Contacts of the helix formed by residues 135 - 156 (chain A) in PDB entry 3DBD
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 THR 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A ARG* 3.8 1.1 - - - +
134A VAL* 1.3 77.1 - - - +
136A GLU* 1.3 64.9 + - - +
137A PRO* 3.8 12.9 - - - +
138A GLU* 2.6 38.5 + - - +
139A ALA* 3.2 17.7 + - - +
231A LEU* 4.9 0.2 - - - -
308A PRO* 4.2 21.3 - - + -
309A PRO* 4.1 10.4 - - + +
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Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL 3.9 0.8 + - - -
135A THR* 1.3 71.4 - - - +
137A PRO* 1.4 71.5 - - + +
139A ALA* 3.3 4.2 + - - +
140A ARG* 3.0 55.2 + - - +
231A LEU* 4.1 17.8 - - + +
261A ASN* 2.9 44.6 + - - +
264A ALA* 5.0 0.4 - - - +
290A PHE* 3.9 17.8 - - + -
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Residues in contact with PRO 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR* 3.5 14.4 - - - +
136A GLU* 1.4 94.8 - - + +
138A GLU* 1.3 60.6 + - + +
140A ARG* 3.4 5.7 + - + +
141A TYR 3.1 17.0 + - - -
295A TYR* 3.5 42.8 - - + +
297A PRO* 3.4 28.1 - - + +
309A PRO* 6.3 1.6 - - + -
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Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ARG* 2.6 46.4 + - - -
134A VAL* 3.6 7.7 - - + +
135A THR* 2.6 31.5 + - - +
137A PRO* 1.3 76.3 - - + +
139A ALA* 1.3 61.6 + - - +
141A TYR* 3.1 4.2 + - - +
142A PHE* 2.9 44.1 + - + -
300A LEU* 3.9 26.0 - - + +
304A CYS* 3.3 19.4 - - - +
309A PRO* 3.3 19.1 - - + +
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 4.2 12.2 - - + +
135A THR 3.2 6.2 + - - +
136A GLU 3.3 8.7 + - - +
138A GLU* 1.3 77.4 - - - +
140A ARG* 1.3 54.9 + - - +
142A PHE* 4.5 5.6 - - - +
143A MET* 2.8 40.5 + - - +
227A LEU* 4.6 4.5 - - + -
230A LEU* 4.5 10.3 - - + -
231A LEU* 3.9 30.3 - - + -
290A PHE* 4.2 7.2 - - + -
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLU* 3.0 58.9 + - - +
137A PRO* 3.4 12.3 - - - +
138A GLU 3.2 0.2 - - - -
139A ALA* 1.3 76.9 - - - +
141A TYR* 1.3 56.3 + - - +
144A ARG* 3.0 34.1 + - - +
261A ASN* 5.1 0.6 - - - +
290A PHE* 2.6 50.2 + - + +
291A PHE* 3.5 16.0 - - + +
293A SER* 4.0 4.8 + - - -
294A GLY* 3.4 28.9 - - - +
295A TYR 3.2 28.3 + - - +
296A ALA* 3.9 22.0 - - + -
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Residues in contact with TYR 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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137A PRO 3.1 9.0 + - - +
138A GLU 3.1 7.5 + - - +
140A ARG* 1.3 79.6 - - - +
142A PHE* 1.3 79.2 + + - +
144A ARG* 3.8 4.8 - - - +
145A GLN* 3.1 56.0 + - + +
173A ASP 3.8 5.9 + - - -
174A MET* 2.8 35.2 + - - +
175A ASP* 3.4 5.5 + - - -
176A VAL* 4.8 0.7 - - + -
296A ALA* 5.5 0.6 - - - +
297A PRO* 3.4 28.9 + - + +
298A MET 3.2 26.4 + - - -
299A ARG* 3.9 7.6 - - - +
300A LEU* 3.5 38.7 + - + -
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Residues in contact with PHE 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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124A LEU* 3.7 33.0 - - + -
127A LEU* 3.9 26.2 - - + -
134A VAL* 5.1 2.0 - - + -
138A GLU* 2.9 36.1 + - + +
139A ALA 3.9 3.1 - - - +
141A TYR* 1.3 95.8 - + - +
143A MET* 1.3 60.1 + - - +
146A THR* 2.6 33.8 + - - -
170A LEU* 3.9 15.0 - - + -
174A MET* 4.4 7.9 - - + -
176A VAL* 3.7 18.5 - - + +
230A LEU* 4.3 23.3 - - + -
300A LEU* 3.7 22.4 - - + -
304A CYS* 5.2 1.1 - - + -
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Residues in contact with MET 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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139A ALA 2.8 25.0 + - - +
140A ARG* 4.8 0.2 - - - -
142A PHE* 1.3 69.4 - - - +
144A ARG* 1.3 57.0 + - - +
146A THR* 3.1 5.8 + - - -
147A ILE* 2.7 56.6 + - + +
223A LEU* 3.4 41.7 - - + +
226A ILE* 4.0 7.9 - - - -
227A LEU* 3.6 46.0 - - + -
230A LEU* 3.9 16.8 - - + -
271A MET* 4.3 4.7 - - + -
290A PHE* 4.9 0.2 - - + -
291A PHE* 3.7 18.4 - - + -
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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 ARG 3.0 21.2 + - - +
141A TYR* 3.8 5.2 - - - +
143A MET* 1.3 75.6 - - - +
145A GLN* 1.3 60.5 + - + +
147A ILE* 3.7 1.7 - - - +
148A GLN* 2.8 59.3 + - - +
286A LEU* 4.0 41.6 + - + +
291A PHE* 3.6 26.8 - - + +
296A ALA* 6.1 4.7 - - - -
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Residues in contact with GLN 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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98A HIS* 3.3 41.8 - - + +
141A TYR* 3.1 44.9 + - + +
142A PHE 4.1 0.4 - - - +
144A ARG* 1.3 81.2 - - + +
146A THR* 1.3 61.1 + - - +
148A GLN* 3.6 12.4 + - - +
149A GLY 3.2 15.2 + - - -
175A ASP* 3.1 22.1 + - - +
176A VAL* 2.9 40.4 - - + +
298A MET 4.5 2.6 - - - +
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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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124A LEU* 5.2 0.2 - - - +
142A PHE* 2.6 25.6 + - - +
143A MET* 3.5 8.8 - - + -
145A GLN* 1.3 75.9 - - - +
147A ILE* 1.3 57.9 + - - +
149A GLY* 3.1 4.7 + - - -
150A VAL* 2.9 34.4 + - + +
163A LEU* 5.4 0.7 - - + -
168A LEU* 3.6 38.7 - - + +
176A VAL* 3.4 20.3 - - - +
178A ILE* 3.5 6.0 - - + +
223A LEU* 3.6 25.4 - - + -
226A ILE* 5.3 0.2 - - + -
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Residues in contact with ILE 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 MET* 2.7 42.5 + - + +
144A ARG* 3.8 3.8 - - - +
146A THR* 1.3 71.2 - - - +
148A GLN* 1.3 53.1 + - - +
150A VAL* 3.2 7.5 + - - +
151A GLN* 2.7 33.3 + - - +
223A LEU* 4.3 11.7 - - + -
267A LEU* 6.4 0.2 - - + -
271A MET* 5.2 1.3 - - + -
282A VAL* 3.7 20.6 - - + +
285A LEU* 4.0 30.1 - - + -
286A LEU* 3.7 28.9 - - + -
291A PHE* 3.7 28.0 - - + -
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Residues in contact with GLN 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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96A ASN* 4.7 2.9 + - - +
98A HIS* 3.3 30.1 + - + -
144A ARG* 2.8 48.5 + - - +
145A GLN* 3.8 15.4 - - - +
147A ILE* 1.3 75.0 - - - +
149A GLY* 1.3 59.4 + - - +
151A GLN* 3.6 14.8 - - - +
152A TYR* 3.4 19.8 + - - +
286A LEU* 4.1 15.0 - - + +
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Residues in contact with GLY 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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96A ASN* 4.4 5.4 - - - -
98A HIS* 3.8 24.1 - - - +
99A VAL* 4.3 3.9 - - - +
145A GLN 3.2 5.1 + - - -
146A THR 3.1 7.5 + - - -
148A GLN* 1.3 76.8 - - - +
150A VAL* 1.3 63.2 + - - +
152A TYR* 3.4 5.6 + - - +
153A LEU* 3.2 24.1 + - - +
178A ILE* 3.7 13.0 - - - -
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Residues in contact with VAL 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 21.0 + - + +
147A ILE* 3.6 9.9 - - - +
149A GLY* 1.3 74.0 - - - +
151A GLN* 1.3 59.5 + - - +
153A LEU* 3.3 9.7 + - + +
154A HIS* 3.0 56.3 + - + +
163A LEU* 3.9 21.8 - - + -
178A ILE* 3.9 11.4 - - + -
219A ASP* 4.5 7.6 - - + +
220A ILE* 5.4 0.4 - - + -
223A LEU* 4.1 27.1 - - + -
282A VAL* 4.1 7.6 - - + -
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Residues in contact with GLN 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 ILE 2.7 19.9 + - - +
148A GLN* 3.6 13.9 - - - +
149A GLY 3.2 0.2 - - - -
150A VAL* 1.3 72.5 - - - +
152A TYR* 1.3 55.9 + - - +
154A HIS* 3.2 2.9 + - - +
155A ASN* 2.8 54.4 + - - +
282A VAL* 3.6 19.0 - - + +
283A ALA* 3.9 29.1 - - - +
286A LEU* 4.1 17.4 - - + +
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Residues in contact with TYR 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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93A SER 4.0 3.8 + - - -
94A LEU* 3.5 30.8 - - + +
95A ASP* 2.7 40.9 + - - +
96A ASN* 3.4 39.7 - - + +
99A VAL* 4.1 11.7 - - + -
148A GLN 3.4 7.5 + - - +
149A GLY 3.6 7.2 - - - +
150A VAL 3.4 0.4 - - - -
151A GLN* 1.3 79.6 - - - +
153A LEU* 1.3 64.8 + - + +
155A ASN* 3.5 6.8 + - - +
156A ASN* 3.2 51.4 + - - +
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Residues in contact with LEU 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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94A LEU* 3.8 24.2 - - + -
99A VAL* 4.2 9.2 - - + -
149A GLY 3.2 14.5 + - - +
150A VAL* 3.4 17.3 - - + +
151A GLN 3.2 0.2 - - - -
152A TYR* 1.3 80.2 - - + +
154A HIS* 1.3 57.2 + - + +
156A ASN* 3.2 5.0 + - - -
157A ARG 3.2 4.9 + - - -
158A VAL* 2.7 52.0 + - + +
160A HIS* 4.2 22.9 - - + +
178A ILE* 4.6 11.9 - - + -
181A PHE* 3.6 36.1 - - + -
219A ASP* 5.2 2.0 - - - +
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Residues in contact with HIS 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 VAL* 3.0 29.4 + - + +
151A GLN* 3.8 3.6 - - - +
153A LEU* 1.3 76.2 - - + +
155A ASN* 1.3 67.6 + - - +
157A ARG* 3.3 13.0 + - - +
158A VAL 3.5 16.4 + - - -
216A PHE* 3.2 68.7 - + + +
219A ASP* 3.1 30.1 + - + +
220A ILE* 4.6 3.6 - - + -
282A VAL* 3.2 30.4 - - + +
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Residues in contact with ASN 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 GLN* 2.8 42.0 + - - +
152A TYR* 3.8 8.2 - - + +
153A LEU 3.3 0.2 - - - -
154A HIS* 1.3 79.6 - - - +
156A ASN* 1.3 63.0 - - - +
157A ARG* 3.2 8.4 + - - +
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Residues in contact with ASN 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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93A SER 5.6 2.2 + - - -
94A LEU* 5.4 4.9 - - + +
152A TYR* 3.2 49.6 + - + +
153A LEU* 3.2 3.3 + - - +
155A ASN* 1.3 82.2 - - - +
157A ARG* 1.3 69.6 + - - +
158A VAL* 3.3 17.9 + - + +
186A LYS* 4.3 6.8 - - - +
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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
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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