Contacts of the helix formed by residues 128 - 149 (chain A) in PDB entry 4BPU
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 CYS 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A CYS* 3.3 15.3 - - - -
122A CYS* 3.7 4.7 - - - -
127A ILE* 1.3 77.4 - - - +
129A PRO* 1.3 75.3 - - + +
130A LYS* 3.1 26.3 + - - -
131A CYS* 3.2 7.5 + - - -
132A TRP* 3.1 23.6 + - - +
345A PHE* 3.8 8.7 - - - -
1409A ZN 2.0 33.7 - - - -
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Residues in contact with PRO 129 (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 CYS* 1.3 89.8 - - + +
130A LYS* 1.3 64.3 + - + +
131A CYS 3.5 0.3 + - - -
132A TRP* 3.8 13.0 + - + +
133A THR* 3.9 10.6 + - - -
230A ASN* 5.3 1.4 + - - -
345A PHE* 4.1 20.6 - - + -
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Residues in contact with LYS 130 (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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121A CYS* 4.2 19.3 - - - +
128A CYS* 3.1 12.8 - - - -
129A PRO* 1.3 83.8 - - + +
131A CYS* 1.3 57.7 + - - +
133A THR* 4.2 2.8 + - - -
226A TYR* 3.3 24.1 - - - -
230A ASN* 3.6 54.8 + - + +
231A GLN* 3.6 12.0 + - - +
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Residues in contact with CYS 131 (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 MET* 3.7 8.7 - - - +
119A ARG* 3.4 35.4 - - + +
121A CYS* 3.4 9.9 - - - -
127A ILE* 4.0 3.8 - - - -
128A CYS 3.3 20.9 - - - -
130A LYS* 1.3 75.2 - - - +
132A TRP* 1.3 66.3 + - - +
133A THR* 3.1 3.4 - - - -
134A LEU* 3.0 27.0 + - + +
226A TYR* 4.1 7.0 - - - -
231A GLN* 4.1 2.5 - - - +
1409A ZN 2.3 35.0 - - - -
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Residues in contact with TRP 132 (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 MET* 3.5 23.1 - - + -
127A ILE* 4.1 17.5 - - + -
128A CYS 3.1 17.5 + - - +
129A PRO* 3.8 8.7 + - + +
130A LYS 3.6 0.6 - - - -
131A CYS* 1.3 77.2 - - - +
133A THR* 1.3 53.6 + - - +
134A LEU 2.9 0.2 - - - -
135A MET* 2.7 56.6 + - + +
136A THR* 3.4 13.5 + - - -
139A ILE* 5.8 1.3 - - + +
159A TYR* 3.7 25.4 - + - -
163A ARG 4.5 0.7 - - - -
164A GLY 4.3 11.9 - - - -
165A VAL* 4.0 12.6 - - + -
334A ILE* 5.5 0.2 - - + -
339A VAL 5.7 0.6 + - - -
342A PHE* 3.6 46.9 + + - +
344A PRO* 3.7 30.5 - - + +
345A PHE* 5.4 1.1 - - + -
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Residues in contact with THR 133 (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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129A PRO 3.9 12.5 + - - -
130A LYS* 4.2 4.0 + - - -
131A CYS 3.1 0.2 - - - -
132A TRP* 1.3 78.5 - - - +
134A LEU* 1.3 61.3 + - - +
136A THR* 3.1 11.3 + - - -
137A MET* 3.0 25.3 + - + +
222A TYR* 3.9 31.6 - - + -
225A GLU* 5.6 3.9 + - - -
226A TYR* 4.0 31.8 - - + +
230A ASN* 5.3 4.9 + - - -
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Residues in contact with LEU 134 (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 MET* 4.1 12.3 - - - -
115A TYR* 3.6 48.2 + - + -
118A VAL* 5.3 0.7 - - + -
119A ARG* 4.5 9.0 - - + -
131A CYS* 3.0 17.9 + - + +
132A TRP 2.9 0.4 - - - -
133A THR* 1.3 77.7 - - - +
135A MET* 1.3 57.5 + - - +
137A MET* 3.4 21.0 + - + +
138A ALA* 2.9 27.3 + - - +
226A TYR* 3.2 37.2 - - + +
300A TYR 3.6 17.3 - - - +
301A CYS* 3.8 9.6 - - - +
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Residues in contact with MET 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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110A ILE* 3.7 21.3 - - + +
111A ASP 4.0 0.4 - - - -
112A MET* 3.5 54.7 - - + +
115A TYR* 3.7 24.2 - - + -
132A TRP* 2.7 43.3 + - + +
134A LEU* 1.3 71.6 - - - +
136A THR* 1.3 54.2 + - - +
138A ALA* 2.7 22.8 + - - +
139A ILE* 2.7 24.3 + - + +
163A ARG 4.3 0.7 - - - +
164A GLY* 4.0 6.3 - - - -
165A VAL* 3.8 28.7 - - + -
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Residues in contact with THR 136 (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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132A TRP* 3.4 18.7 + - - -
133A THR* 3.1 17.4 + - + -
135A MET* 1.3 79.0 - - - +
137A MET* 1.3 61.4 + - - +
139A ILE* 3.6 6.6 + - - +
140A ARG* 3.1 27.7 + - - +
222A TYR* 3.9 29.6 - - + +
339A VAL* 4.2 17.1 + - + +
340A ASP* 4.0 27.4 + - - +
342A PHE 5.6 0.2 + - - -
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Residues in contact with MET 137 (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 THR* 3.0 25.8 + - + +
134A LEU* 3.7 24.0 - - + +
136A THR* 1.3 76.7 - - - +
138A ALA* 1.3 58.9 + - - +
140A ARG* 4.0 4.0 - - - +
141A ILE* 2.8 48.4 + - + +
218A ILE* 4.9 3.6 - - + +
219A ILE* 4.2 17.7 - - - +
222A TYR* 3.7 41.7 - - + -
226A TYR* 4.3 11.7 - - + -
301A CYS* 3.7 40.6 - - + +
303A PRO* 5.3 0.2 - - - -
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Residues in contact with ALA 138 (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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110A ILE* 3.9 25.8 - - + -
115A TYR* 3.8 16.2 - - - +
134A LEU 2.9 14.1 + - - +
135A MET* 2.7 19.8 + - - +
137A MET* 1.3 70.4 - - - +
139A ILE* 1.3 65.4 + - + +
142A ILE* 3.0 31.2 + - - +
303A PRO* 3.9 17.0 - - + +
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Residues in contact with ILE 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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132A TRP* 5.8 2.0 - - + +
135A MET* 2.7 26.6 + - + +
136A THR* 4.0 4.5 - - - +
138A ALA* 1.3 71.8 - - - +
140A ARG* 1.3 58.5 + - + +
143A ASP* 2.8 35.9 + - + +
157A TRP* 3.9 34.0 - - + -
165A VAL* 4.0 17.7 - - + -
334A ILE* 3.9 28.7 - - + -
336A LEU* 3.8 28.7 - - + -
339A VAL* 3.9 24.7 - - + -
342A PHE* 6.0 1.8 - - + -
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Residues in contact with ARG 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 THR* 3.1 21.6 + - - +
137A MET 4.0 1.8 - - - +
139A ILE* 1.3 76.5 - - + +
141A ILE* 1.3 62.5 + - - +
143A ASP* 4.8 2.0 - - - -
144A ARG* 3.1 27.0 + - - +
218A ILE* 3.9 26.1 - - + +
221A LYS* 4.6 15.6 - - - +
222A TYR* 3.0 37.2 + - - -
339A VAL* 4.0 19.0 - - + +
340A ASP* 3.6 18.1 + - - -
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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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137A MET* 2.8 31.1 + - + +
138A ALA* 3.9 3.1 - - - +
140A ARG* 1.3 78.7 - - - +
142A ILE* 1.3 65.2 + - + +
144A ARG* 3.8 7.3 + - - +
145A ALA* 3.5 17.0 + - - +
211A PHE* 4.6 5.1 - - + -
215A SER* 3.5 26.4 + - - +
218A ILE* 3.9 25.1 - - + -
219A ILE* 3.8 32.8 - - + -
302A PHE* 3.8 21.3 - - + -
303A PRO* 4.0 22.9 - - + -
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Residues in contact with ILE 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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108A PHE* 4.9 8.3 - - + -
110A ILE* 3.5 29.4 - - + -
138A ALA 3.0 11.8 + - - +
141A ILE* 1.3 77.4 - - + +
143A ASP* 1.3 63.3 + - - +
144A ARG 3.1 1.3 - - - -
145A ALA* 2.7 23.8 + - - +
146A LEU* 2.9 32.9 + - + +
157A TRP* 4.0 12.6 - - + -
189A LEU* 4.5 20.0 - - + +
211A PHE* 6.0 0.2 - - + -
302A PHE* 5.9 0.4 - - + -
303A PRO* 3.7 28.9 - - + -
305A LEU* 3.9 23.6 - - + -
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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 ILE 2.8 24.7 + - - +
140A ARG* 4.4 2.0 - - - +
142A ILE* 1.3 74.2 - - - +
144A ARG* 1.3 63.3 + - - +
146A LEU* 3.3 5.6 + - - +
147A LYS* 2.9 25.1 + - - +
155A ARG* 2.6 40.1 + - - -
157A TRP* 2.9 32.4 + - - +
336A LEU* 3.6 18.5 - - + +
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Residues in contact with ARG 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 ARG 3.1 21.1 + - - +
141A ILE 3.8 6.4 + - - +
142A ILE 3.1 0.2 - - - -
143A ASP* 1.3 78.1 + - - +
145A ALA* 1.3 60.6 + - - +
147A LYS* 4.7 5.2 - - - +
148A GLU* 2.8 75.7 + - - +
149A ASP* 2.9 40.4 + - - -
211A PHE* 3.6 31.1 + - - +
214A LYS* 3.4 35.6 - - - +
215A SER* 5.1 1.8 + - - +
218A ILE* 4.2 16.1 - - + +
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Residues in contact with ALA 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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141A ILE 3.5 4.3 + - - +
142A ILE 2.7 9.2 + - - +
144A ARG* 1.3 92.3 - - - +
146A LEU* 1.3 66.0 + - - +
149A ASP* 3.0 27.5 + - - +
150A PHE* 3.1 12.4 + - - -
188A TYR* 4.6 2.0 - - + -
189A LEU* 3.6 28.5 - - + -
211A PHE* 3.8 19.1 - - + -
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Residues in contact with LEU 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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108A PHE* 3.9 25.4 - - + -
142A ILE* 2.9 32.6 + - + +
143A ASP* 3.7 5.4 - - - +
145A ALA* 1.3 77.3 - - - +
147A LYS* 1.3 55.5 + - - +
150A PHE* 3.5 9.9 - - + +
151A GLY 3.2 8.0 + - - -
152A PHE* 2.9 53.7 + - + +
155A ARG* 3.6 18.4 - - - -
167A CYS* 3.8 17.7 - - - -
169A VAL* 3.7 22.4 - - + -
185A ILE* 4.7 1.8 - - + -
189A LEU* 4.5 10.8 - - + -
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Residues in contact with LYS 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* 2.9 21.0 + - - +
144A ARG* 4.0 3.8 - - - +
146A LEU* 1.3 76.8 - - - +
148A GLU* 1.3 82.0 + - + +
151A GLY* 3.2 22.2 + - - -
152A PHE 3.6 8.9 - - - +
155A ARG* 3.6 30.7 - - - +
204B ASP* 4.4 3.8 - - - +
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Residues in contact with GLU 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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144A ARG* 2.8 59.8 + - + +
147A LYS* 1.3 98.6 + - + +
149A ASP* 1.3 56.1 + - - +
214A LYS* 4.3 10.3 + - - +
203B GLU* 3.6 6.3 - - - +
204B ASP* 2.6 33.4 + - - +
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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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144A ARG* 2.9 40.5 + - - -
145A ALA* 3.0 12.9 + - - +
148A GLU* 1.3 79.5 - - - +
150A PHE* 1.3 67.3 + - + +
188A TYR* 2.5 34.8 + - + +
211A PHE* 3.9 4.2 + - - +
214A LYS* 4.2 8.4 + - - -
201B TYR* 6.4 0.2 - - - -
202B LEU* 3.4 28.4 - - + +
203B GLU 3.4 12.1 + - - -
204B ASP 3.8 0.2 - - - -
205B GLY* 3.2 14.6 + - - -
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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
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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