Contacts of the helix formed by residues 136 - 160 (chain A) in PDB entry 3DAN
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 ARG 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ASN* 3.7 33.9 + - - +
133A SER* 2.8 8.5 + - - +
135A ASN* 1.3 82.1 - - + +
137A VAL* 1.3 67.4 + - - +
138A ILE 3.5 1.1 - - - -
139A PRO* 3.5 3.9 - - - +
140A GLN* 2.9 41.4 + - + +
178A ARG 3.4 15.3 + - - -
179A ALA* 2.8 32.0 + - - +
180A TYR 3.1 19.4 + - - -
181A PHE* 4.1 1.8 - - - +
182A ASN* 3.8 35.1 + - - +
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU 5.5 0.4 - - - +
133A SER* 3.1 32.9 + - - +
134A SER* 3.9 11.9 - - - +
135A ASN 3.6 1.2 - - - -
136A ARG* 1.3 75.9 - - - +
138A ILE* 1.3 60.7 + - + +
141A PHE* 2.9 32.2 + - - +
175A PHE* 3.5 19.6 - - + -
179A ALA* 4.5 4.0 - - + +
431A PHE* 4.0 17.0 - - + -
434A LEU* 3.7 29.2 - - + -
435A ILE* 4.2 7.4 - - + -
438A LEU* 4.1 11.7 - - + -
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Residues in contact with ILE 138 (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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134A SER 4.9 2.8 + - - +
137A VAL* 1.3 77.7 - - + +
139A PRO* 1.3 74.4 - - + +
141A PHE* 3.2 2.4 + - - +
142A GLU* 3.0 46.5 + - + +
319A VAL* 3.5 42.0 - - + +
320A THR* 4.1 15.3 - - - -
321A LEU* 4.1 24.0 - - + +
324A ILE* 4.7 3.6 - - + -
434A LEU* 5.0 3.8 - - + -
438A LEU* 4.2 21.5 - - + -
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Residues in contact with PRO 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ASN 3.8 15.9 - - - +
136A ARG* 3.5 14.6 - - - +
138A ILE* 1.3 97.1 - - + +
140A GLN* 1.3 66.3 + - - +
142A GLU* 3.5 14.5 + - - +
143A THR* 3.1 31.8 + - - -
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Residues in contact with GLN 140 (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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136A ARG* 2.9 39.9 + - + +
137A VAL 4.2 1.1 - - - +
139A PRO* 1.3 84.2 + - - +
141A PHE* 1.3 64.5 + - - +
143A THR* 3.9 10.5 + - - +
144A THR* 2.8 31.9 + - - -
175A PHE* 3.8 8.5 - - + -
178A ARG* 3.5 48.2 + - + +
179A ALA 4.3 2.9 - - - +
182A ASN* 5.1 10.1 - - - +
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Residues in contact with PHE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL 2.9 19.9 + - - +
138A ILE 3.6 3.4 - - - +
140A GLN* 1.3 76.7 - - - +
142A GLU* 1.3 61.0 + - + +
145A TYR* 2.9 68.7 + + - +
175A PHE* 3.5 29.3 - + + -
285A PHE* 4.0 11.4 - + - -
435A ILE* 3.6 17.5 - - + -
438A LEU* 3.4 43.5 - - + -
439A PHE* 3.4 26.9 - - + -
442A GLU* 3.8 14.4 - - + -
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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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138A ILE* 3.0 35.1 + - + +
139A PRO* 3.7 14.0 - - - +
141A PHE* 1.3 78.0 - - + +
143A THR* 1.3 60.9 + - - +
145A TYR 3.9 0.2 - - - -
146A THR* 2.8 33.7 + - - +
319A VAL* 3.4 15.6 + - + +
438A LEU* 6.0 1.8 - - + -
442A GLU* 3.7 26.6 - - + +
445A ARG* 3.0 27.2 + - - -
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Residues in contact with THR 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PRO 3.1 15.7 + - - -
140A GLN* 3.9 13.4 + - - +
141A PHE 3.3 0.2 - - - -
142A GLU* 1.3 80.6 - - - +
144A THR* 1.3 61.3 + - - +
146A THR* 3.7 4.9 - - - -
147A GLU* 3.0 39.9 + - + +
178A ARG* 3.9 20.9 - - - +
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Residues in contact with THR 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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140A GLN 2.8 21.1 + - - -
141A PHE 3.9 2.0 - - - -
143A THR* 1.3 78.2 - - - +
145A TYR* 1.3 61.4 + - + +
147A GLU* 3.3 10.1 + - - +
148A LEU* 3.1 21.0 + - - +
171A ALA* 3.2 30.5 - - - +
174A ARG* 3.3 27.5 + - - +
175A PHE* 3.7 19.4 - - + +
178A ARG* 2.9 21.9 + - - +
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Residues in contact with TYR 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 PHE* 2.9 57.4 + + + +
142A GLU 4.6 0.7 - - - +
144A THR* 1.3 79.7 - - + +
146A THR* 1.3 60.0 + - - +
147A GLU 3.2 0.2 - - - -
148A LEU* 3.6 30.6 - - + +
149A PHE* 2.9 48.5 + + + -
164A PHE* 5.2 1.3 - + - -
168A GLY 4.3 2.4 + - - -
171A ALA* 4.3 5.8 - - + -
172A ALA* 3.4 25.3 + - - +
175A PHE* 4.0 19.2 - + + -
281A VAL* 4.6 0.3 - - - +
285A PHE* 3.4 25.7 - + - -
439A PHE* 3.9 30.5 - + - -
442A GLU* 4.6 3.8 - - + -
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Residues in contact with THR 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* 2.8 25.4 + - - +
143A THR* 3.7 5.8 - - - -
145A TYR* 1.3 75.8 - - - +
147A GLU* 1.3 65.1 + - + +
149A PHE* 3.3 8.7 + - - +
150A GLU* 2.9 52.5 + - + +
442A GLU* 3.9 10.4 + - - -
446A ARG* 4.2 13.9 + - - +
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Residues in contact with GLU 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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143A THR* 3.0 28.1 - - + +
144A THR* 3.4 5.3 - - - +
146A THR* 1.3 79.5 - - + +
148A LEU* 1.3 63.1 + - - +
150A GLU* 3.4 16.1 + - - +
151A GLY* 3.0 19.1 + - - -
174A ARG* 2.8 38.4 + - - +
178A ARG* 2.9 28.4 + - - -
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Residues in contact with LEU 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 THR 3.1 13.5 + - - +
145A TYR* 3.6 39.3 - - + +
146A THR 3.2 0.2 - - - -
147A GLU* 1.3 76.5 - - - +
149A PHE* 1.3 63.2 + - + +
151A GLY* 3.1 3.7 + - - -
152A LEU* 2.9 38.3 + - + +
164A PHE* 3.8 23.6 - - + -
167A VAL* 3.5 46.0 - - + +
168A GLY* 4.0 4.3 - - - +
171A ALA* 3.9 13.7 - - + -
174A ARG* 4.2 3.5 - - - +
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Residues in contact with PHE 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 TYR* 2.9 32.9 + + + +
146A THR* 3.9 5.2 - - - +
148A LEU* 1.3 83.0 - - + +
150A GLU* 1.3 61.3 + - - +
152A LEU* 3.7 16.6 - - + +
153A GLU* 2.8 31.9 + - - +
164A PHE* 5.1 2.0 - + - -
439A PHE* 4.3 25.8 - + - -
442A GLU* 3.7 37.9 - - + -
443A LEU* 3.8 28.9 - - + -
446A ARG* 3.7 18.8 - - - -
447A TYR* 3.4 27.5 + + - +
465A LEU* 6.2 0.9 - - + -
468A LEU* 6.5 0.2 - - + -
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Residues in contact with GLU 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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146A THR* 2.9 40.0 + - - +
147A GLU* 3.6 16.4 - - - +
149A PHE* 1.3 75.9 - - - +
151A GLY* 1.3 57.6 + - - +
153A GLU* 3.5 5.3 - - - +
154A ALA* 3.1 28.4 + - - +
446A ARG* 3.3 29.9 + - - +
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Residues in contact with GLY 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 GLU 3.0 14.3 + - - -
148A LEU* 3.5 4.0 - - - -
150A GLU* 1.3 75.1 - - - +
152A LEU* 1.3 59.2 + - - +
154A ALA* 3.4 6.1 + - - +
155A GLU* 3.0 28.7 + - - +
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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 LEU* 2.9 34.9 + - + +
149A PHE* 3.8 15.7 - - + +
151A GLY* 1.3 73.4 - - - +
153A GLU* 1.3 60.5 + - - +
155A GLU* 3.3 8.6 + - - +
156A LEU* 2.9 31.4 + - - +
162A ALA* 3.7 19.2 - - + +
163A ALA 3.6 26.2 - - - +
164A PHE* 3.8 27.6 - - + -
167A VAL* 3.7 14.8 - - + -
465A LEU* 3.9 21.3 - - + -
468A LEU* 4.6 5.2 - - + -
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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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149A PHE 2.8 11.2 + - - +
150A GLU* 3.5 7.2 - - - +
152A LEU* 1.3 77.8 - - - +
154A ALA* 1.3 62.9 + - - +
156A LEU* 3.4 4.3 + - + +
157A ALA* 3.0 25.2 + - - +
446A ARG* 2.9 28.1 + - - -
447A TYR* 2.8 35.5 + - + +
468A LEU* 3.9 17.9 - - + +
470A ARG* 3.2 32.7 + - + +
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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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150A GLU 3.1 14.7 + - - +
151A GLY* 3.7 6.7 - - - +
152A LEU 3.3 0.2 - - - -
153A GLU* 1.3 80.4 - - - +
155A GLU* 1.3 62.4 + - - +
157A ALA* 3.3 7.6 + - - +
158A LYS* 3.1 24.4 + - - +
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Residues in contact with GLU 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 GLY 3.0 17.8 + - - +
152A LEU* 3.3 11.4 + - - +
154A ALA* 1.3 75.5 - - - +
156A LEU* 1.3 59.3 + - - +
158A LYS* 3.3 0.6 + - - -
159A ASN* 2.8 50.3 + - - +
161A LYS 3.5 13.4 - - - +
162A ALA* 3.6 20.7 - - + +
163A ALA* 4.0 13.5 + - - +
167A VAL* 5.1 7.3 - - - +
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Residues in contact with LEU 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 17.1 + - - +
153A GLU* 3.7 4.5 - - - +
155A GLU* 1.3 77.9 - - - +
157A ALA* 1.3 60.0 + - - +
160A GLY* 2.7 61.3 + - - +
161A LYS* 3.4 14.6 - - - +
162A ALA* 4.1 3.6 - - + +
465A LEU* 3.6 14.6 - - + +
466A THR 3.9 7.9 - - - +
467A PHE* 3.7 29.8 - - + +
468A LEU* 3.8 27.1 - - + +
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Residues in contact with ALA 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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153A GLU 3.0 16.6 + - - +
154A ALA* 3.3 7.8 + - - +
156A LEU* 1.3 77.8 - - - +
158A LYS* 1.3 60.2 + - - +
160A GLY 4.9 0.3 + - - -
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Residues in contact with LYS 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 ALA 3.1 16.0 + - - +
155A GLU* 4.9 0.2 - - - -
157A ALA* 1.3 79.5 - - + +
159A ASN* 1.3 79.9 + - - +
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Residues in contact with ASN 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 GLU* 2.8 45.7 + - + +
158A LYS* 1.3 100.6 + - - +
160A GLY* 1.3 55.0 + - - +
161A LYS* 3.2 17.9 + - + +
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Residues in contact with GLY 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 LEU* 2.7 34.9 + - - +
157A ALA 4.7 0.2 - - - -
158A LYS 3.9 0.4 - - - -
159A ASN* 1.3 71.6 - - - +
161A LYS* 1.3 70.3 + - - +
466A THR* 4.1 9.9 - - - +
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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
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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