5.0 + - - +
148A THR* 3.1 23.7 + - - -
124B VAL* 4.2 10.1 - - + +
125B GLY 4.6 0.2 - - - -
126B TYR* 4.1 10.8 - - + +
149B ASP* 2.7 35.7 + - - -
153B ARG* 3.4 47.2 + - - +
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Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A TYR 4.1 3.3 - - - +
127A GLY* 4.1 8.0 - - - -
128A VAL* 3.8 10.7 + - - +
141A LYS* 3.0 61.3 + - + +
144A LYS* 1.3 75.0 - - + +
146A ALA* 1.3 61.1 + - - +
148A THR* 4.0 6.0 - - - +
149A ASP* 2.8 34.0 + - + +
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Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLN* 3.8 11.2 - - - +
107A VAL* 3.5 25.6 - - + +
109A ALA* 3.7 16.0 - - + +
125A GLY* 3.6 8.0 - - - -
126A TYR 3.6 12.8 - - - +
127A GLY* 3.6 1.2 - - - +
142A ALA 3.1 18.4 + - - +
143A ARG 3.6 5.4 - - - +
144A LYS 3.1 0.2 - - - -
145A GLU* 1.3 77.9 - - - +
147A VAL* 1.3 57.8 + - - +
150A GLY 2.9 24.6 + - - -
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Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A HIS* 5.2 6.3 - - + +
88A ILE* 3.8 29.2 - - + -
91A GLN* 3.5 16.8 - - - +
109A ALA* 3.9 11.4 - - + -
111A VAL* 3.6 6.9 - - + +
143A ARG 3.3 0.6 + - - +
144A LYS 3.2 7.9 + - - +
146A ALA* 1.3 76.7 - - - +
148A THR* 1.3 58.6 + - - +
150A GLY* 3.1 2.8 + - - -
151A LEU* 2.8 28.1 + - + +
122B GLU 4.5 3.4 - - - +
123B ASP* 3.2 30.3 - - - +
124B VAL* 3.4 26.0 - - + -
153B ARG* 4.9 0.4 - - - +
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Residues in contact with THR 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLY* 4.1 26.7 - - - +
72A ILE* 6.5 0.4 - - + -
144A LYS 3.1 15.5 + - - -
145A GLU* 4.0 6.3 - - - -
147A VAL* 1.3 78.3 - - - +
149A ASP* 1.3 64.1 + - - +
151A LEU* 3.2 11.1 + - + +
152A LYS* 2.9 33.0 + - + +
123B ASP* 5.2 1.9 + - - -
153B ARG* 3.8 17.2 + - - -
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Residues in contact with ASP 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A GLY* 3.3 4.7 - - - -
126A TYR 2.8 27.7 + - - +
145A GLU* 2.8 23.3 + - + +
146A ALA 3.6 3.4 - - - +
148A THR* 1.3 76.8 - - - +
150A GLY* 1.3 55.7 + - - +
152A LYS* 3.3 18.7 + - - +
153A ARG* 3.0 38.4 + - - +
156A ARG* 5.2 4.0 + - - -
140K GLU* 5.3 0.2 - - - -
144K LYS* 2.8 31.7 + - - -
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Residues in contact with GLY 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 3.7 16.5 - - - +
123A ASP* 4.5 3.0 - - - +
124A VAL 4.0 5.2 - - - -
125A GLY* 3.3 23.0 - - - -
146A ALA 2.9 12.7 + - - -
147A VAL 3.6 2.9 - - - -
149A ASP* 1.3 74.7 - - - +
151A LEU* 1.3 64.9 + - - +
153A ARG* 3.3 1.6 + - - +
154A ALA* 2.9 25.5 + - - +
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 5.5 1.8 - - + -
72A ILE* 4.4 26.0 - - + -
84A TRP* 3.9 9.6 - - + -
86A HIS* 3.8 50.7 - - + +
111A VAL* 3.7 14.1 - - + +
113A VAL* 4.7 5.2 - - + -
147A VAL* 2.8 15.0 + - + +
148A THR* 3.2 12.8 + - + +
150A GLY* 1.3 75.3 - - - +
152A LYS* 1.3 67.0 + - + +
154A ALA* 3.7 0.9 - - - +
155A LEU* 3.0 43.4 + - + +
123B ASP* 6.2 0.2 - - - +
157B SER* 5.1 0.4 - - - +
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Residues in contact with LYS 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A TYR* 4.3 16.0 - - - +
66A ILE* 2.8 34.7 + - + +
67A GLU* 4.9 0.2 - - - +
68A GLY* 4.1 13.6 - - - +
71A VAL* 3.8 30.3 - - + -
148A THR* 2.9 27.9 + - + +
149A ASP* 3.7 20.0 + - - +
151A LEU* 1.3 78.9 - - + +
153A ARG* 1.3 62.9 + - - +
155A LEU* 3.4 7.2 + - - +
156A ARG* 3.1 44.3 + - - +
162A LEU 4.6 2.1 - - - +
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Residues in contact with ARG 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ASP* 2.5 57.0 + - + +
124A VAL* 2.9 22.5 + - - +
149A ASP* 3.0 24.0 + - - +
150A GLY 3.3 2.0 + - - +
152A LYS* 1.3 76.5 - - - +
154A ALA* 1.3 63.7 + - - +
156A ARG* 3.1 46.2 + - - +
157A SER* 3.8 5.2 + - - -
144K LYS* 3.5 57.7 + - - +
147K VAL* 5.0 0.2 - - - +
148K THR* 3.9 16.6 + - - -
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL 3.8 15.3 - - - +
113A VAL* 3.3 26.8 - - + +
121A HIS* 3.8 16.5 - - - +
122A GLU 4.8 1.3 - - - -
123A ASP* 3.7 12.2 - - - +
150A GLY 2.9 17.4 + - - +
151A LEU* 3.7 4.9 - - - +
153A ARG* 1.3 75.2 - - - +
155A LEU* 1.3 64.1 + - - +
157A SER* 3.2 23.9 + - - -
158A PHE* 4.5 1.2 + - - -
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 3.9 22.4 - - + +
75A ALA* 4.6 9.9 - - + -
79A PHE* 5.0 4.7 - - + -
84A TRP* 4.2 17.0 - - + -
113A VAL* 3.5 28.9 - - + -
151A LEU* 3.0 47.7 + - + +
152A LYS 3.7 4.5 - - - +
153A ARG 3.2 0.2 - - - -
154A ALA* 1.3 78.1 - - - +
156A ARG* 1.3 62.7 + - - +
157A SER 3.0 0.9 + - - -
158A PHE* 3.0 30.2 + - + -
162A LEU* 3.5 34.6 - - + +
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Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A TYR* 6.1 3.2 - - - +
66A ILE* 4.9 8.5 - - - +
71A VAL* 6.1 1.2 - - - +
149A ASP* 5.2 4.8 + - - -
152A LYS* 3.1 40.7 + - - +
153A ARG* 3.1 35.3 + - - +
155A LEU* 1.3 74.6 - - - +
157A SER* 1.3 63.2 + - - +
159A GLY 2.9 14.4 + - - +
162A LEU 3.7 12.0 + - - +
163A GLY* 3.7 24.7 + - - +
164A ASN* 3.3 30.8 - - - +
166A ILE* 3.9 25.1 - - - +
167A LEU* 4.2 15.3 - - - +
72K ILE* 5.3 3.1 - - + -
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Residues in contact with SER 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A HIS* 3.3 34.3 - - - +
123A ASP* 5.2 2.9 + - - -
153A ARG 4.0 4.5 + - - -
154A ALA* 3.2 12.2 + - - -
155A LEU 3.0 0.8 + - - -
156A ARG* 1.3 78.5 - - - +
158A PHE* 1.3 55.9 + - - +
159A GLY 3.3 0.4 - - - -
72K ILE* 3.5 22.1 - - - +
76K ASN* 3.0 24.1 + - - +
84K TRP* 3.8 8.8 - - - -
86K HIS* 3.5 18.0 - - - -
151K LEU* 5.2 0.9 - - - +
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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