Contacts of the helix formed by residues 134 - 160 (chain A) in PDB entry 4HKC
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 ALA 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ARG* 5.1 3.9 - - - +
132A VAL 3.8 1.8 + - - -
133A ALA* 1.4 70.7 - - - +
135A GLY* 1.3 68.3 + - - +
136A ASP* 4.2 7.9 - - + +
137A ASP* 2.8 36.6 + - - +
138A LYS* 2.9 9.0 + - - +
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Residues in contact with GLY 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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133A ALA 3.6 2.8 + - - -
134A ALA* 1.3 71.4 - - - +
136A ASP* 1.3 63.5 + - - +
137A ASP 3.6 0.3 + - - -
138A LYS* 3.7 18.5 + - - +
139A LYS* 4.5 3.3 + - - +
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Residues in contact with ASP 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ALA* 2.8 6.1 + - + +
135A GLY* 1.3 81.0 - - - +
137A ASP* 1.3 64.4 + - - +
139A LYS* 4.7 5.4 + - - +
140A GLY 5.5 0.5 + - - -
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Residues in contact with ASP 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ALA* 5.4 0.2 - - - -
134A ALA* 2.8 27.5 + - + +
136A ASP* 1.3 78.7 - - - +
138A LYS* 1.3 66.1 + - - +
139A LYS 3.4 2.0 + - - -
140A GLY* 3.4 5.6 + - - -
141A ILE* 3.3 37.4 + - + +
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Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ALA* 4.2 16.2 - - - +
133A ALA* 3.7 25.3 - - + +
134A ALA 2.9 13.7 + - - +
135A GLY* 3.8 12.6 - - - +
136A ASP 3.5 1.0 - - - -
137A ASP* 1.3 76.2 - - - +
139A LYS* 1.3 63.4 + - - +
141A ILE* 3.2 2.7 + - - +
142A VAL* 2.9 46.8 + - + +
181A ILE* 4.5 18.9 + - - +
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Residues in contact with LYS 139 (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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135A GLY 4.5 4.1 + - - +
136A ASP 4.7 4.6 + - - +
137A ASP 3.4 1.4 - - - -
138A LYS* 1.3 76.8 - - - +
140A GLY* 1.3 60.6 + - - +
142A VAL* 3.4 5.7 + - - +
143A ASP* 2.9 45.8 + - - +
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Residues in contact with GLY 140 (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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136A ASP 5.5 0.8 + - - -
137A ASP 3.4 6.7 + - - -
138A LYS 3.3 0.6 - - - -
139A LYS* 1.3 83.0 - - - +
141A ILE* 1.4 57.9 + - - +
143A ASP* 3.4 9.0 + - - +
144A GLN* 3.0 33.2 + - - +
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Residues in contact with ILE 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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91A ARG* 6.6 0.4 - - - -
126A TYR* 3.3 37.9 - - + +
129A LEU* 3.8 19.7 - - + +
130A ALA* 3.4 18.2 - - + +
133A ALA* 3.8 20.2 - - + -
137A ASP* 3.3 26.0 + - + +
138A LYS* 3.2 7.4 + - - +
140A GLY* 1.4 72.1 - - - +
142A VAL* 1.3 65.9 + - - +
144A GLN* 3.2 9.0 + - - +
145A SER* 3.0 22.2 + - - -
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Residues in contact with VAL 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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130A ALA* 4.0 7.4 - - + -
138A LYS* 2.9 41.9 + - + +
139A LYS* 3.7 5.6 - - - +
141A ILE* 1.3 75.3 - - - +
143A ASP* 1.3 61.9 + - - +
145A SER* 3.2 8.1 + - - -
146A GLN* 3.0 30.1 + - - +
177A PHE* 3.7 10.2 - - + -
181A ILE* 3.7 23.1 - - + +
182A LEU* 3.5 32.1 - - + -
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Residues in contact with ASP 143 (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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139A LYS* 2.9 40.8 + - - +
140A GLY* 3.5 8.5 - - - +
142A VAL* 1.3 80.6 - - - +
144A GLN* 1.3 57.8 + - + +
146A GLN* 3.5 10.2 + - - +
147A GLN* 3.0 50.2 + - - +
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Residues in contact with GLN 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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122A LYS* 4.2 14.9 + - - -
126A TYR* 3.7 45.5 + - + +
140A GLY 3.0 19.4 + - - +
141A ILE* 3.2 7.4 + - - +
143A ASP* 1.3 76.1 - - - +
145A SER* 1.3 62.6 + - - +
147A GLN* 3.6 22.0 + - - +
148A ALA* 3.2 23.7 + - - +
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Residues in contact with SER 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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123A GLY* 2.8 25.9 + - - -
126A TYR* 3.6 22.5 - - - +
127A ARG* 3.5 7.1 + - - -
130A ALA* 5.8 0.4 - - - -
141A ILE 3.0 9.3 + - - -
142A VAL* 3.2 9.6 + - - -
144A GLN* 1.3 75.8 - - - +
146A GLN* 1.3 63.6 + - - +
148A ALA 3.2 1.9 + - - -
149A TYR* 3.0 39.8 + - - -
177A PHE* 3.5 15.9 - - - -
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Residues in contact with GLN 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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142A VAL* 3.0 17.8 + - - +
143A ASP* 3.9 11.8 - - - +
145A SER* 1.3 75.9 - - - +
147A GLN* 1.3 58.3 + - + +
149A TYR* 3.4 6.1 + - - +
150A GLN* 2.8 36.4 + - + +
174A PHE* 4.2 8.4 - - + -
177A PHE* 3.6 17.2 - - + -
178A TYR* 3.4 28.7 + - - -
182A LEU* 3.5 25.8 - - - +
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Residues in contact with GLN 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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143A ASP* 3.0 40.3 + - - +
144A GLN* 4.1 20.9 + - - +
146A GLN* 1.3 74.7 - - + +
148A ALA* 1.3 60.7 + - - +
150A GLN* 3.8 6.1 - - - +
151A GLU* 3.0 29.8 + - - +
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Residues in contact with ALA 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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119A LEU* 3.5 32.8 - - + +
122A LYS* 3.7 24.7 - - + +
123A GLY 3.6 14.6 - - - +
144A GLN 3.2 17.9 + - - +
145A SER 3.2 1.1 + - - +
147A GLN* 1.3 77.3 - - - +
149A TYR* 1.3 63.9 + - - +
151A GLU* 3.8 0.9 - - - -
152A ALA* 3.0 23.2 + - - +
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Residues in contact with TYR 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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120A LYS* 3.6 18.4 - - + -
123A GLY* 3.4 9.6 - - - -
124A ASP* 2.5 34.5 + - - -
127A ARG* 2.9 21.5 + - - -
145A SER* 3.0 41.4 + - - +
146A GLN 3.7 0.2 - - - +
148A ALA* 1.3 76.6 - - - +
150A GLN* 1.3 51.5 + - - +
152A ALA* 3.3 5.8 + - - +
153A PHE* 2.8 35.2 + - - +
170A LEU* 3.7 19.3 - - + +
173A ASN* 4.0 16.5 - - + +
174A PHE* 3.5 39.2 - + + -
177A PHE* 3.7 20.9 - + + -
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Residues in contact with GLN 150 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A GLN* 2.8 26.4 + - + +
147A GLN* 3.8 7.4 - - - +
149A TYR* 1.3 71.2 - - - +
151A GLU* 1.3 63.5 + - - +
153A PHE* 3.2 16.7 + - - +
154A GLU* 3.0 61.4 + - + +
174A PHE* 3.5 23.5 - - + -
178A TYR* 4.2 6.9 + - - -
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Residues in contact with GLU 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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119A LEU* 3.7 32.7 - - + +
147A GLN 3.0 17.9 + - - +
148A ALA* 3.8 3.3 - - - +
150A GLN* 1.3 75.8 - - - +
152A ALA* 1.3 63.1 + - - +
154A GLU* 3.3 9.3 + - + +
155A ILE* 3.2 33.0 + - + +
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Residues in contact with ALA 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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116A VAL* 3.8 22.6 - - + +
119A LEU* 3.7 24.1 - - + +
120A LYS* 3.8 6.7 - - - +
148A ALA 3.0 14.2 + - - +
149A TYR 3.5 7.9 - - - +
151A GLU* 1.3 75.6 - - - +
153A PHE* 1.3 56.7 + - - +
155A ILE* 3.4 1.8 + - - -
156A SER* 2.9 25.3 + - - -
170A LEU* 3.4 24.4 - - + +
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Residues in contact with PHE 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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149A TYR 2.8 17.4 + - - +
150A GLN* 3.3 25.8 - - - +
152A ALA* 1.3 73.8 - - - +
154A GLU* 1.3 65.1 + - - +
156A SER* 3.0 5.9 + - - -
157A LYS* 3.0 67.6 + - + +
167A ARG* 6.1 1.3 - - + -
170A LEU* 3.5 17.0 - - + -
171A ALA* 4.9 9.9 - - + -
174A PHE* 4.0 18.8 - + + -
191A LEU* 3.6 31.9 - - + -
194A THR* 6.5 0.2 - - + -
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Residues in contact with GLU 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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150A GLN* 3.0 48.9 + - + +
151A GLU* 3.3 8.7 + - + +
153A PHE* 1.3 79.5 - - - +
155A ILE* 1.3 65.8 + - + +
157A LYS* 3.4 10.6 + - - +
158A LYS* 3.1 23.2 + - - +
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Residues in contact with ILE 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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112A ALA* 4.2 13.2 - - + +
115A LYS* 4.4 27.1 - - + +
116A VAL* 3.6 21.1 - - + -
119A LEU* 3.8 23.6 - - + -
151A GLU* 3.2 31.6 + - + +
152A ALA* 4.9 0.2 - - - -
154A GLU* 1.3 78.2 - - + +
156A SER* 1.4 56.8 + - - +
158A LYS* 3.2 4.9 + - - -
159A GLU* 2.9 43.3 + - + +
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Residues in contact with SER 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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116A VAL* 3.7 15.8 - - - +
152A ALA 2.9 15.6 + - - -
153A PHE* 3.0 18.2 + - - -
155A ILE* 1.4 75.9 - - - +
157A LYS* 1.3 56.9 + - - +
160A MET* 3.0 55.4 + - - +
167A ARG* 3.6 21.9 + - - +
170A LEU* 3.6 12.5 - - - +
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Residues in contact with LYS 157 (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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153A PHE* 3.0 51.4 + - + +
154A GLU* 3.7 10.8 - - - +
156A SER* 1.3 80.6 + - - +
158A LYS* 1.3 59.4 + - - +
160A MET 4.2 1.9 - - - +
167A ARG* 3.7 31.2 + - - +
194A THR* 4.9 7.1 - - - +
198A GLU* 3.7 24.2 + - - -
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Residues in contact with LYS 158 (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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154A GLU 3.1 17.0 + - - +
155A ILE* 3.2 5.8 + - - +
157A LYS* 1.3 79.5 - - - +
159A GLU* 1.3 76.6 + - - +
160A MET 3.8 0.2 - - - -
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Residues in contact with GLU 159 (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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112A ALA* 3.8 30.7 - - + -
115A LYS* 5.9 0.8 + - - +
155A ILE* 2.9 23.6 + - + +
158A LYS* 1.3 96.5 - - + +
160A MET* 1.3 64.5 + - + +
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Residues in contact with MET 160 (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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112A ALA* 4.7 1.3 - - + -
113A GLU* 3.5 38.6 - - + +
116A VAL* 4.1 17.0 - - + -
156A SER* 3.0 33.8 + - - +
157A LYS 4.2 2.8 - - - +
158A LYS 5.1 0.3 - - - +
159A GLU* 1.3 85.6 - - + +
161A GLN* 1.3 63.8 + - - +
162A PRO* 4.4 0.2 - - - +
164A HIS* 3.9 37.5 - - + +
166A ILE* 4.2 5.6 - - + -
167A ARG* 2.7 41.9 + - - -
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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
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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