Contacts of the helix formed by residues 145 - 167 (chain B) in PDB entry 2NP5
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 GLU 145 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B THR 3.6 0.6 + - - -
144B PRO* 1.3 74.2 - - + +
146B ALA* 1.3 65.0 + - - +
147B GLU 3.4 2.2 - - - -
148B THR* 3.2 14.1 + - - -
149B ARG* 2.9 30.8 + - + +
178D HIS* 2.9 36.7 + - - -
182D ILE* 3.7 22.3 - - + +
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Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B SER* 4.6 1.8 - - - +
138B LEU* 3.6 15.7 - - + +
139B ILE* 3.6 40.4 - - + +
143B THR* 3.5 17.4 + - - +
144B PRO 3.1 5.6 + - - -
145B GLU* 1.3 74.1 - - - +
147B GLU* 1.3 57.9 + - - +
149B ARG* 3.3 1.1 + - - -
150B ALA* 2.9 30.7 + - - +
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Residues in contact with GLU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ARG* 4.9 13.7 + - - +
135B SER* 3.6 23.1 + - - +
139B ILE* 5.4 7.5 - - + +
145B GLU 3.4 0.8 - - - -
146B ALA* 1.3 78.7 - - - +
148B THR* 1.3 58.4 + - - +
150B ALA* 3.5 3.6 + - - +
151B ALA* 3.1 22.0 + - - +
175D TYR* 3.8 10.9 + - + +
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Residues in contact with THR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLU* 3.2 18.5 + - - -
147B GLU* 1.3 77.4 - - - +
149B ARG* 1.3 60.6 + - - +
151B ALA* 3.2 3.5 + - - +
152B LEU* 2.9 28.5 + - + +
175D TYR* 3.8 18.3 + - + +
178D HIS* 3.3 28.2 + - + -
179D ALA* 3.7 32.5 - - + -
182D ILE* 4.0 15.9 - - + -
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Residues in contact with ARG 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 4.0 11.0 - - + -
143B THR* 3.8 8.6 - - - +
144B PRO* 3.2 33.0 + - - +
145B GLU* 2.9 22.6 + - - +
146B ALA 3.8 3.4 - - - +
148B THR* 1.3 76.3 - - - +
150B ALA* 1.3 57.6 + - - +
152B LEU* 3.3 4.0 + - - -
153B LEU* 2.9 26.7 + - - +
186B MSE 3.8 2.8 + - - -
187B ILE* 2.7 60.2 + - + +
189B GLN* 2.9 28.1 + - - +
182D ILE* 4.1 17.8 - - + +
186D MSE 3.8 27.1 - - - +
189D GLN* 5.5 4.4 + - - -
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ARG* 4.0 5.8 - - - +
134B LEU* 3.7 21.6 - - + +
135B SER* 3.2 44.2 - - - +
138B LEU* 3.6 8.6 - - + +
146B ALA 2.9 15.0 + - - +
147B GLU 3.5 1.8 - - - +
149B ARG* 1.3 74.7 - - - +
151B ALA* 1.3 63.4 + - - +
153B LEU* 3.3 6.0 + - - +
154B LEU* 3.2 18.5 + - - +
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ARG* 3.6 31.9 - - - +
147B GLU 3.1 7.6 + - - +
148B THR* 3.2 5.8 + - + +
150B ALA* 1.3 75.5 - - - +
152B LEU* 1.3 59.3 + - + +
154B LEU* 3.4 3.3 + - - +
155B ALA* 3.0 29.4 + - - +
160D LEU* 4.9 3.6 - - + +
171D TYR* 4.9 7.2 + - + -
175D TYR* 3.0 36.3 - - + +
179D ALA* 5.8 1.1 - - + -
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B THR* 2.9 22.7 + - + +
149B ARG* 3.5 6.5 - - - +
150B ALA 3.2 0.2 - - - -
151B ALA* 1.3 73.9 - - - +
153B LEU* 1.3 67.0 + - - +
155B ALA* 3.3 1.9 + - - -
156B THR* 2.9 28.0 + - - -
183B GLN* 4.6 0.7 - - - -
187B ILE* 4.5 3.6 - - + -
156D THR* 3.6 24.2 - - + +
160D LEU* 4.0 10.5 - - + -
179D ALA* 3.5 41.1 - - + +
182D ILE* 3.5 28.5 - - + -
183D GLN* 3.6 20.2 - - + +
186D MSE 3.7 11.7 - - + -
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 4.2 26.2 - - + -
89B MSE 3.9 23.1 - - + -
134B LEU* 4.2 9.9 - - + -
138B LEU* 5.8 1.8 - - + -
149B ARG 2.9 16.5 + - - +
150B ALA* 3.3 7.4 + - - +
152B LEU* 1.3 77.7 - - - +
154B LEU* 1.3 62.2 + - - +
156B THR* 3.3 5.0 + - - -
157B VAL* 3.1 27.8 + - + +
180B LEU* 4.0 22.9 - - + -
183B GLN* 3.8 25.6 - - + +
184B ILE* 4.1 15.5 - - + -
187B ILE* 4.5 16.9 - - + +
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B MSE 4.4 6.1 - - - -
92B LEU* 4.0 21.1 - - + -
127B LEU* 3.6 26.0 - - + +
130B ILE* 3.8 38.6 - - + -
131B ARG* 3.7 25.4 - - + -
134B LEU* 4.1 7.3 - - + +
150B ALA 3.2 10.4 + - - +
151B ALA 3.7 7.9 - - - +
153B LEU* 1.3 78.8 - - - +
155B ALA* 1.3 58.2 + - - +
157B VAL* 3.2 7.6 + - + +
158B ASP* 3.0 44.2 + - - +
163D ASP* 4.7 1.8 - - - +
171D TYR* 5.1 1.3 - - - +
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ALA 3.0 17.9 + - - +
152B LEU* 3.7 4.7 - - - +
154B LEU* 1.3 77.2 - - - +
156B THR* 1.3 51.0 + - - +
158B ASP 3.1 1.1 + - - +
159B GLY* 2.7 32.4 + - - -
155D ALA 3.9 0.2 - - - +
156D THR* 3.9 6.7 - - + +
159D GLY* 3.3 8.6 - - - -
160D LEU* 3.7 42.8 - - + +
163D ASP* 3.6 16.1 + - - +
171D TYR* 5.8 0.2 - - + -
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Residues in contact with THR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU 2.9 15.6 + - - -
153B LEU* 3.4 9.9 - - + +
155B ALA* 1.3 74.1 - - - +
157B VAL* 1.3 58.0 + - + +
159B GLY 3.6 0.3 - - - -
160B LEU* 2.7 48.1 + - + +
180B LEU* 5.5 2.0 - - + -
183B GLN* 3.3 27.9 + - + -
152D LEU* 3.5 29.6 - - + -
155D ALA* 4.2 1.3 - - + +
156D THR* 2.7 30.3 + - - +
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B MSE 3.8 34.5 - - + +
92B LEU* 3.5 44.9 - - + +
93B LEU* 3.5 17.4 - - + +
153B LEU* 3.1 13.9 + - + +
154B LEU 3.4 9.0 - - - +
156B THR* 1.3 84.4 - - + +
158B ASP* 1.3 60.6 + - - +
160B LEU* 4.6 0.9 - - + -
161B ALA* 3.0 28.4 + - - +
180B LEU* 4.0 15.0 - - + -
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Residues in contact with ASP 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 5.2 5.1 - - - +
123B ARG* 4.4 3.4 + - - -
127B LEU* 3.8 14.3 - - - +
154B LEU* 3.0 28.3 + - - +
155B ALA 3.7 3.8 - - - +
157B VAL* 1.3 79.6 - - - +
159B GLY* 1.3 57.5 + - - +
161B ALA* 3.4 6.9 + - - +
162B LEU* 3.0 28.8 + - - +
159D GLY* 4.3 5.6 - - - +
162D LEU* 4.6 10.8 - - + +
163D ASP* 2.6 37.8 - - - +
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Residues in contact with GLY 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ALA 2.7 15.3 + - - -
158B ASP* 1.3 70.9 - - - +
160B LEU* 1.3 53.8 + - - +
162B LEU* 3.3 4.8 + - - +
163B ASP* 2.7 40.8 + - - +
155D ALA* 3.1 28.5 - - - -
158D ASP* 4.3 1.8 - - - -
159D GLY* 3.5 12.7 - - - -
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Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 4.0 15.0 - - + -
156B THR* 2.7 42.0 + - + +
157B VAL* 3.8 4.7 - - + +
159B GLY* 1.3 69.8 - - - +
161B ALA* 1.3 60.7 + - - +
163B ASP* 3.8 2.7 - - - +
164B ALA* 2.9 32.1 + - - +
171B TYR* 4.1 22.9 - - + -
175B TYR* 5.2 0.9 - - + -
176B LEU* 3.9 25.0 - - + +
179B ALA* 3.9 29.8 - - + -
180B LEU* 4.5 9.4 - - + +
151D ALA* 5.0 3.6 - - + +
152D LEU* 4.2 3.1 - - + -
155D ALA* 3.7 20.8 - - + +
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Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU 4.0 11.0 - - - +
93B LEU* 4.3 0.6 - - - +
94B PRO* 3.7 27.8 - - + -
103B ALA* 4.2 13.7 - - + +
157B VAL 3.0 18.1 + - - +
158B ASP* 3.6 7.2 - - - +
160B LEU* 1.3 75.6 - - - +
162B LEU* 1.3 58.3 + - - +
164B ALA* 3.1 2.3 + - - +
165B ILE* 2.9 36.8 + - - +
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ALA* 3.9 26.0 - - + -
158B ASP 3.0 18.0 + - - +
159B GLY 3.6 3.4 - - - +
161B ALA* 1.3 74.7 - - - +
163B ASP* 1.3 67.3 + - - +
164B ALA 3.2 0.9 + - - -
165B ILE* 3.4 23.3 + - + +
166B GLY* 3.8 3.1 + - - -
107D ALA* 4.6 8.1 - - + +
110D ALA* 3.7 33.6 - - + +
111D VAL* 4.4 8.5 - - + -
123D ARG* 4.4 10.1 + - - +
158D ASP* 4.1 26.9 - - + +
162D LEU* 4.2 25.4 - - + -
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Residues in contact with ASP 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B GLY 2.7 25.5 + - - +
160B LEU 4.0 3.1 - - - +
162B LEU* 1.3 72.8 - - - +
164B ALA* 1.3 56.6 + - - +
166B GLY* 3.6 1.6 + - - -
167B SER* 3.2 28.4 + - - -
171B TYR* 3.7 30.9 + - + -
123D ARG* 2.8 24.4 + - - +
127D LEU* 3.9 14.1 - - + +
154D LEU* 4.5 1.6 - - - +
155D ALA* 3.5 22.2 + - - +
158D ASP* 2.6 32.6 - - - +
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B PRO* 3.8 19.7 - - + -
160B LEU 2.9 19.6 + - - +
161B ALA 3.1 4.7 + - - +
163B ASP* 1.3 72.2 - - - +
165B ILE* 1.3 63.9 + - - +
166B GLY 3.1 2.5 - - - -
168B PRO* 3.1 28.1 - - - +
171B TYR* 3.6 33.8 - - + +
176B LEU* 4.2 4.0 - - + -
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Residues in contact with ILE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B PRO* 4.7 7.4 - - + -
100B SER* 4.3 10.8 - - - +
103B ALA* 3.6 27.1 - - + +
104B HIS* 4.0 21.8 - - + +
107B ALA* 3.8 28.3 - - + -
161B ALA 2.9 20.4 + - - +
162B LEU* 3.4 22.4 - - + +
164B ALA* 1.3 72.8 - - - +
166B GLY* 1.3 62.6 + - - +
168B PRO* 4.1 9.0 - - - +
110D ALA 4.6 8.1 - - - +
111D VAL* 4.7 3.4 - - - -
114D ALA* 3.5 35.8 - - + +
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Residues in contact with GLY 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU 3.8 2.1 + - - -
163B ASP 3.6 5.0 + - - -
164B ALA 3.1 0.4 - - - -
165B ILE* 1.3 83.3 - - - +
167B SER* 1.3 60.8 + - - +
168B PRO* 2.8 15.9 - - - +
110D ALA 4.6 2.2 - - - -
113D ALA* 3.9 28.7 - - - +
114D ALA 4.3 0.2 - - - -
120D ALA* 3.4 22.6 - - - +
123D ARG* 5.6 4.3 - - - -
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Residues in contact with SER 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ASP 3.2 12.9 + - - -
164B ALA 3.4 4.3 - - - +
166B GLY* 1.3 77.6 - - - +
168B PRO* 1.4 63.9 - - - +
169B ALA* 3.2 3.4 - - - -
170B LEU* 3.1 19.0 + - - -
171B TYR* 3.0 27.4 + - - +
120D ALA 4.0 2.4 + - - -
123D ARG* 4.4 2.8 - - - +
124D ARG* 3.5 39.1 + - - +
127D LEU* 4.1 6.6 - - - +
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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
------------------------------------------------------------
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