Contacts of the helix formed by residues 140 - 161 (chain A) in PDB entry 4BZN
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 GLN 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A ARG* 6.0 1.8 - - - +
138A ALA 3.8 2.2 + - - -
139A LEU* 1.3 72.6 - - - +
141A GLU* 1.3 60.8 + - - +
142A GLU* 4.4 6.4 - - + +
143A LEU* 3.1 8.5 + - + +
144A ALA* 2.9 24.3 + - - +
303A HIS* 3.3 35.1 + - + +
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Residues in contact with GLU 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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139A LEU 4.2 2.2 - - - +
140A GLN* 1.3 74.8 - - - +
142A GLU* 1.3 58.1 + - - +
144A ALA* 4.3 2.5 - - - -
145A ARG* 2.7 38.5 + - - +
236A VAL* 4.4 12.6 - - + -
258A ARG* 4.3 7.7 + - - +
259A VAL* 3.5 10.4 - - - -
260A SER* 2.7 52.7 + - - -
263A CYS* 4.1 5.6 - - - -
289A TRP* 2.8 35.4 + - + +
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Residues in contact with GLU 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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140A GLN* 3.2 5.1 - - + +
141A GLU* 1.3 78.2 - - - +
143A LEU* 1.3 62.5 + - - +
145A ARG* 3.5 22.5 - - - +
146A SER* 3.2 21.8 + - - -
294A LEU* 3.6 36.5 + - + +
302A ILE* 3.8 12.0 - - - +
303A HIS* 2.8 29.3 + - + +
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PHE* 3.7 31.2 - - + -
136A ARG* 4.0 15.5 - - - +
139A LEU* 4.1 14.8 - - + -
140A GLN* 3.1 12.1 + - + +
142A GLU* 1.3 77.5 - - - +
144A ALA* 1.3 67.4 + - - +
146A SER* 3.2 3.6 + - - -
147A PHE* 2.9 49.2 + - + +
299A THR* 3.5 29.6 - - + -
303A HIS* 3.7 32.4 + - + +
304A LEU* 4.7 1.1 - - + -
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Residues in contact with ALA 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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139A LEU* 4.3 7.5 - - + +
140A GLN 2.9 14.0 + - - +
141A GLU 3.7 3.8 - - - +
143A LEU* 1.3 76.1 - - - +
145A ARG* 1.3 54.3 + - - +
147A PHE* 4.4 1.1 - - - -
148A PHE* 2.7 38.1 + - - +
232A LEU* 4.4 0.4 - - + -
235A MET* 3.8 24.6 - - + +
236A VAL* 3.5 31.9 - - + -
289A TRP* 3.8 6.7 - - + -
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Residues in contact with ARG 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 GLU* 2.7 26.8 + - - +
142A GLU* 3.5 34.0 - - - +
143A LEU 3.1 0.2 - - - -
144A ALA* 1.3 72.3 - - - +
146A SER* 1.3 58.1 + - - +
149A TRP* 2.9 33.4 + - - +
289A TRP* 2.7 61.2 + - + +
290A MET* 3.6 17.1 - - + +
291A GLN 3.4 23.9 + - - -
292A ASP 4.3 3.7 + - - -
293A VAL* 3.9 22.7 - - + +
294A LEU 5.3 0.4 - - - +
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Residues in contact with SER 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 GLU 3.2 10.8 + - - -
143A LEU 3.2 7.4 + - - -
145A ARG* 1.3 81.0 - - - +
147A PHE* 1.3 62.4 + - - +
149A TRP* 3.5 2.4 + - - +
150A GLN* 3.1 38.1 + - - +
293A VAL* 3.4 18.9 - - - +
294A LEU* 4.0 10.2 + - - -
299A THR* 2.7 39.7 + - - +
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Residues in contact with PHE 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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129A LEU* 3.7 18.8 - - + -
132A PHE* 3.8 17.0 - + - -
139A LEU* 3.9 11.4 - - + -
143A LEU* 2.9 38.8 + - + +
144A ALA 3.8 2.7 - - - +
146A SER* 1.3 83.4 - - - +
148A PHE* 1.3 63.1 + - - +
150A GLN* 3.2 3.5 + - - -
151A VAL* 3.0 25.6 + - - +
175A ILE* 3.7 32.5 - - + -
180A GLY 4.8 2.7 - - - -
182A LEU* 3.5 35.3 - - + +
235A MET* 3.9 12.6 - - + -
299A THR* 3.9 10.3 - - + -
304A LEU* 4.2 18.8 - - + -
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Residues in contact with PHE 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 ALA 2.7 22.6 + - - +
145A ARG 4.0 2.0 - - - +
147A PHE* 1.3 72.2 - - - +
149A TRP* 1.3 57.3 + - - +
151A VAL* 3.1 3.3 + - - +
152A LEU* 2.8 63.5 + - + +
228A LEU* 3.2 55.2 - - + -
229A GLY 4.9 0.2 - - - -
231A LEU* 4.4 12.8 - - + -
232A LEU* 3.7 41.3 - - + -
235A MET* 4.0 11.0 - - + +
266A LEU* 4.2 2.9 - - + -
270A CYS* 4.9 6.1 - - - -
284A ILE* 3.9 13.9 - - + -
289A TRP* 4.3 0.9 - + + -
290A MET* 3.7 14.8 - - + -
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Residues in contact with TRP 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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145A ARG 2.9 19.4 + - - +
146A SER 3.5 4.3 - - - +
148A PHE* 1.3 76.2 - - - +
150A GLN* 1.3 65.4 + - + +
152A LEU* 3.1 10.0 + - - +
153A GLU* 2.9 48.3 + - + +
285A GLN* 3.5 59.0 - - + -
290A MET* 3.8 37.1 - - + +
291A GLN* 5.3 0.2 - - - -
293A VAL* 3.7 33.7 - - + +
294A LEU 5.8 0.2 - - - -
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Residues in contact with GLN 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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100A PHE* 5.1 1.2 - - - -
102A GLY* 5.5 0.9 - - - -
146A SER* 3.1 30.4 + - - +
147A PHE* 3.6 7.1 - - - +
149A TRP* 1.3 80.9 - - + +
151A VAL* 1.3 66.4 + - - +
153A GLU* 3.4 7.4 + - - +
154A ALA* 3.0 23.4 + - - +
180A GLY 2.8 22.4 + - - -
181A GLU* 3.2 8.5 - - - +
182A LEU* 2.9 47.9 + - + +
294A LEU 5.7 0.2 + - - -
296A PRO* 3.7 23.2 - - + +
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Residues in contact with VAL 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 PHE 3.0 21.7 + - - +
148A PHE* 3.1 7.4 + - + +
150A GLN* 1.3 75.6 - - - +
152A LEU* 1.3 58.4 + - - +
154A ALA* 3.1 7.6 + - + +
155A VAL* 2.9 37.5 + - + +
168A ILE* 4.3 6.3 - - + -
173A ILE* 3.8 28.5 - - + -
182A LEU* 3.9 15.5 - - + -
184A LEU* 5.5 3.6 - - + -
228A LEU* 3.7 26.9 - - + -
231A LEU* 3.9 15.7 - - + -
235A MET* 4.4 2.0 - - + -
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Residues in contact with LEU 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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148A PHE* 2.8 33.4 + - + +
149A TRP* 3.4 9.0 - - - +
151A VAL* 1.3 77.8 - - - +
153A GLU* 1.3 56.8 + - - +
155A VAL* 3.8 4.5 - - - +
156A ARG* 2.9 35.7 + - - +
228A LEU* 3.8 28.5 - - + -
281A PHE* 3.9 15.0 - - + -
284A ILE* 3.4 36.1 - - + -
285A GLN* 3.9 21.3 - - + +
290A MET* 3.6 21.8 - - - -
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Residues in contact with GLU 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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100A PHE* 3.9 18.8 - - + -
149A TRP* 2.9 42.8 + - + +
150A GLN* 3.7 9.4 - - - +
152A LEU* 1.3 74.6 - - - +
154A ALA* 1.3 57.2 + - - +
156A ARG* 3.3 25.8 + - - +
157A HIS* 3.0 28.1 + - - +
285A GLN* 2.7 23.5 + - - +
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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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100A PHE* 3.7 12.0 - - - -
102A GLY* 3.3 31.4 - - - +
103A VAL* 3.8 4.2 - - + +
150A GLN 3.0 14.7 + - - +
151A VAL* 3.5 10.1 - - + +
153A GLU* 1.3 72.7 - - - +
155A VAL* 1.3 61.6 + - - +
157A HIS* 3.2 4.3 + - - +
158A CYS* 3.0 32.2 + - - -
182A LEU 5.6 0.9 - - - +
184A LEU* 4.4 11.2 - - + -
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Residues in contact with VAL 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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151A VAL* 2.9 33.6 + - + +
152A LEU* 3.9 3.4 - - - +
154A ALA* 1.3 72.8 - - - +
156A ARG* 1.3 66.4 + - - +
158A CYS* 3.1 9.1 + - + +
159A HIS* 2.9 51.1 + - + +
165A HIS* 5.8 2.2 - - + -
168A ILE* 3.6 32.1 - - + -
184A LEU* 4.1 14.1 - - + -
228A LEU* 4.5 2.9 - - + -
281A PHE* 3.6 20.0 - - + -
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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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152A LEU 2.9 21.9 + - - +
153A GLU* 3.3 26.2 + - - +
155A VAL* 1.3 75.8 - - - +
157A HIS* 1.3 58.1 + - - +
159A HIS* 3.2 8.7 + - - +
160A ASN* 2.7 32.8 + - - +
281A PHE* 3.8 31.6 - - + +
282A GLU* 6.5 0.7 - - - -
285A GLN* 2.9 37.3 + - - -
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Residues in contact with HIS 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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96A VAL* 2.7 34.4 + - + -
98A SER* 3.6 25.1 + - - -
100A PHE* 3.6 34.4 + + + +
103A VAL* 3.9 14.6 - - + -
153A GLU 3.0 15.0 + - - +
154A ALA 3.4 7.2 - - - +
155A VAL 3.2 0.2 - - - -
156A ARG* 1.3 77.1 - - - +
158A CYS* 1.3 63.9 + - - +
160A ASN* 3.3 9.1 + - - +
161A CYS* 3.0 42.8 + - - -
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Residues in contact with CYS 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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96A VAL* 3.9 12.3 - - - -
103A VAL* 3.7 13.5 - - - -
154A ALA 3.0 19.3 + - - -
155A VAL* 3.1 9.2 + - + +
157A HIS* 1.3 76.1 - - - +
159A HIS* 1.3 63.5 + - + +
161A CYS* 2.9 10.2 + - - -
162A GLY 3.1 0.2 + - - -
163A VAL* 2.8 41.8 + - + +
165A HIS* 5.3 4.0 - - + +
184A LEU* 3.9 11.0 - - - -
187A PHE* 3.6 34.5 - - + -
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Residues in contact with HIS 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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155A VAL* 2.9 43.6 + - + +
156A ARG* 3.7 6.6 - - - +
158A CYS* 1.3 78.2 - - + +
160A ASN* 1.3 58.4 + - - +
162A GLY* 3.0 15.6 + - - -
163A VAL 3.2 18.4 - - - +
164A LEU* 3.6 23.1 - - + +
165A HIS 4.9 2.2 + - - -
168A ILE* 5.8 0.2 - - - +
193A LEU* 3.5 27.6 - - + +
221A ARG* 3.9 31.9 + - + +
224A ALA* 3.9 11.6 - - + +
281A PHE* 3.6 27.5 - + - -
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Residues in contact with ASN 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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156A ARG 2.7 22.4 + - - +
157A HIS* 3.7 9.6 + - - +
159A HIS* 1.3 72.0 - - - +
161A CYS* 1.3 63.9 + - - +
162A GLY 3.2 1.1 + - - -
221A ARG* 5.7 0.7 - - - +
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Residues in contact with CYS 161 (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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95A LYS* 3.2 53.3 + - - +
96A VAL* 3.9 10.5 - - + -
157A HIS* 3.0 45.1 + - - +
158A CYS 2.9 6.9 + - - +
160A ASN* 1.3 81.9 - - - +
162A GLY* 1.3 57.8 + - - +
163A VAL* 3.4 1.5 + - - +
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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