Contacts of the helix formed by residues 148 - 169 (chain D) in PDB entry 2WZJ
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 LYS 148 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ARG* 3.4 30.8 + - + +
147D MET* 1.3 76.3 - - - +
149D GLU* 1.3 67.8 + - - +
150D LYS* 3.2 4.7 - - + +
151D GLU* 3.0 20.8 + - + +
152D ALA 3.2 6.2 + - - -
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Residues in contact with GLU 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ARG* 4.4 7.5 + - - +
147D MET 3.8 0.8 + - - -
148D LYS* 1.3 73.8 - - - +
150D LYS* 1.3 62.9 + - - +
152D ALA* 3.1 6.6 + - - +
153D ARG* 3.0 34.8 + - - +
244D VAL* 4.5 17.3 - - + +
272D TYR 4.2 4.3 - - - +
273D MET* 3.9 5.0 - - - +
274D SER* 2.6 46.9 + - - -
277D CYS* 4.1 6.3 - - + +
303D TRP* 2.6 40.5 + - + +
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Residues in contact with LYS 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D LYS* 3.1 4.3 + - + +
149D GLU* 1.3 78.2 - - - +
151D GLU* 1.3 62.9 + - - +
152D ALA 3.4 0.2 + - - -
153D ARG* 3.6 20.8 + - - +
154D ALA* 3.5 18.0 + - - +
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Residues in contact with GLU 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D TYR* 3.0 26.2 + - - -
147D MET* 3.5 27.6 - - + +
148D LYS* 3.0 14.5 + - + +
150D LYS* 1.3 78.7 - - - +
152D ALA* 1.3 62.1 + - - +
154D ALA* 3.3 15.1 + - + +
155D LYS* 3.4 41.8 + - - +
187D MET* 5.2 1.4 - - - +
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Residues in contact with ALA 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D MET* 4.1 17.7 - - + +
148D LYS 3.2 10.1 + - - +
149D GLU* 3.1 12.4 + - - +
151D GLU* 1.3 74.2 - - - +
153D ARG* 1.3 56.5 + - - +
154D ALA 3.1 1.3 - - - -
155D LYS* 3.0 2.9 + - - +
156D PHE* 2.7 36.9 + - - +
240D LEU* 5.5 0.2 - - + -
243D LEU* 4.1 24.5 - - + +
244D VAL* 4.4 10.5 - - + -
303D TRP* 4.0 11.0 - - + -
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Residues in contact with ARG 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D GLU* 3.0 18.0 + - - +
150D LYS* 3.6 36.9 - - - +
152D ALA* 1.3 75.5 - - - +
154D ALA* 1.3 56.3 + - - +
156D PHE* 4.3 0.2 - - - -
157D ARG* 2.8 41.9 + - + +
303D TRP* 2.7 66.8 + - + +
304D MET 3.7 18.4 - - - +
306D VAL* 3.5 52.6 + - - +
308D HIS* 4.4 6.1 - - + +
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Residues in contact with ALA 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D LYS 3.5 9.0 + - - +
151D GLU* 3.3 13.8 + - + +
152D ALA 3.1 1.0 - - - -
153D ARG* 1.3 82.0 - - - +
155D LYS* 1.3 67.5 + - + +
157D ARG* 3.8 7.9 + - - +
158D GLN* 3.6 28.2 + - - +
308D HIS* 6.0 1.6 - - - -
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Residues in contact with LYS 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D VAL* 5.4 0.9 - - + -
140D TYR* 5.3 0.7 - - - -
147D MET* 3.7 22.9 - - + -
151D GLU* 3.4 43.8 + - - +
152D ALA 3.0 4.5 + - - +
154D ALA* 1.3 80.6 - - - +
156D PHE* 1.3 61.6 - - - +
158D GLN* 3.2 8.0 + - - +
159D ILE* 3.0 36.4 + - + +
183D LEU* 4.2 16.2 - - + -
187D MET* 3.3 44.6 + - - +
189D ILE* 3.9 16.9 - - + +
243D LEU* 4.8 7.6 - - + -
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Residues in contact with PHE 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ALA 2.7 24.4 + - - +
153D ARG* 4.0 5.4 - - - +
155D LYS* 1.3 70.4 - - - +
157D ARG* 1.3 61.2 + - - +
159D ILE* 3.5 11.8 - - + +
160D VAL* 2.9 46.1 + - + +
236D LEU* 3.7 27.4 - - + -
239D ILE* 4.4 3.4 - - + -
240D LEU* 3.6 39.0 - - + -
243D LEU* 4.1 18.1 - - + +
284D PHE* 3.8 28.3 - + - -
303D TRP* 4.2 10.1 - + + -
304D MET* 3.6 28.9 - - - -
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Residues in contact with ARG 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ARG* 2.8 27.5 + - + +
154D ALA* 3.8 7.4 - - - +
156D PHE* 1.3 79.0 - - - +
158D GLN* 1.3 61.9 + - + +
160D VAL* 3.3 1.7 + - - +
161D SER* 3.1 23.6 + - - -
304D MET* 2.9 40.6 + - + +
305D ASN* 3.2 18.8 + - - -
308D HIS* 3.3 43.7 + - - -
311D ASP* 3.1 29.1 + - - -
313D LEU* 3.6 41.2 - - + +
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Residues in contact with GLN 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ASN* 3.4 37.5 - - - +
154D ALA* 3.6 18.1 + - - +
155D LYS* 3.2 8.1 + - - +
157D ARG* 1.3 79.1 - - + +
159D ILE* 1.3 63.0 + - - +
161D SER* 3.5 4.6 + - - -
162D ALA* 3.1 24.6 + - - +
187D MET 4.5 1.5 + - - +
188D ASN* 3.1 28.3 + - - +
189D ILE* 2.8 34.3 + - + +
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Residues in contact with ILE 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D LYS* 3.0 25.8 + - + +
156D PHE* 3.2 16.3 + - + +
158D GLN* 1.3 78.0 - - - +
160D VAL* 1.3 62.9 + - - +
162D ALA* 3.5 1.7 + - - +
163D VAL* 3.2 27.3 + - + +
176D LEU* 6.0 0.7 - - + -
181D LEU* 3.8 38.4 - - + -
189D ILE* 3.8 27.4 - - + -
191D ILE* 4.0 6.9 - - + +
236D LEU* 3.6 28.3 - - + -
239D ILE* 4.5 11.2 - - + -
243D LEU* 4.6 7.2 - - + -
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Residues in contact with VAL 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D PHE* 2.9 49.9 + - + +
157D ARG 4.0 2.9 - - - +
159D ILE* 1.3 75.2 - - - +
161D SER* 1.3 66.4 + - - +
163D VAL* 3.4 0.9 + - - -
164D GLN* 2.8 23.4 + - - +
236D LEU* 4.6 12.6 - - + -
284D PHE* 4.7 5.8 - - + -
295D LEU* 4.1 22.1 - - + +
298D ILE* 5.3 1.3 - - + -
299D MET* 3.9 30.7 - - + +
304D MET* 3.9 12.6 - - + -
313D LEU* 4.2 4.3 - - + -
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Residues in contact with SER 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D HIS* 3.2 19.1 + - - -
111D ASN* 5.4 0.2 - - - -
157D ARG 3.1 16.3 + - - -
158D GLN* 3.8 5.8 - - - -
160D VAL* 1.3 77.3 - - - +
162D ALA* 1.3 57.8 + - - +
164D GLN* 3.8 2.4 - - - +
165D TYR* 2.9 31.4 + - - +
299D MET* 4.0 11.6 - - - +
313D LEU* 4.6 11.2 - - - +
314D LYS 4.8 3.6 + - - -
316D TYR* 3.4 23.4 + - - +
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Residues in contact with ALA 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D HIS* 3.4 26.2 + - + +
111D ASN* 4.1 4.3 - - + -
112D ILE* 3.8 12.4 - - + +
158D GLN 3.1 12.0 + - - +
159D ILE 3.8 0.2 - - - +
161D SER* 1.3 79.8 - - - +
163D VAL* 1.3 62.5 + - - +
165D TYR* 3.2 5.7 - - - +
166D CYS* 3.2 24.8 + - - -
191D ILE* 3.3 28.3 - - + -
194D PHE* 4.5 2.7 - - - -
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Residues in contact with VAL 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ILE* 3.2 21.7 + - + +
162D ALA* 1.3 72.4 - - - +
164D GLN* 1.3 67.3 + - - +
166D CYS* 3.1 3.8 + - - +
167D HIS* 2.9 49.9 + - + +
176D LEU* 4.2 19.7 - - + -
191D ILE* 4.2 10.3 - - + -
194D PHE* 3.9 20.0 - - + -
232D ASP* 4.1 14.8 - - + +
236D LEU* 4.3 8.5 - - + -
295D LEU* 3.8 12.8 - - + -
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Residues in contact with GLN 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D VAL 2.8 22.8 + - - +
161D SER 3.9 1.4 - - - +
163D VAL* 1.3 73.7 - - - +
165D TYR* 1.3 65.9 + - - +
167D HIS* 2.9 18.1 + - + +
168D GLN* 3.0 49.5 + - - +
295D LEU* 3.8 27.3 - - + +
296D GLU* 4.1 20.1 + - + +
299D MET* 3.4 24.6 - - + +
315D PRO* 3.7 23.7 - - - +
316D TYR 4.4 0.7 + - - -
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Residues in contact with TYR 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D VAL 3.8 2.9 + - - -
107D LEU* 4.0 17.3 - - + -
108D ASN 3.1 34.4 + - - -
109D HIS* 3.9 27.1 - + + -
112D ILE* 4.0 9.4 - - + -
161D SER 2.9 14.1 + - - +
162D ALA 3.2 8.5 - - - +
164D GLN* 1.3 83.8 + - - +
166D CYS* 1.3 63.0 + - - +
168D GLN* 3.4 27.5 + - - +
169D LYS* 3.6 31.0 + - - +
316D TYR* 3.8 30.3 - + + -
318D GLU* 3.2 28.2 + - + -
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Residues in contact with CYS 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LEU* 4.0 17.5 - - - -
112D ILE* 3.6 14.8 - - - -
162D ALA 3.2 7.2 + - - -
163D VAL 3.1 8.3 + - - +
165D TYR* 1.3 75.9 - - - +
167D HIS* 1.3 58.1 + - - +
169D LYS* 3.4 5.5 + - - +
170D PHE 3.2 2.8 + - - -
171D ILE* 2.7 53.6 + - + +
194D PHE* 3.3 45.5 - - + -
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Residues in contact with HIS 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D VAL* 2.9 31.7 + - + +
164D GLN* 2.9 13.9 + - + +
166D CYS* 1.3 74.0 - - + +
168D GLN* 1.3 57.0 + - - +
169D LYS 3.0 2.0 - - - -
170D PHE* 2.6 33.5 + - - +
171D ILE 3.5 16.6 - - - +
172D VAL* 4.3 4.0 - - + -
229D PRO* 3.5 49.2 - - + +
232D ASP* 2.9 26.9 + - + +
233D VAL* 4.6 3.3 - - + +
295D LEU* 4.2 22.0 + - + +
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Residues in contact with GLN 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C PHE* 4.4 5.4 - - - -
120C GLU* 4.7 6.2 - - - +
164D GLN* 3.0 45.3 + - - +
165D TYR* 3.5 22.3 + - + +
167D HIS* 1.3 74.1 - - - +
169D LYS* 1.3 62.2 + - + +
170D PHE* 3.2 17.8 - - - -
315D PRO* 4.2 8.5 - - - +
316D TYR 3.9 19.3 + - - +
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Residues in contact with LYS 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C PHE* 3.9 9.3 - - + +
102C ARG* 2.5 38.4 + - - +
106D VAL* 4.8 15.9 + - + +
107D LEU* 4.4 16.8 - - + -
165D TYR* 3.6 45.7 - - + +
166D CYS 3.4 7.0 + - - +
167D HIS 3.0 0.8 - - - -
168D GLN* 1.3 80.8 - - + +
170D PHE* 1.3 66.0 + - - +
171D ILE* 3.2 13.0 - - + -
318D GLU* 4.3 11.1 + - - -
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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