Contacts of the helix formed by residues 139 - 160 (chain B) in PDB entry 3AG9
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 SER 139 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ARG* 4.2 9.3 + - - +
138B PHE* 1.3 76.8 - - - +
140B GLU* 1.3 65.5 + - - +
141B PRO* 3.3 12.6 - - - +
142B HIS* 3.2 23.3 + - - +
143B ALA* 2.9 21.4 + - - +
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PHE 3.9 0.4 + - - +
139B SER* 1.3 71.9 - - - +
141B PRO* 1.4 66.4 - - + +
143B ALA* 4.4 3.4 - - - -
144B ARG* 2.8 39.9 + - - +
232B ALA* 5.0 5.4 - - + -
260B HIS* 3.7 8.3 + - - +
261B PHE* 3.6 9.5 - - + -
262B SER* 2.6 50.4 + - - -
265B LEU* 3.6 20.3 - - + +
296B TRP* 2.9 31.2 + - - +
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Residues in contact with PRO 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B SER* 3.3 14.1 - - - +
140B GLU* 1.4 93.9 - - + +
142B HIS* 1.3 55.7 + - - +
144B ARG* 3.4 24.7 + - - +
145B PHE* 3.1 28.2 + - - +
313B PRO* 5.4 0.7 - - - -
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Residues in contact with HIS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ILE* 5.1 5.2 - - + -
138B PHE* 3.7 35.2 - + + +
139B SER* 3.1 20.8 + - - +
141B PRO* 1.3 76.6 - - - +
143B ALA* 1.3 64.2 + - - +
145B PHE* 3.2 12.0 + - - +
146B TYR* 2.8 56.7 + + - -
313B PRO* 3.4 34.4 - - + +
314B PHE* 3.9 17.8 - + + -
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PHE* 4.1 6.2 - - + +
139B SER 2.9 19.7 + - - +
140B GLU* 3.7 6.5 - - - +
142B HIS* 1.3 73.2 - - - +
144B ARG* 1.3 51.1 + - - +
146B TYR* 3.3 2.6 + - - -
147B ALA* 2.8 31.7 + - - +
228B ILE 4.9 1.6 - - - +
231B MET* 3.3 43.4 - - + +
232B ALA* 4.5 11.7 - - + +
296B TRP* 4.0 12.6 - - + -
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Residues in contact with ARG 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLU* 2.8 26.7 + - - +
141B PRO* 3.6 34.3 - - - +
143B ALA* 1.3 70.3 - - - +
145B PHE* 1.3 67.4 + - - +
147B ALA* 3.8 0.8 - - - +
148B ALA* 2.9 24.8 + - - +
296B TRP* 2.7 69.7 + - + +
297B PHE* 3.9 11.1 - - + -
299B THR* 3.9 21.2 + - - +
300B THR* 3.6 25.4 - - + +
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Residues in contact with PHE 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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141B PRO 3.1 14.8 + - - +
142B HIS 3.2 7.6 + - - +
144B ARG* 1.3 78.2 - - - +
146B TYR* 1.3 72.6 + + - +
148B ALA* 3.6 10.8 + - - +
149B GLN* 3.1 38.4 + - - +
178B GLY 3.4 21.5 - - - -
179B TYR* 3.6 44.6 - + - -
305B ILE* 3.9 18.2 - - + +
310B VAL* 4.0 20.2 - - + -
311B GLU 4.1 6.5 - - - -
312B ALA* 3.8 7.9 - - - -
313B PRO* 3.2 28.7 - - + -
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Residues in contact with TYR 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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128B MET* 3.6 18.4 - - + -
138B PHE* 3.6 18.2 - + - -
142B HIS* 2.8 46.1 + + - -
143B ALA 3.3 5.2 + - - +
145B PHE* 1.3 95.9 - + - +
147B ALA* 1.3 66.0 + - - +
149B GLN* 3.0 17.3 + - - +
150B ILE* 3.2 15.1 + - - +
174B ILE* 4.2 12.3 - - + +
178B GLY 3.6 18.3 + - - -
180B ILE* 3.5 31.4 - - + +
227B LEU* 6.0 0.2 - - + -
231B MET* 3.8 18.8 - - + -
313B PRO* 4.6 1.8 - - + +
314B PHE* 3.4 22.9 - - - -
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Residues in contact with ALA 147 (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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143B ALA 2.8 21.1 + - - +
144B ARG 3.3 4.5 + - - +
146B TYR* 1.3 72.6 - - - +
148B ALA* 1.3 56.2 + - - +
150B ILE* 3.2 7.5 + - - +
151B VAL* 2.9 32.8 + - - +
224B LEU* 4.2 6.1 - - - +
228B ILE* 3.6 36.8 - - + -
231B MET* 4.1 5.3 - - + +
296B TRP* 4.1 4.5 - - + -
297B PHE* 3.8 11.4 - - + -
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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
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144B ARG 2.9 18.0 + - - +
145B PHE* 3.7 6.1 - - - +
146B TYR 3.1 0.2 - - - -
147B ALA* 1.3 77.7 - - - +
149B GLN* 1.3 61.8 + - - +
151B VAL 3.3 0.7 + - - -
152B LEU* 3.2 22.0 + - - +
297B PHE* 3.9 2.9 - - + -
300B THR* 3.8 20.4 - - + -
302B TRP* 3.3 35.7 - - + -
305B ILE* 4.3 13.7 - - + -
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Residues in contact with GLN 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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102B PHE* 3.4 39.0 - - + -
145B PHE* 3.1 54.7 + - - +
146B TYR* 3.0 12.1 + - - +
148B ALA* 1.3 74.1 - - - +
150B ILE* 1.3 60.6 + - - +
152B LEU 3.4 0.9 + - - -
153B THR* 2.8 34.7 + - - -
179B TYR* 3.4 10.6 - - - -
180B ILE* 2.8 37.2 + - + +
305B ILE* 3.7 16.4 - - + -
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Residues in contact with ILE 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 TYR 3.7 11.7 - - - +
147B ALA* 3.2 7.0 + - - +
149B GLN* 1.3 77.0 - - - +
151B VAL* 1.3 57.0 + - - +
153B THR* 3.2 4.8 + - - +
154B PHE* 2.8 65.1 + - + +
167B LEU* 4.0 9.9 - - + -
172B LEU* 3.9 28.0 - - + -
180B ILE* 4.1 16.2 - - + -
182B VAL* 3.9 15.9 - - + -
224B LEU* 3.9 14.8 - - + -
227B LEU* 3.9 19.5 - - + -
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Residues in contact with VAL 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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147B ALA 2.9 19.5 + - - +
148B ALA 3.7 7.0 - - - +
149B GLN 3.3 0.2 - - - -
150B ILE* 1.3 76.4 - - - +
152B LEU* 1.3 58.7 + - - +
154B PHE 3.3 0.2 + - - -
155B GLU* 2.9 26.9 + - - +
221B TRP* 3.6 12.3 - - + -
224B LEU* 3.6 25.1 - - + -
288B VAL* 3.7 24.7 - - + -
291B ILE* 3.8 18.8 - - + -
292B LYS* 3.8 22.0 - - + -
297B PHE* 4.2 12.1 - - + -
302B TRP* 3.9 7.0 - - + -
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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
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100B PHE* 3.5 25.2 - - + -
102B PHE* 4.1 6.7 - - + -
148B ALA 3.2 16.8 + - - +
149B GLN 3.8 2.9 - - - +
151B VAL* 1.3 73.8 - - - +
153B THR* 1.3 66.8 + - - +
155B GLU* 3.3 22.5 + - - +
156B TYR 3.0 18.0 + - - -
292B LYS* 3.9 10.1 - - - +
302B TRP* 3.7 44.9 - - + +
305B ILE* 3.8 19.7 - - + -
306B TYR* 4.1 14.4 - - + +
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Residues in contact with THR 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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100B PHE* 3.6 11.3 - - + -
102B PHE* 3.3 24.8 - - - +
103B LEU* 3.6 36.1 - - + -
149B GLN 2.8 24.8 + - - -
150B ILE* 3.2 8.8 + - - +
152B LEU* 1.3 76.1 - - - +
154B PHE* 1.3 61.6 + - + +
156B TYR* 3.3 3.5 + - - +
157B LEU* 2.9 38.5 + - + +
182B VAL* 4.5 11.6 - - + +
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Residues in contact with PHE 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 ILE* 2.8 42.5 + - + +
153B THR* 1.3 76.3 - - + +
155B GLU* 1.3 57.8 + - - +
157B LEU* 4.4 13.2 - - + +
158B HIS* 2.8 44.7 + - + -
164B TYR* 3.9 25.8 - + + -
167B LEU* 3.9 27.6 - - + -
182B VAL* 6.3 2.2 - - + -
220B ASP* 3.2 51.8 - - + -
221B TRP* 3.5 34.5 - + + -
224B LEU* 4.5 2.2 - - + -
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Residues in contact with GLU 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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16B LYS* 4.2 18.1 - - - +
19B LEU* 4.4 18.4 - - + +
151B VAL 2.9 16.5 + - - +
152B LEU* 3.5 16.2 - - - +
154B PHE* 1.3 76.7 - - - +
156B TYR* 1.3 61.4 + - - +
158B HIS* 4.1 3.0 - - - +
159B SER* 3.2 23.4 + - - -
221B TRP* 4.3 6.0 - - - -
288B VAL* 3.5 31.5 - - + +
289B ASN* 5.1 1.0 - - - +
292B LYS* 2.6 34.7 + - - +
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Residues in contact with TYR 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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18B PHE* 4.3 7.2 - + - -
19B LEU* 4.3 8.5 - - + -
22B ALA* 3.8 31.9 + - + -
26B PHE* 5.1 0.5 - - - +
97B ALA 4.4 1.6 + - - -
98B VAL* 3.4 24.5 - - + +
99B ASN* 2.9 39.8 + - - +
100B PHE* 3.5 39.0 - + + -
103B LEU* 4.1 4.9 - - + -
152B LEU 3.0 14.2 + - - +
153B THR 3.4 7.0 - - - +
155B GLU* 1.3 73.6 - - - +
157B LEU* 1.3 78.4 + - + +
159B SER* 2.6 25.1 + - - -
160B LEU* 3.5 31.1 + - + +
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Residues in contact with LEU 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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98B VAL* 4.4 2.5 - - + -
103B LEU* 4.1 7.9 - - + -
153B THR* 2.9 38.5 + - + +
154B PHE* 4.0 8.5 - - + +
156B TYR* 1.3 88.5 - - + +
158B HIS* 1.3 61.6 + - + +
160B LEU* 3.0 12.9 + - - +
162B LEU* 2.9 62.6 + - + +
163B ILE 5.6 0.2 - - - -
164B TYR* 4.0 28.7 - - + -
182B VAL* 6.3 0.2 - - + -
185B PHE* 4.1 28.3 - - + -
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Residues in contact with HIS 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 PHE* 2.8 32.7 + - + +
155B GLU* 4.3 2.9 - - - +
157B LEU* 1.3 76.5 - - + +
159B SER* 1.3 56.5 + - - +
161B ASP* 2.9 17.6 + - - +
162B LEU 3.2 20.2 - - - +
217B LYS* 3.2 70.7 + - + +
220B ASP* 2.7 32.9 + - + +
221B TRP* 3.4 32.1 + + + -
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Residues in contact with SER 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 3.5 35.2 + - - +
22B ALA* 5.7 0.2 - - - +
23B LYS* 4.3 18.6 + - - +
155B GLU 3.2 14.6 + - - -
156B TYR* 2.6 22.0 + - - -
158B HIS* 1.3 76.7 - - - +
160B LEU* 1.3 67.7 + - - +
161B ASP* 3.3 4.5 + - - +
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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
----------------------------------------------------------
22B ALA* 4.1 2.9 - - + +
23B LYS* 3.6 42.4 - - + +
26B PHE* 3.8 35.0 - - + -
98B VAL* 4.1 0.4 - - + -
156B TYR* 3.5 50.5 - - + +
157B LEU 3.0 7.8 + - - +
159B SER* 1.3 81.9 - - - +
161B ASP* 1.3 66.2 + - - +
162B LEU* 3.1 19.1 + - + +
190B ARG* 2.9 30.2 + - - +
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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
------------------------------------------------------------
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