Contacts of the helix formed by residues 153 - 174 (chain A) in PDB entry 4I93
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 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLN* 4.7 26.5 - - - +
151A PRO 4.4 4.5 + - - +
152A MSE 1.3 77.2 - - - +
154A TRP* 1.3 65.8 + - - +
155A ALA* 4.2 6.7 - - + +
156A MSE 3.1 11.1 + - + +
157A ARG* 3.0 20.3 + - - +
273A LEU* 4.2 0.2 - - - -
276A GLN* 3.5 16.2 - - - +
323A GLN 4.0 10.6 + - - -
324A LEU* 3.1 46.7 + - + +
325A LEU 4.9 1.2 + - - -
326A GLY* 4.8 5.7 - - - +
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Residues in contact with TRP 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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153A LYS* 1.3 70.9 - - - +
155A ALA* 1.3 66.6 + - - +
157A ARG* 3.1 11.0 + - + +
158A LEU* 3.0 54.7 + - + +
246A LEU* 4.3 8.3 - - + -
269A MSE 3.9 20.9 - - + -
273A LEU* 3.5 27.1 - - + +
276A GLN* 2.8 45.4 + - + +
277A PHE* 3.4 26.7 - + + +
281A ASP* 4.3 23.4 + - + +
282A GLY* 4.1 19.1 - - - -
285A LEU* 4.1 21.1 - - + -
313A LEU* 4.9 1.1 + - + -
315A LYS* 4.6 14.1 - - + +
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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
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153A LYS* 3.2 4.2 - - + +
154A TRP* 1.3 82.1 - - + +
156A MSE 1.3 57.4 + - - +
158A LEU* 3.5 12.1 + - - +
159A ARG* 3.0 27.2 + - - +
276A GLN* 4.8 0.2 + - - -
314A GLN* 4.8 0.9 - - - +
315A LYS* 3.4 34.3 + - + +
316A ASP* 3.7 22.9 - - + +
324A LEU* 4.1 13.5 - - + +
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Residues in contact with MSE 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 MSE 3.9 18.8 - - + -
153A LYS* 3.1 15.4 + - + +
155A ALA* 1.3 77.6 - - - +
157A ARG* 1.3 65.0 + - - +
159A ARG* 3.2 18.5 + - + -
160A VAL* 2.9 45.5 + - + +
189A PHE* 4.1 14.8 - - + -
193A ALA 4.7 1.6 - - - +
195A PRO* 4.2 9.2 - - + -
321A SER* 4.1 17.0 - - - +
324A LEU* 3.6 37.7 - - + +
325A LEU* 4.1 23.1 - - + -
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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
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144A LEU* 3.6 20.1 + - + +
151A PRO* 3.7 8.9 - - - +
152A MSE 2.8 56.9 + - + +
153A LYS 3.0 14.2 + - - +
154A TRP* 3.1 12.1 + - + +
156A MSE 1.3 75.8 - - - +
158A LEU* 1.3 63.1 + - + +
160A VAL* 3.4 4.6 + - - +
161A ALA* 3.0 22.2 + - - +
245A LEU* 2.8 60.0 + - + +
248A GLY 3.9 2.4 - - - +
270A ASP* 2.9 39.8 + - - +
273A LEU* 3.5 24.6 - - - +
285A LEU* 6.3 2.5 - - + -
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Residues in contact with LEU 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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154A TRP* 3.0 63.3 + - + +
155A ALA* 3.8 7.0 - - - +
157A ARG* 1.3 75.8 - - + +
159A ARG* 1.3 59.8 + - - +
161A ALA* 3.3 5.2 + - + +
162A LEU 2.9 24.1 + - - -
281A ASP* 6.4 0.2 - - + -
285A LEU* 4.1 23.3 - - + -
310A MSE 5.3 2.8 - - - +
313A LEU* 3.2 45.8 - - + +
314A GLN* 3.3 26.2 + - - +
315A LYS* 4.4 6.3 - - + -
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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
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155A ALA 3.0 16.5 + - - +
156A MSE 3.2 17.9 + - + +
158A LEU* 1.3 74.0 - - - +
160A VAL* 1.3 60.8 + - - +
162A LEU* 3.4 1.5 + - - -
163A HIS* 2.9 65.3 + - + +
194A ASN* 4.9 0.8 + - - -
195A PRO* 4.5 1.8 - - + -
314A GLN* 3.6 11.6 + - - +
315A LYS 4.5 2.4 + - - -
316A ASP 2.9 21.8 + - - -
317A LEU* 3.5 24.0 + - + +
319A ILE 2.9 29.9 + - - -
320A ALA* 4.3 0.4 - - - +
321A SER* 3.0 38.3 + - - +
324A LEU* 3.5 15.3 - - - +
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Residues in contact with VAL 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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140A LEU* 4.2 15.9 - - + -
152A MSE 4.4 10.3 - - - -
156A MSE 2.9 36.9 + - + +
157A ARG 3.5 7.0 - - - +
158A LEU 3.3 0.2 - - - -
159A ARG* 1.3 76.2 - - - +
161A ALA* 1.3 63.9 + - - +
163A HIS 3.3 0.3 + - - -
164A ILE* 2.9 30.6 + - + +
187A VAL* 3.9 25.6 - - + -
189A PHE* 4.0 13.5 - - + -
195A PRO* 3.9 16.8 - - + -
241A LEU* 5.3 1.6 - - + -
245A LEU* 4.3 10.5 - - + -
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Residues in contact with ALA 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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157A ARG 3.0 13.6 + - - +
158A LEU* 3.3 9.6 + - - +
160A VAL* 1.3 77.4 - - - +
162A LEU* 1.3 64.5 + - - +
164A ILE* 3.5 1.1 + - - -
165A ALA* 3.0 24.9 + - - +
238A PHE* 3.5 12.7 - - + -
241A LEU* 5.8 1.1 - - - -
242A LEU* 3.8 28.7 - - + -
245A LEU* 4.0 10.3 - - + +
285A LEU* 5.4 3.1 - - + -
310A MSE 4.0 13.7 - - - -
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Residues in contact with LEU 162 (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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158A LEU 2.9 16.8 + - - +
159A ARG 3.7 3.1 - - - +
161A ALA* 1.3 77.2 - - - +
163A HIS* 1.3 69.6 + - + +
165A ALA* 3.2 2.9 + - - +
166A GLN* 2.9 55.0 + - - +
307A VAL* 4.1 13.5 - - + -
310A MSE 3.9 24.1 - - + +
311A ILE* 4.0 21.5 - - + -
314A GLN* 3.7 33.9 - - + +
317A LEU* 5.5 5.6 - - + -
217B ALA* 5.4 5.8 - - + -
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Residues in contact with HIS 163 (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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114A ARG* 3.5 48.6 + - - +
159A ARG* 2.9 47.8 + - + +
162A LEU* 1.3 89.2 - - + +
164A ILE* 1.3 59.1 + - - +
166A GLN* 3.4 18.8 + - - +
167A ALA* 2.9 26.9 + - - +
194A ASN* 4.9 8.8 - - - +
195A PRO* 3.8 34.1 + - + +
317A LEU* 6.2 1.8 - - - +
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Residues in contact with ILE 164 (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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114A ARG 5.0 0.2 - - - +
160A VAL* 2.9 28.5 + - + +
161A ALA 4.1 1.8 - - - +
163A HIS* 1.3 78.1 - - - +
165A ALA* 1.3 64.1 + - - +
167A ALA* 3.1 3.5 + - - +
168A LEU* 2.9 29.5 + - + +
182A LEU* 4.7 3.8 - - + -
187A VAL* 3.9 23.6 - - + -
195A PRO* 4.8 2.9 - - + -
196A ARG* 3.7 13.0 - - - +
197A LEU* 3.7 48.2 - - + +
238A PHE* 4.2 13.2 - - + -
241A LEU* 4.2 19.3 - - + -
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Residues in contact with ALA 165 (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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161A ALA 3.0 18.7 + - - +
162A LEU* 3.5 7.6 - - - +
164A ILE* 1.3 76.7 - - - +
166A GLN* 1.3 56.2 + - - +
168A LEU* 3.2 9.5 + - - +
169A GLU* 2.9 28.1 + - - +
238A PHE* 3.8 12.7 - - + -
303A PRO* 4.8 3.1 - - - +
306A LEU* 4.0 25.1 - - + +
307A VAL* 3.9 19.7 - - + +
310A MSE 4.9 0.9 - - + -
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Residues in contact with GLN 166 (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 ASN* 5.4 0.4 + - - -
114A ARG* 3.0 41.6 + - + +
162A LEU* 2.9 35.8 + - + +
163A HIS* 3.6 15.5 - - - +
165A ALA* 1.3 71.7 - - - +
167A ALA* 1.3 59.7 + - - +
169A GLU* 3.2 7.8 + - - +
170A TYR* 2.9 28.4 + - - +
307A VAL* 4.1 24.3 - - + +
311A ILE* 5.3 3.4 - - - +
217B ALA* 5.5 6.1 - - - +
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Residues in contact with ALA 167 (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 ASN* 5.0 0.2 - - - +
114A ARG* 3.7 28.6 - - + +
115A MSE 3.9 6.9 - - - +
163A HIS 2.9 14.6 + - - +
164A ILE* 3.1 9.6 + - - +
166A GLN* 1.3 76.8 - - - +
168A LEU* 1.3 56.8 + - - +
170A TYR* 3.2 7.3 + - - +
171A CYS* 2.9 34.0 + - - -
197A LEU* 3.7 23.3 - - + -
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Residues in contact with LEU 168 (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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164A ILE* 2.9 17.0 + - + +
165A ALA* 3.6 8.5 - - - +
167A ALA* 1.3 73.1 - - - +
169A GLU* 1.3 65.8 + - - +
171A CYS* 3.3 7.6 + - + +
172A THR* 3.0 29.6 + - - +
179A TYR* 4.4 14.1 - - + -
182A LEU* 4.3 11.9 - - + -
197A LEU* 3.8 22.0 - - + -
202A LEU* 6.3 0.2 - - + -
234A VAL* 4.0 30.3 - - + -
235A ILE* 5.4 3.4 - - + -
238A PHE* 4.0 31.6 - - + -
303A PRO* 4.6 9.6 - - + -
306A LEU* 5.0 7.0 - - + -
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Residues in contact with GLU 169 (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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165A ALA 2.9 14.8 + - - +
166A GLN* 3.5 10.1 - - - +
168A LEU* 1.3 76.7 - - - +
170A TYR* 1.3 62.3 + - - +
172A THR* 3.4 4.2 + - + -
173A SER* 3.0 24.5 + - - -
303A PRO* 3.9 18.1 - - + +
304A LYS* 3.4 41.0 - - + +
307A VAL* 3.5 27.5 - - + +
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Residues in contact with TYR 170 (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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109A GLN 4.5 1.9 + - - -
110A LEU* 3.5 30.6 - - + -
111A ARG* 2.9 35.3 + - - +
112A ASN* 3.6 39.9 - - + +
115A MSE 4.6 5.4 - - + -
166A GLN 2.9 12.4 + - - +
167A ALA* 3.2 8.9 + - - +
169A GLU* 1.3 77.6 - - - +
171A CYS* 1.3 74.1 + - - +
173A SER* 2.7 27.3 + - - -
174A LYS* 3.2 37.7 + - + +
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Residues in contact with CYS 171 (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 LEU* 4.0 12.1 - - + -
115A MSE 3.5 33.7 - - - -
167A ALA 2.9 21.4 + - - +
168A LEU* 3.3 8.7 + - + +
170A TYR* 1.3 80.0 - - - +
172A THR* 1.3 63.6 + - - +
174A LYS* 3.0 10.7 + - - +
175A GLY 3.3 0.2 + - - -
176A ARG* 2.9 37.2 + - - +
197A LEU* 4.7 4.7 - - - -
202A LEU* 3.9 23.1 - - + -
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Residues in contact with THR 172 (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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168A LEU* 3.0 17.8 + - - +
169A GLU* 3.7 7.2 - - - +
171A CYS* 1.3 77.5 - - - +
173A SER* 1.3 61.5 + - - +
175A GLY* 3.1 13.9 + - - -
176A ARG 4.3 0.2 - - - -
177A ALA* 3.8 35.0 + - + +
231A PRO* 5.9 1.8 - - + +
303A PRO* 4.1 20.1 - - + +
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Residues in contact with SER 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLU* 3.0 15.8 + - - -
170A TYR* 2.7 24.9 + - - -
172A THR* 1.3 76.7 - - - +
174A LYS* 1.3 76.4 + - - +
175A GLY 3.3 1.1 + - - -
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Residues in contact with LYS 174 (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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109A GLN 5.9 1.3 - - - +
110A LEU* 3.8 27.7 - - + +
170A TYR* 3.2 48.4 + - + +
171A CYS 3.0 8.7 + - - +
173A SER* 1.3 91.9 + - - +
175A GLY* 1.3 61.1 + - - +
176A ARG* 3.4 3.4 + - - +
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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