Contacts of the helix formed by residues 134 - 160 (chain B) in PDB entry 4ZDR
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 ALA 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ARG* 5.2 3.1 - - - +
132B VAL 3.9 1.0 + - - -
133B ALA* 1.3 74.5 - - - +
135B GLY* 1.3 70.0 + - - +
136B ASP 3.3 2.5 + - - +
137B ASP* 3.6 7.5 + - + +
138B LYS* 3.2 20.9 + - - +
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Residues in contact with GLY 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ALA* 1.3 75.5 - - - +
136B ASP* 1.3 63.0 + - - +
138B LYS* 3.3 16.2 + - - +
139B LYS* 4.2 3.5 + - - +
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Residues in contact with ASP 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ALA* 3.3 2.2 + - - +
135B GLY* 1.3 76.6 - - - +
137B ASP* 1.3 71.7 + - - +
138B LYS 3.4 0.2 + - - -
139B LYS* 4.2 8.7 + - - +
140B GLY 5.1 0.5 + - - -
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Residues in contact with ASP 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ALA* 5.0 2.9 - - + -
134B ALA* 3.6 8.2 + - - +
135B GLY 3.5 0.2 - - - -
136B ASP* 1.3 85.8 - - - +
138B LYS* 1.3 63.8 + - - +
139B LYS 3.5 0.4 - - - -
140B GLY* 3.5 3.9 + - - -
141B ILE* 3.2 37.8 + - + +
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Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ALA* 4.0 18.0 + - - +
133B ALA* 4.1 27.6 + - + +
134B ALA 3.2 19.0 + - - +
135B GLY* 3.5 8.7 - - - +
136B ASP 3.2 1.2 - - - -
137B ASP* 1.3 75.3 - - - +
139B LYS* 1.3 67.5 - - - +
140B GLY 2.9 0.7 + - - -
141B ILE* 3.0 3.4 + - - +
142B VAL* 2.9 41.7 + - + +
181B ILE* 5.1 10.7 + - - +
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Residues in contact with LYS 139 (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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135B GLY 4.2 3.9 + - - +
136B ASP 4.2 6.3 + - - +
137B ASP 3.5 0.8 - - - -
138B LYS* 1.3 78.3 - - - +
140B GLY* 1.3 56.6 + - - +
142B VAL* 3.6 8.3 - - - +
143B ASP* 3.1 24.9 + - - +
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Residues in contact with GLY 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASP 5.1 1.0 + - - -
137B ASP 3.5 4.8 + - - -
138B LYS 3.1 0.6 - - - -
139B LYS* 1.3 77.9 - - - +
141B ILE* 1.3 60.9 + - - +
142B VAL 3.3 0.2 - - - -
143B ASP* 3.2 6.2 + - - +
144B GLN* 2.9 34.9 + - - +
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TYR* 3.3 33.4 - - + +
129B LEU* 3.6 23.6 - - + -
130B ALA* 3.4 15.7 - - - +
133B ALA* 3.7 23.6 - - + -
137B ASP* 3.2 26.5 + - + +
138B LYS* 3.0 6.6 + - - +
140B GLY* 1.3 71.9 - - - +
142B VAL* 1.3 68.1 + - - +
144B GLN* 3.1 9.3 + - - +
145B SER* 3.0 21.3 + - - -
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ALA* 4.0 9.2 - - + -
138B LYS* 2.9 40.4 + - + +
139B LYS* 3.6 7.4 - - - +
141B ILE* 1.3 75.3 - - - +
143B ASP* 1.3 65.3 + - - +
145B SER* 3.1 9.7 + - - -
146B GLN* 3.0 20.0 + - - +
177B PHE* 3.5 12.9 - - + -
181B ILE* 3.7 22.2 - - + +
182B LEU* 3.6 31.2 - - + -
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Residues in contact with ASP 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LYS 3.1 17.7 + - - +
140B GLY* 3.2 7.4 + - - +
141B ILE 3.2 0.4 - - - -
142B VAL* 1.3 78.5 - - + +
144B GLN* 1.3 60.3 + - - +
146B GLN* 3.9 18.2 - - - +
147B GLN* 2.9 37.1 + - - +
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Residues in contact with GLN 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LYS* 4.5 10.7 + - - -
126B TYR* 3.5 48.9 + - + +
140B GLY 2.9 17.1 + - - +
141B ILE* 3.4 9.2 - - - +
143B ASP* 1.3 79.0 + - - +
145B SER* 1.3 62.0 + - - +
147B GLN* 4.2 6.3 - - - +
148B ALA* 3.2 24.8 + - - +
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Residues in contact with SER 145 (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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123B GLY* 2.7 26.5 + - - -
126B TYR* 3.5 20.8 - - - +
127B ARG* 3.3 16.7 + - - +
141B ILE 3.0 9.9 + - - -
142B VAL* 3.3 10.3 - - - -
144B GLN* 1.3 79.3 - - - +
146B GLN* 1.3 56.8 + - - +
148B ALA 3.5 0.2 + - - -
149B TYR* 3.0 41.2 + - - -
177B PHE* 3.5 12.2 - - - -
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Residues in contact with GLN 146 (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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142B VAL* 3.0 13.3 + - - +
143B ASP* 3.3 20.2 + - - +
145B SER* 1.3 74.0 - - - +
147B GLN* 1.3 56.7 + - - +
148B ALA 3.1 1.3 - - - -
149B TYR* 3.3 4.7 + - - +
150B GLN* 2.6 43.8 + - + +
174B PHE* 4.3 8.9 - - + -
177B PHE* 3.6 26.3 - - + -
178B TYR* 3.5 28.3 + - - -
182B LEU* 4.0 15.8 - - - +
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Residues in contact with GLN 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASP* 2.9 25.8 + - - +
144B GLN* 4.3 8.3 - - - +
146B GLN* 1.3 76.8 - - - +
148B ALA* 1.3 61.9 + - - +
150B GLN* 3.7 7.0 - - - +
151B GLU* 3.1 25.8 + - - +
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 3.6 27.7 - - + +
122B LYS* 3.9 22.0 - - + +
123B GLY* 3.6 14.1 - - - +
144B GLN 3.2 18.3 + - - +
145B SER 3.7 1.1 - - - +
146B GLN 3.1 0.4 - - - -
147B GLN* 1.3 75.3 - - - +
149B TYR* 1.3 68.3 + - - +
150B GLN 3.1 0.5 + - - -
151B GLU* 3.3 4.0 + - - +
152B ALA* 3.0 24.1 + - - +
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Residues in contact with TYR 149 (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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119B LEU 4.2 0.6 + - - -
120B LYS* 3.8 11.2 - - + -
123B GLY* 3.4 19.7 - - - -
124B ASP* 2.5 38.2 + - - -
127B ARG* 2.6 25.3 + - - -
145B SER* 3.0 27.7 + - - +
146B GLN 3.6 3.8 - - - +
148B ALA* 1.3 77.0 - - - +
150B GLN* 1.3 56.8 + - - +
152B ALA* 3.5 6.3 + - - +
153B PHE* 2.9 28.1 + - - +
170B LEU* 4.0 17.7 - - + +
173B ASN* 3.8 18.4 - - + +
174B PHE* 3.4 27.2 - + + -
177B PHE* 3.7 32.5 - + + -
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Residues in contact with GLN 150 (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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146B GLN* 2.6 27.5 + - + +
147B GLN* 3.7 9.0 - - - +
148B ALA 3.1 0.2 - - - -
149B TYR* 1.3 73.4 - - - +
151B GLU* 1.3 55.6 + - - +
153B PHE* 2.6 41.4 + - - +
154B GLU* 3.1 37.7 + - - +
174B PHE* 3.5 21.0 - - - -
178B TYR* 4.3 7.4 + - - -
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Residues in contact with GLU 151 (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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119B LEU* 3.7 30.1 - - + +
147B GLN 3.1 15.8 + - - +
148B ALA* 3.9 1.4 - - - +
150B GLN* 1.3 77.9 - - - +
152B ALA* 1.3 61.7 + - - +
153B PHE 3.2 0.5 + - - -
154B GLU* 3.5 12.2 + - - +
155B ILE* 3.3 38.3 + - + +
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Residues in contact with ALA 152 (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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116B VAL* 3.7 19.3 - - + +
119B LEU* 3.5 32.8 - - + +
120B LYS* 4.0 6.3 - - - +
148B ALA 3.0 12.1 + - - +
149B TYR 3.6 5.2 - - - +
151B GLU* 1.3 76.5 - - - +
153B PHE* 1.3 61.9 + - - +
155B ILE* 3.7 2.6 + - - +
156B SER* 3.1 25.1 + - - -
170B LEU* 3.4 15.2 - - + +
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Residues in contact with PHE 153 (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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149B TYR 2.9 13.2 + - - +
150B GLN* 2.6 34.6 + - - +
152B ALA* 1.3 72.5 - - - +
154B GLU* 1.3 61.8 + - + +
156B SER* 2.9 24.1 + - - -
157B LYS* 3.0 18.8 + - + +
167B ARG* 5.7 5.2 - - + -
170B LEU* 3.5 18.6 - - + -
171B ALA* 5.0 11.2 - - + -
174B PHE* 4.0 20.2 - + + -
191B LEU* 4.6 30.5 - - + -
195B ALA* 6.3 1.1 - - + -
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Residues in contact with GLU 154 (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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150B GLN* 3.1 47.3 + - - +
151B GLU* 4.1 8.7 - - - +
152B ALA 3.5 0.2 - - - -
153B PHE* 1.3 73.6 - - + +
155B ILE* 1.3 66.1 + - + +
157B LYS* 3.4 5.5 + - - +
158B LYS* 3.0 29.0 + - - +
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Residues in contact with ILE 155 (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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112B ALA* 3.9 26.2 - - + +
115B LYS* 4.7 12.6 - - + -
116B VAL* 3.5 22.0 - - + -
119B LEU* 4.2 18.8 - - + -
151B GLU* 3.3 29.3 + - + +
152B ALA 4.0 0.2 - - - +
154B GLU* 1.3 76.5 - - + +
156B SER* 1.3 58.8 + - - +
158B LYS* 3.3 5.5 + - - -
159B GLU* 2.8 41.6 + - + +
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Residues in contact with SER 156 (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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116B VAL* 3.8 18.8 - - - +
152B ALA 3.1 13.6 + - - -
153B PHE* 2.9 14.3 + - - -
155B ILE* 1.3 79.9 - - - +
157B LYS* 1.3 62.0 + - - +
160B MET* 2.9 43.0 + - - +
167B ARG* 3.6 29.2 + - - +
170B LEU* 3.7 12.1 - - - +
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Residues in contact with LYS 157 (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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153B PHE* 3.0 23.4 + - + +
154B GLU* 4.1 5.6 - - - +
156B SER* 1.3 82.5 + - - +
158B LYS* 1.3 61.1 + - - +
159B GLU 3.6 0.2 + - - -
160B MET 3.9 8.3 - - - +
167B ARG* 3.9 27.3 + - - +
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Residues in contact with LYS 158 (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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154B GLU 3.0 20.3 + - - +
155B ILE* 3.9 4.9 - - - +
157B LYS* 1.3 79.1 - - - +
159B GLU* 1.3 75.7 + - + +
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Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ALA* 3.5 33.4 - - + +
155B ILE* 2.8 25.3 + - + +
158B LYS* 1.3 101.6 + - + +
160B MET* 1.3 64.1 + - + +
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Residues in contact with MET 160 (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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112B ALA 4.7 0.2 - - - -
113B GLU* 3.4 30.1 - - + +
116B VAL* 3.4 42.0 - - + -
156B SER* 2.9 19.3 + - - +
157B LYS 3.9 5.4 - - - +
159B GLU* 1.3 85.6 - - + +
161B GLN* 1.3 64.1 + - - +
162B PRO* 4.3 0.2 - - - +
164B HIS* 3.5 40.8 - - + -
166B ILE* 4.1 6.3 - - + -
167B ARG* 2.9 36.8 + - + -
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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) + - + + + + + -
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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