Contacts of the helix formed by residues 137 - 157 (chain A) in PDB entry 1BAD
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 TRP 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A THR* 3.7 40.2 - - + +
138A TRP* 1.3 67.9 + - - +
139A ALA* 2.9 9.9 - - - +
140A ILE* 3.3 30.7 + - + +
141A SER* 2.9 27.2 + - - +
189A TRP* 5.7 5.4 - - + -
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Residues in contact with TRP 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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137A TRP* 1.3 79.1 - - - +
139A ALA* 1.3 60.8 + - + +
141A SER* 3.2 8.2 + - - -
142A THR* 2.8 74.7 + - + -
145A MET* 5.9 0.9 - - + -
186A PRO* 3.6 41.2 + - + +
187A VAL* 4.0 20.9 - - + +
189A TRP* 4.5 16.0 - + + -
190A LEU* 4.0 39.0 - - + +
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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
----------------------------------------------------------
137A TRP* 2.9 7.1 - - - +
138A TRP* 1.3 91.2 - - + +
140A ILE* 1.3 58.0 + - + +
142A THR* 3.0 6.7 + - - -
143A ALA* 2.9 25.7 + - - +
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Residues in contact with ILE 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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117A ILE* 4.3 33.3 - - + +
121A THR* 5.8 0.9 - - + +
137A TRP* 3.3 36.9 + - + +
139A ALA* 1.3 77.9 - - + +
141A SER* 1.3 65.7 + - - +
143A ALA* 3.6 10.2 - - + +
144A ALA* 2.9 27.9 + - - +
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Residues in contact with SER 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216 RET 4.7 7.0 - - - +
117A ILE* 6.5 0.2 - - - -
118A MET* 4.1 32.4 - - - +
137A TRP* 2.9 18.4 + - - +
138A TRP* 3.5 16.2 - - - -
139A ALA 3.1 0.2 - - - -
140A ILE* 1.3 81.7 - - - +
142A THR* 1.3 59.4 - - - +
144A ALA* 3.4 6.9 + - - +
145A MET* 2.9 27.0 + - - +
186A PRO* 5.5 4.9 - - - -
189A TRP* 5.3 6.9 - - - -
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Residues in contact with THR 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 TRP* 2.8 61.3 + - + -
139A ALA 3.0 5.6 + - - -
141A SER* 1.3 77.0 - - - +
143A ALA* 1.3 59.1 + - - +
145A MET* 3.3 22.6 - - + +
146A LEU* 3.0 31.8 + - + +
186A PRO* 5.1 2.2 - - - +
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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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139A ALA 2.9 12.7 + - - +
140A ILE* 3.6 17.0 - - + +
141A SER 3.3 0.2 - - - -
142A THR* 1.3 74.5 - - - +
144A ALA* 1.3 63.0 + - - +
146A LEU* 3.2 7.7 + - - +
147A TYR* 3.0 24.1 + - - +
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Residues in contact with ALA 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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114A ALA* 4.0 26.7 - - + +
117A ILE* 5.7 6.7 - - + -
118A MET* 4.4 5.4 - - + -
140A ILE 2.9 18.2 + - - +
141A SER* 3.6 9.0 - - - +
142A THR 3.2 0.2 - - - -
143A ALA* 1.3 73.8 - - - +
145A MET* 1.3 61.2 + - - +
147A TYR* 3.2 8.4 + - - +
148A ILE* 2.9 36.8 + - - +
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Residues in contact with MET 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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216 RET 3.6 34.7 - - + +
138A TRP* 5.9 1.8 - - + -
141A SER 2.9 15.8 + - - +
142A THR* 3.3 27.1 - - + +
144A ALA* 1.3 76.7 - - - +
146A LEU* 1.3 73.5 + - + +
148A ILE* 3.2 3.7 + - - +
149A LEU* 3.0 47.0 + - + +
182A TRP 3.6 22.0 - - - +
183A SER* 3.9 20.9 - - - +
186A PRO* 3.9 17.5 - - + -
187A VAL* 5.9 0.7 - - + -
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Residues in contact with LEU 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 THR* 3.0 19.2 + - + +
143A ALA* 3.2 7.2 + - - +
145A MET* 1.3 85.4 - - + +
147A TYR* 1.3 57.9 + - - +
149A LEU* 3.3 15.4 + - + +
150A TYR* 3.0 31.5 + - + +
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Residues in contact with TYR 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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110A ALA* 3.8 30.3 - - + +
143A ALA 3.0 13.6 + - - +
144A ALA* 3.4 12.6 - - - +
145A MET 3.2 0.2 - - - -
146A LEU* 1.3 75.6 - - - +
148A ILE* 1.3 63.4 + - + +
150A TYR* 3.2 15.9 + + - +
151A VAL* 2.9 54.2 + - + +
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Residues in contact with ILE 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216 RET 4.0 28.9 - - + -
94A LEU* 5.3 5.2 - - + -
110A ALA* 4.8 7.2 - - + +
111A LEU* 4.7 18.8 - - + +
114A ALA* 3.8 28.3 - - + -
118A MET* 5.4 0.2 - - + -
144A ALA 2.9 24.2 + - - +
145A MET* 3.2 4.9 + - - +
147A TYR* 1.3 79.5 - - + +
149A LEU* 1.3 67.6 + - - +
151A VAL* 3.3 5.5 + - - +
152A LEU* 3.2 32.2 + - + +
182A TRP* 3.9 27.8 - - + -
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Residues in contact with LEU 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 MET* 3.0 49.7 + - + +
146A LEU* 3.4 20.6 - - + +
148A ILE* 1.3 80.4 - - + +
150A TYR* 1.3 62.8 + - - +
152A LEU* 3.2 10.4 + - - +
153A PHE* 2.9 36.4 + - + -
179A VAL* 4.2 33.7 - - + +
182A TRP* 3.9 33.0 - - + -
183A SER* 6.3 0.9 - - - -
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Residues in contact with TYR 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 LEU* 3.0 20.1 + - + +
147A TYR* 3.2 19.9 + + - +
149A LEU* 1.3 76.8 - - - +
151A VAL* 1.3 69.8 + - + +
152A LEU 3.3 0.2 + - - -
153A PHE* 3.3 7.8 + - + +
154A PHE* 2.8 77.4 + + + +
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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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106A GLY 5.4 1.1 - - - +
107A THR* 4.2 38.2 + - + +
110A ALA* 4.9 6.1 - - + -
147A TYR* 2.9 55.8 + - + +
148A ILE* 3.7 7.2 - - - +
149A LEU 3.2 0.2 - - - -
150A TYR* 1.3 83.9 - - + +
152A LEU* 1.3 61.0 + - + +
154A PHE* 3.8 4.5 - - - +
155A GLY* 2.9 27.2 + - - -
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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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94A LEU* 4.1 18.4 - - + -
97A LEU* 4.0 18.6 - - + -
98A ALA* 6.0 6.5 - - + +
107A THR* 4.4 21.8 - - + +
148A ILE* 3.2 27.4 + - + +
149A LEU* 3.2 9.9 + - - +
151A VAL* 1.3 83.2 - - + +
153A PHE* 1.3 65.8 + - + +
155A GLY* 3.6 0.7 - - - -
156A PHE* 2.8 32.2 + - - +
178A THR* 5.8 0.4 - - + -
182A TRP* 3.8 28.5 - - + -
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Residues in contact with PHE 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 LEU* 2.9 48.1 + - + -
150A TYR* 3.9 6.5 - - - +
152A LEU* 1.3 82.4 - - + +
154A PHE* 1.3 57.6 + - - +
156A PHE* 3.7 9.9 - + + +
157A THR* 2.8 38.6 + - - +
175A ARG* 4.7 21.3 - - + -
178A THR* 6.2 2.5 - - + -
179A VAL* 3.9 23.1 - - + -
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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 TYR* 2.8 58.8 + + + +
151A VAL* 3.8 4.9 - - - +
153A PHE* 1.3 79.9 - - - +
155A GLY* 1.3 64.5 + - - +
157A THR* 3.7 16.9 + - - -
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Residues in contact with GLY 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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107A THR* 6.1 0.9 - - - -
151A VAL 2.9 17.5 + - - -
152A LEU 3.6 0.7 - - - -
154A PHE* 1.3 83.0 - - - +
156A PHE* 1.3 63.1 + - - +
157A THR 4.2 3.3 - - - -
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Residues in contact with PHE 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 2.8 18.7 + - - +
153A PHE* 3.7 10.5 - + + +
155A GLY* 1.3 74.9 - - - +
157A THR* 1.3 73.7 + - - +
171A PHE* 3.7 54.7 - + + -
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Residues in contact with THR 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 PHE* 2.8 20.2 + - - +
154A PHE* 4.0 15.0 - - - -
155A GLY 3.3 4.0 - - - -
156A PHE* 1.3 87.8 - - - +
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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
------------------------------------------------------------
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