Contacts of the helix formed by residues 139 - 160 (chain A) in PDB entry 1Q62
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ARG* 4.2 8.6 + - - +
138A PHE* 1.3 75.2 - - - +
140A GLU* 1.3 67.9 + - - +
141A PRO* 3.7 13.5 - - - +
142A HIS* 3.0 24.9 + - - +
143A ALA* 2.8 19.8 + - - +
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Residues in contact with GLU 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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138A PHE 3.7 0.8 + - - +
139A SER* 1.3 70.1 - - - +
141A PRO* 1.3 62.5 - - + +
143A ALA* 3.0 7.8 + - - +
144A ARG* 2.7 44.3 + - - +
232A ALA* 5.1 5.8 - - + -
260A HIS* 3.6 7.5 + - - +
261A PHE* 3.6 10.4 - - - -
262A SER* 2.7 51.2 + - - -
265A LEU* 3.8 15.2 - - + +
296A TRP* 2.9 23.6 + - + +
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Residues in contact with PRO 141 (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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139A SER* 3.5 13.9 - - - +
140A GLU* 1.3 94.9 - - + +
142A HIS* 1.3 54.9 + - - +
144A ARG* 3.5 22.7 - - - +
145A PHE* 3.1 27.9 + - - +
313A PRO* 5.2 3.3 - - + +
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Residues in contact with HIS 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 5.3 4.9 - - + -
138A PHE* 3.7 31.9 - + + +
139A SER* 3.0 27.1 + - - +
141A PRO* 1.3 78.2 - - - +
143A ALA* 1.3 65.2 + - - +
145A PHE* 3.3 13.0 + - - +
146A TYR* 3.1 58.1 + + - -
313A PRO* 4.1 23.3 + - + +
314A PHE* 3.5 30.6 - + + +
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Residues in contact with ALA 143 (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 PHE* 4.1 8.0 - - + +
139A SER 2.8 15.1 + - - +
140A GLU* 3.4 11.4 - - - +
142A HIS* 1.3 71.7 - - - +
144A ARG* 1.3 51.3 + - - +
146A TYR* 3.1 5.7 + - - +
147A ALA* 2.8 34.3 + - - +
228A ILE* 5.0 2.5 - - + +
231A MET* 3.6 35.1 - - + +
232A ALA* 4.6 11.4 - - + +
296A TRP* 4.1 11.4 - - + -
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Residues in contact with ARG 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 GLU* 2.7 24.7 + - - +
141A PRO* 3.5 35.5 - - - +
143A ALA* 1.3 71.0 - - - +
145A PHE* 1.3 65.5 + - - +
147A ALA* 3.9 1.2 - - - +
148A ALA* 2.9 24.1 + - - +
296A TRP* 2.8 71.9 + - + +
297A PHE* 3.9 10.3 - - + -
299A THR* 3.5 23.2 + - - +
300A THR* 3.5 25.8 - - + +
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Residues in contact with PHE 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 PRO 3.1 13.6 + - - +
142A HIS 3.4 7.9 - - - +
144A ARG* 1.3 78.7 - - - +
146A TYR* 1.3 77.0 + + - +
148A ALA* 3.5 9.7 + - - +
149A GLN* 3.1 41.6 + - - +
178A GLY 3.5 21.3 - - - -
179A TYR* 3.6 28.9 - + - -
300A THR* 6.5 0.2 - - - -
305A ILE* 3.9 17.2 - - + +
310A VAL* 3.7 27.1 - - + -
312A ALA* 3.7 13.0 - - + -
313A PRO* 3.4 28.3 - - + -
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Residues in contact with TYR 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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128A MET* 3.9 17.5 - - + -
138A PHE* 3.6 24.4 - + - -
142A HIS* 3.1 47.1 + + - -
143A ALA 3.1 5.8 + - - +
145A PHE* 1.3 91.7 - + - +
147A ALA* 1.3 67.5 + - - +
149A GLN* 3.1 17.4 + - - +
150A ILE* 3.3 16.7 + - + +
174A ILE* 4.0 13.9 - - + +
178A GLY 3.8 21.2 + - - -
180A ILE* 3.5 28.9 - - + +
227A LEU* 6.1 0.2 - - + -
231A MET* 3.9 14.8 - - + -
313A PRO* 5.2 0.8 - - + +
314A PHE* 3.7 22.0 + - - +
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Residues in contact with ALA 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 ALA 2.8 16.3 + - - +
144A ARG* 3.9 6.7 - - - +
145A PHE 3.4 0.2 - - - -
146A TYR* 1.3 78.1 - - - +
148A ALA* 1.3 60.8 + - - +
150A ILE* 3.1 10.7 + - - +
151A VAL* 3.1 26.7 + - - +
224A LEU* 4.5 2.8 - - + +
228A ILE* 3.8 35.4 - - + -
231A MET* 4.3 5.1 - - + +
296A TRP* 4.3 1.1 - - + -
297A PHE* 4.0 11.7 - - + -
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Residues in contact with ALA 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 ARG 2.9 18.4 + - - +
145A PHE* 3.8 5.4 - - - +
146A TYR 3.2 0.2 - - - -
147A ALA* 1.3 75.8 - - - +
149A GLN* 1.3 63.6 + - - +
151A VAL 3.1 9.9 + - - -
152A LEU* 3.2 12.3 + - - +
297A PHE* 4.0 4.5 - - + -
300A THR* 3.8 21.5 - - + -
302A TRP* 3.2 35.7 - - + -
305A ILE* 4.3 11.7 - - + -
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Residues in contact with GLN 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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102A PHE* 3.6 29.7 - - + +
145A PHE* 3.1 54.1 + - - +
146A TYR* 3.1 12.3 + - - +
148A ALA* 1.3 80.2 - - - +
150A ILE* 1.3 53.2 + - - +
152A LEU* 3.7 1.2 + - - +
153A THR* 2.7 34.3 + - - -
179A TYR* 3.2 16.8 - - - -
180A ILE* 3.0 33.3 + - + +
305A ILE* 3.5 24.7 - - + -
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Residues in contact with ILE 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 TYR* 3.6 13.5 - - + +
147A ALA* 3.1 8.6 + - - +
149A GLN* 1.3 77.9 - - - +
151A VAL* 1.3 64.9 + - - +
153A THR* 3.6 3.5 - - + -
154A PHE* 3.1 56.6 + - + +
167A LEU* 3.8 11.7 - - + -
172A LEU* 3.9 31.6 - - + -
180A ILE* 4.1 15.9 - - + -
182A VAL* 4.3 10.5 - - + -
224A LEU* 4.2 14.8 - - + -
227A LEU* 4.1 17.3 - - + -
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Residues in contact with VAL 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 ALA 3.1 16.8 + - - +
148A ALA 3.1 8.2 + - - +
150A ILE* 1.3 78.1 - - - +
152A LEU* 1.3 57.2 + - - +
155A GLU* 3.0 26.4 + - - +
221A TRP* 3.8 13.0 - - + -
224A LEU* 3.8 23.1 - - + -
288A VAL* 3.8 12.6 - - + -
291A ILE* 3.8 18.2 - - + -
292A LYS* 3.8 30.3 - - + -
297A PHE* 4.2 10.3 - - + -
302A TRP* 3.9 9.4 - - + -
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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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15A VAL* 6.6 0.2 - - + -
100A PHE* 3.4 24.3 - - + -
102A PHE* 4.2 5.6 - - + -
148A ALA 3.2 10.4 + - - +
149A GLN 4.0 4.5 - - - +
150A ILE 3.3 0.2 - - - -
151A VAL* 1.3 78.2 - - - +
153A THR* 1.3 64.1 + - - +
155A GLU* 3.3 10.2 + - - +
156A TYR* 3.1 17.7 + - - +
292A LYS* 4.0 23.3 - - - +
302A TRP* 3.7 46.9 - - + +
305A ILE* 3.9 23.8 - - + -
306A TYR* 3.9 17.9 - - + +
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Residues in contact with THR 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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100A PHE* 3.5 18.2 - - + -
102A PHE* 3.6 13.5 - - - +
103A LEU* 3.8 33.2 - - + -
149A GLN 2.7 21.6 + - - -
150A ILE* 3.6 8.7 - - - -
151A VAL 3.3 0.2 - - - -
152A LEU* 1.3 77.2 - - - +
154A PHE* 1.3 62.8 + - + +
156A TYR* 3.4 3.3 + - - +
157A LEU* 2.9 36.3 + - + +
182A VAL* 4.1 13.8 - - + +
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Residues in contact with PHE 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 ILE* 3.1 38.0 + - + +
153A THR* 1.3 80.6 - - + +
155A GLU* 1.3 61.1 + - - +
157A LEU* 4.2 13.7 - - + +
158A HIS* 2.7 44.7 + + - +
164A TYR* 3.9 25.4 - + + -
167A LEU* 4.0 26.2 - - + -
182A VAL* 6.2 2.7 - - + -
220A ASP* 3.3 46.9 - - + -
221A TRP* 3.5 33.4 - + + -
224A LEU* 4.5 2.5 - - + -
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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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15A VAL* 3.7 23.4 - - - +
16A LYS* 3.8 11.9 + - - +
19A LEU* 4.4 10.6 - - + +
151A VAL 3.0 15.0 + - - +
152A LEU* 3.5 16.5 - - - +
154A PHE* 1.3 77.6 - - - +
156A TYR* 1.3 61.7 + - - +
158A HIS* 4.1 3.1 - - - +
159A SER* 3.2 23.0 + - - -
221A TRP* 4.3 6.7 - - - -
288A VAL* 3.3 32.3 - - + +
289A ASN* 5.0 1.0 - - - +
292A LYS* 2.8 31.2 + - - -
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Residues in contact with TYR 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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18A PHE* 4.7 2.5 - + - -
19A LEU* 4.6 15.5 - - + -
22A ALA* 4.0 28.4 + - + -
26A PHE* 4.8 3.1 - - - +
97A ALA 4.7 0.7 + - - -
98A VAL* 3.5 10.1 - - + -
99A ASN 2.9 38.7 + - - -
100A PHE* 3.6 41.7 - + + -
103A LEU* 4.0 14.4 - - + -
152A LEU 3.1 15.6 + - - +
153A THR 3.6 5.4 - - - +
155A GLU* 1.3 76.0 - - - +
157A LEU* 1.3 74.0 + - + +
159A SER* 2.7 26.4 + - - -
160A LEU* 3.3 32.4 + - + +
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Residues in contact with LEU 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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98A VAL* 4.6 1.3 - - + -
103A LEU* 3.9 24.2 - - + -
153A THR* 2.9 35.2 + - + +
154A PHE* 3.8 10.5 - - + +
156A TYR* 1.3 83.7 - - + +
158A HIS* 1.3 61.5 + - + +
160A LEU* 2.9 21.5 + - - +
162A LEU* 3.2 46.8 + - + +
164A TYR* 4.1 28.3 - - + -
182A VAL* 5.9 0.4 - - + -
185A PHE* 3.9 26.0 - - + -
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Residues in contact with HIS 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 PHE* 2.7 35.3 + + + +
155A GLU* 4.3 3.4 - - - +
157A LEU* 1.3 73.4 - - + +
159A SER* 1.3 56.9 + - - +
161A ASP* 2.9 21.3 + - - +
162A LEU 2.9 20.7 + - - -
163A ILE* 4.4 0.9 - - - -
164A TYR 4.7 0.2 - - - -
217A LYS* 3.5 36.2 + - + +
220A ASP* 2.8 44.7 + - + +
221A TRP* 3.7 29.9 + + - -
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Residues in contact with SER 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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19A LEU* 4.0 28.3 + - - +
23A LYS* 3.2 26.9 + - - +
155A GLU 3.2 14.8 + - - -
156A TYR* 2.7 21.8 + - - -
158A HIS* 1.3 76.4 - - - +
160A LEU* 1.3 67.8 + - - +
161A ASP* 3.2 2.3 + - - +
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Residues in contact with LEU 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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19A LEU 5.1 0.9 - - - +
22A ALA 4.5 1.6 - - - +
23A LYS* 3.9 36.6 - - + +
26A PHE* 3.7 33.9 - - + -
98A VAL* 4.4 0.2 - - + -
156A TYR* 3.4 49.6 - - + +
157A LEU 2.9 9.9 + - - +
159A SER* 1.3 92.9 + - - +
161A ASP* 1.3 74.3 + - - +
162A LEU* 3.1 18.4 + - + +
190A ARG* 3.1 22.0 + - - -
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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