Contacts of the helix formed by residues 131 - 159 (chain A) in PDB entry 3O8H
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 131 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU* 6.1 6.3 - - - -
73A LEU* 5.7 0.3 - - - +
127A ALA* 2.9 19.6 + - - +
128A ARG 3.5 9.7 - - - +
129A ALA 3.7 0.6 - - - -
130A THR* 1.3 81.3 - - - +
132A VAL* 1.3 59.1 + - - +
133A GLU* 3.5 14.7 + - - +
134A VAL* 3.0 30.6 + - - +
135A ALA* 2.9 23.7 + - - +
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A THR 4.2 0.8 + - - -
131A SER* 1.3 73.6 + - - +
133A GLU* 1.3 77.1 + - + +
135A ALA* 3.8 6.3 - - - +
136A GLU* 2.8 37.1 + - - +
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Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 3.7 32.2 - - + +
131A SER* 3.5 12.1 + - - +
132A VAL* 1.3 92.4 + - + +
134A VAL* 1.3 62.6 + - - +
136A GLU* 3.9 7.3 - - - +
137A LEU* 2.9 28.9 + - - +
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU 5.6 1.8 - - - +
72A LEU* 5.3 4.9 - - + -
73A LEU* 3.9 32.1 - - + +
76A LEU* 4.3 17.9 - - + +
124A GLY* 3.4 26.7 - - - +
127A ALA* 3.8 13.0 - - + +
128A ARG* 3.8 14.1 - - + +
131A SER* 3.0 30.1 + - - +
133A GLU* 1.3 74.9 - - - +
135A ALA* 1.3 62.3 + - - +
137A LEU* 3.2 3.5 + - - +
138A TRP* 3.0 23.0 + - - +
217A O8H 5.3 0.2 - - + -
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Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ARG* 3.6 34.6 + - + +
131A SER 2.9 11.7 + - - +
132A VAL* 3.9 7.2 - - - +
134A VAL* 1.3 75.9 - - - +
136A GLU* 1.3 57.4 + - - +
138A TRP* 3.5 1.8 + - - +
139A SER* 2.9 32.2 + - - -
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Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL* 2.8 24.7 + - - +
133A GLU* 3.9 6.3 - - - +
135A ALA* 1.3 74.8 - - - +
137A LEU* 1.3 60.7 + - - +
139A SER* 3.8 5.0 - - - -
140A THR* 2.8 42.7 + - - +
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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
----------------------------------------------------------
73A LEU* 4.1 13.9 - - + -
76A LEU* 3.4 29.2 - - + +
77A ASP* 3.5 47.8 - - + +
80A VAL* 4.7 4.7 - - + +
133A GLU 2.9 18.5 + - - +
134A VAL 3.2 4.5 + - - +
136A GLU* 1.3 78.9 - - - +
138A TRP* 1.3 63.1 + - - +
140A THR* 3.4 4.0 + - - -
141A PHE* 3.2 56.4 + - + -
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Residues in contact with TRP 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 4.8 2.2 - - + +
80A VAL* 3.7 29.2 - - + -
114A PHE* 3.7 6.3 - + - -
128A ARG* 3.3 39.2 - - + +
134A VAL 3.0 15.7 + - - +
135A ALA 3.9 2.9 - - - +
137A LEU* 1.3 78.1 - - - +
139A SER* 1.3 59.1 + - - +
141A PHE* 3.3 3.3 + - + -
142A MET* 2.9 55.8 + - + +
145A TRP* 3.9 15.3 - + - -
180A GLU* 2.8 24.7 + - + -
217A O8H 3.3 80.1 - + + -
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Residues in contact with SER 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ALA 2.9 19.2 + - - -
136A GLU* 3.8 5.4 - - - -
138A TRP* 1.3 79.8 - - - +
140A THR* 1.3 60.9 + - - +
142A MET* 3.4 5.9 + - - +
143A GLN* 3.0 46.0 + - - +
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Residues in contact with THR 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLU* 2.8 33.9 + - - +
137A LEU* 3.7 6.2 - - - -
139A SER* 1.3 72.0 + - - +
141A PHE* 1.3 74.6 + - + +
143A GLN* 3.5 12.0 + - - +
144A LYS* 3.2 33.2 + - - +
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Residues in contact with PHE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASP* 5.1 0.2 - - - -
80A VAL* 3.4 26.7 - - + -
81A ASN* 3.5 27.4 - - - -
84A ASP* 3.6 30.3 - - + -
137A LEU* 3.2 35.7 + - + +
138A TRP* 4.0 3.8 - - + +
140A THR* 1.3 88.7 - - + +
142A MET* 1.3 66.2 + - - +
144A LYS* 3.1 24.1 + - - +
145A TRP* 2.9 58.7 + + + -
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Residues in contact with MET 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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138A TRP* 2.9 61.1 + - + +
139A SER* 3.8 6.3 - - - +
141A PHE* 1.3 75.1 - - - +
143A GLN* 1.3 58.7 + - + +
145A TRP* 3.3 17.5 + - + +
146A ILE* 2.8 45.3 + - + +
176A ASN* 3.6 43.5 - - + +
177A LEU* 4.1 11.4 - - + -
180A GLU* 3.5 17.3 - - + +
217A O8H 4.0 7.9 - - - +
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Residues in contact with GLN 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A SER* 3.0 40.7 + - - +
140A THR* 3.8 9.5 + - - +
142A MET* 1.3 75.6 - - + +
144A LYS* 1.3 58.0 + - - +
146A ILE* 3.8 8.1 - - + +
147A ALA* 2.9 30.5 + - - +
169A HIS* 5.3 1.8 + - - -
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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
----------------------------------------------------------
84A ASP* 3.5 23.8 - - - +
88A GLN* 5.7 1.8 - - + +
140A THR* 3.2 25.6 + - - +
141A PHE* 3.1 41.4 + - - +
143A GLN* 1.3 77.0 - - - +
145A TRP* 1.3 58.4 + - + +
147A ALA* 3.4 6.9 + - - +
148A TYR* 2.9 27.4 + - + +
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Residues in contact with TRP 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 3.9 19.3 - - + -
84A ASP* 2.8 31.4 + - - +
87A LEU* 3.7 17.9 - - + +
110A PHE* 3.5 34.4 - + - -
114A PHE* 4.2 16.6 - + - -
138A TRP* 3.9 24.2 - + - -
141A PHE* 2.9 47.0 + + + +
142A MET* 3.9 21.1 - - - +
144A LYS* 1.3 77.1 - - + +
146A ILE* 1.3 60.4 + - - +
148A TYR* 3.3 6.1 + - + +
149A THR* 3.0 33.7 + - - -
176A ASN* 4.0 4.7 - - - +
217A O8H 3.8 24.5 - + - +
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Residues in contact with ILE 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 MET* 2.8 36.2 + - + +
143A GLN* 3.8 6.7 - - + +
145A TRP* 1.3 73.1 - - - +
147A ALA* 1.3 59.2 + - - +
149A THR* 3.2 3.1 + - - -
150A ALA* 2.8 28.4 + - - +
169A HIS* 3.5 23.6 - - + +
172A ALA* 3.6 4.2 - - + +
173A THR* 3.4 51.4 - - + +
176A ASN* 3.5 35.4 - - + +
177A LEU* 5.3 3.4 - - + -
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Residues in contact with ALA 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 GLN 2.9 18.8 + - - +
144A LYS* 3.7 6.5 - - - +
146A ILE* 1.3 75.3 - - - +
148A TYR* 1.3 58.9 + - - +
150A ALA* 3.3 7.4 + - - +
151A ALA* 2.9 28.6 + - - +
169A HIS* 4.5 11.9 + - + +
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Residues in contact with TYR 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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87A LEU* 4.1 24.0 - - + -
91A ALA* 3.1 40.1 + - + +
144A LYS* 2.9 17.6 + - + +
145A TRP* 3.8 7.4 - - + +
147A ALA* 1.3 72.1 - - - +
149A THR* 1.3 66.7 + - - +
151A ALA* 3.1 11.6 + - + +
152A VAL* 2.9 38.1 + - + +
217A O8H 3.0 52.6 - + - -
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Residues in contact with THR 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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103A TRP* 4.1 4.2 - - + -
145A TRP 3.0 14.8 + - - -
146A ILE 3.5 7.9 - - - -
148A TYR* 1.3 74.7 - - - +
150A ALA* 1.3 57.7 + - - +
152A VAL* 3.3 4.9 + - - +
153A ILE* 2.9 40.4 + - + +
172A ALA* 3.6 19.1 - - + -
175A LEU* 5.3 0.7 - - + -
176A ASN* 3.0 18.0 + - - +
207A TRP* 3.5 24.7 - - + -
217A O8H 3.5 26.8 + - - +
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Residues in contact with ALA 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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146A ILE 2.8 16.3 + - - +
147A ALA* 3.7 4.0 - - - +
149A THR* 1.3 77.7 - - - +
151A ALA* 1.3 56.7 + - - +
153A ILE* 3.3 5.7 + - - +
154A ASP* 2.8 37.4 + - - +
168A ALA* 3.9 8.8 - - + +
169A HIS* 3.9 40.4 - - + +
172A ALA* 3.8 5.6 - - + +
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Residues in contact with ALA 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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147A ALA 2.9 16.6 + - - +
148A TYR* 3.6 14.1 - - + +
150A ALA* 1.3 78.2 - - - +
152A VAL* 1.3 56.9 + - + +
154A ASP* 3.4 11.3 + - - +
155A ALA* 3.0 27.0 + - - +
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Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A MET* 3.8 22.9 - - + -
103A TRP* 3.4 32.8 - - + -
148A TYR* 2.9 53.6 + - + +
149A THR 3.8 2.5 - - - +
151A ALA* 1.3 73.3 - - - +
153A ILE* 1.3 65.2 + - - +
155A ALA* 3.2 8.4 + - + +
156A GLU* 3.0 23.4 + - + +
217A O8H 3.8 9.9 - - - +
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Residues in contact with ILE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TRP* 4.2 4.7 - - + -
149A THR* 2.9 35.5 + - + +
150A ALA 3.5 6.3 - - - +
152A VAL* 1.3 76.8 - - - +
154A ASP* 1.3 57.6 + - - +
156A GLU* 3.2 9.6 + - - +
157A ARG* 2.9 56.6 + - + +
162A ALA* 5.6 0.2 - - + -
168A ALA* 3.6 30.1 - - + +
171A LEU* 4.2 14.4 - - + -
172A ALA* 4.3 1.8 - - - +
175A LEU* 4.9 0.4 - - + -
211A ILE* 4.1 41.1 - - + +
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Residues in contact with ASP 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 ALA* 2.8 28.5 + - - +
151A ALA* 3.5 10.0 - - - +
153A ILE* 1.3 71.3 - - - +
155A ALA* 1.3 59.0 + - - +
157A ARG* 3.3 11.0 + - - +
158A ASP* 2.8 41.2 + - - +
164A ARG* 5.3 4.1 + - - +
168A ALA* 3.5 19.1 - - - +
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ALA 3.0 13.8 + - - +
152A VAL* 3.2 12.3 + - + +
154A ASP* 1.3 77.2 - - - +
156A GLU* 1.3 58.5 + - - +
158A ASP* 3.2 8.4 + - - +
159A ARG* 2.9 34.5 + - - +
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Residues in contact with GLU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 4.2 0.5 - - - +
102A MET* 4.0 20.9 - - + +
103A TRP* 4.7 2.5 - - + -
152A VAL* 3.0 20.1 + - + +
153A ILE* 3.2 12.1 + - - +
155A ALA* 1.3 76.9 - - - +
157A ARG* 1.3 58.5 + - - +
159A ARG* 2.7 48.7 + - - +
160A GLY 3.3 2.4 + - - -
161A ALA* 2.9 29.0 + - - -
162A ALA* 3.0 20.3 + - + -
211A ILE* 5.2 0.7 - - + -
212A TYR* 2.6 34.9 + - + +
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Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ILE* 2.9 35.5 + - - +
154A ASP* 3.6 12.5 + - - +
156A GLU* 1.3 74.6 - - - +
158A ASP* 1.3 60.0 + - - +
160A GLY* 3.0 18.5 + - - -
162A ALA* 3.4 27.9 - - + +
163A PRO 3.4 14.4 + - - +
164A ARG* 3.5 43.1 + - + +
165A THR* 3.3 26.2 + - - +
166A LEU 2.6 31.5 + - - +
167A PRO* 4.5 1.2 - - - +
168A ALA* 3.6 16.1 - - - +
171A LEU* 4.2 16.4 - - - +
211A ILE 5.4 2.6 + - - -
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Residues in contact with ASP 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASP* 2.8 28.4 + - - +
155A ALA* 3.2 8.6 + - - +
157A ARG* 1.3 72.8 - - - +
159A ARG* 1.3 59.0 + - - +
160A GLY* 3.6 0.5 + - - -
164A ARG* 2.7 33.4 + - - +
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Residues in contact with ARG 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 4.6 14.5 - - - +
102A MET* 5.8 0.2 - - - +
155A ALA 2.9 19.0 + - - +
156A GLU* 2.7 48.1 + - - +
158A ASP* 1.3 78.5 - - - +
160A GLY* 1.3 55.9 + - - +
161A ALA* 3.3 22.9 + - + +
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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