Contacts of the helix formed by residues 140 - 154 (chain A) in PDB entry 1B3U
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 PHE 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A ARG* 5.3 5.2 - - - -
138A ASP 3.7 4.4 + - - -
139A TRP* 1.3 82.1 - + - +
141A THR* 1.3 86.0 + - + +
143A ARG* 3.1 31.3 + - - +
144A THR* 3.0 38.7 + - + +
177A THR* 4.3 11.4 - - + +
179A MET* 3.8 44.2 - - + -
180A VAL* 4.2 2.0 - - + +
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Residues in contact with THR 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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96A ALA 3.9 1.5 - - - +
97A THR* 3.6 14.8 + - - +
98A VAL 4.4 3.6 - - - +
99A GLU* 5.1 5.8 - - + +
104A ARG* 3.7 35.7 + - - +
139A TRP* 3.4 27.8 - - + +
140A PHE* 1.3 98.7 - - + +
142A SER* 1.3 60.8 + - - +
144A THR* 2.7 21.8 + - - -
145A SER* 3.0 18.4 + - - -
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Residues in contact with SER 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA 4.6 4.5 - - - -
97A THR* 3.3 28.6 + - - +
134A LEU* 3.3 37.4 - - - +
137A GLY* 4.3 12.3 - - - -
139A TRP* 2.9 16.0 + - - +
141A THR* 1.3 78.5 + - - +
143A ARG* 1.3 64.0 + - - +
145A SER* 3.4 4.9 + - - -
146A ALA 3.2 17.2 + - - -
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Residues in contact with ARG 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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134A LEU 3.5 11.4 - - - +
135A ALA* 3.1 26.0 - - - +
136A GLY* 4.7 1.1 - - - -
137A GLY 2.8 29.2 + - - +
138A ASP 3.6 16.2 + - - -
139A TRP 4.4 0.7 - - - +
140A PHE* 3.1 29.1 + - - +
142A SER* 1.3 75.2 - - - +
144A THR* 1.3 65.1 + - - +
146A ALA* 3.4 12.4 + - - +
147A CYS* 3.5 15.4 + - - -
172A LEU* 4.0 14.2 - - + +
175A ASP* 2.7 32.7 + - - -
177A THR* 3.3 24.9 + - - -
180A VAL* 4.0 8.5 - - + +
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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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104A ARG* 4.3 11.1 + - - +
140A PHE* 3.0 31.8 + - + +
141A THR* 2.7 27.9 + - - -
143A ARG* 1.3 76.5 - - - +
145A SER* 1.3 62.8 + - - +
147A CYS* 3.4 18.2 + - - +
148A GLY 4.3 1.0 + - - -
179A MET* 4.0 23.8 - - + +
180A VAL* 4.1 10.8 - - + -
183A ALA* 4.2 16.8 - - + +
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Residues in contact with SER 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA* 2.9 31.4 + - - -
104A ARG* 3.9 16.3 + - - +
108A VAL* 4.0 23.1 - - - +
134A LEU* 4.8 5.4 - - - -
141A THR 3.0 12.5 + - - -
142A SER* 3.7 5.8 - - - -
143A ARG 3.2 0.2 - - - -
144A THR* 1.3 78.6 + - - +
146A ALA* 1.3 64.6 + - - +
148A GLY* 3.3 11.8 + - - -
149A LEU* 3.8 12.9 - - - +
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Residues in contact with ALA 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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131A VAL* 4.2 6.0 - - + +
134A LEU* 3.8 6.6 - - + +
135A ALA* 3.6 38.1 - - + +
142A SER 3.2 9.5 + - - +
143A ARG 3.6 9.6 - - - +
144A THR 3.3 0.6 - - - -
145A SER* 1.3 75.9 - - - +
147A CYS* 1.3 53.4 + - - +
149A LEU* 2.8 39.0 + - - +
150A PHE* 3.2 17.8 - - + -
172A LEU* 4.5 1.6 - - + -
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Residues in contact with CYS 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 ARG 3.6 15.0 - - - -
144A THR* 3.5 11.4 - - - +
145A SER 3.2 0.2 - - - -
146A ALA* 1.3 78.5 - - - +
148A GLY* 1.3 60.2 + - - +
149A LEU 3.4 0.9 + - - -
150A PHE* 3.6 20.8 + - - +
151A SER 5.4 0.3 + - - -
169A PHE* 4.1 6.4 - - + -
172A LEU* 3.9 17.5 - - - -
180A VAL* 4.2 4.5 - - - -
183A ALA* 3.9 21.5 - - + +
184A ALA* 3.7 31.4 - - - +
187A LYS* 3.6 19.7 - - + +
190A GLU* 4.9 1.0 - - - +
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Residues in contact with GLY 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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108A VAL* 4.6 9.9 - - - -
112A ARG* 3.2 34.8 + - - +
144A THR 4.3 1.0 + - - -
145A SER 3.3 7.2 + - - -
146A ALA 2.9 1.6 + - - -
147A CYS* 1.3 78.2 - - - +
149A LEU* 1.3 64.8 + - - +
150A PHE 3.6 0.7 - - - -
151A SER* 4.8 2.2 + - - -
152A VAL* 5.2 0.2 - - - +
187A LYS* 4.1 22.6 - - - +
190A GLU* 4.6 1.8 - - - -
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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
----------------------------------------------------------
108A VAL* 4.2 17.7 - - + +
111A LEU* 3.8 36.3 - - + -
112A ARG* 4.5 4.5 - - + -
127A PHE* 3.9 10.8 - - + -
130A LEU* 5.0 4.7 - - + -
131A VAL* 4.1 25.6 - - + -
134A LEU* 3.6 31.6 - - + -
145A SER 3.8 13.2 - - - +
146A ALA* 2.8 17.1 + - - +
148A GLY* 1.3 78.4 - - - +
150A PHE* 1.3 65.0 + - - +
151A SER 3.6 0.9 - - - -
152A VAL* 3.3 20.7 - - - +
153A CYS* 3.6 10.9 - - - -
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Residues in contact with PHE 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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131A VAL* 4.1 17.5 - - + -
135A ALA* 4.8 3.6 - - + -
146A ALA* 3.2 24.0 - - + -
147A CYS* 3.6 12.5 + - - +
148A GLY 3.6 1.2 - - - -
149A LEU* 1.3 76.5 - - - +
151A SER* 1.3 65.3 + - - +
152A VAL 3.3 0.3 + - - -
153A CYS* 3.4 7.8 + - - -
154A TYR* 3.1 25.8 + - - +
165A LEU* 3.5 47.5 - - + +
168A TYR* 3.9 13.0 - - + -
169A PHE* 3.7 28.3 - + + -
172A LEU* 3.6 31.0 - - + -
191A PHE* 4.0 20.9 - + + -
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Residues in contact with SER 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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112A ARG* 3.5 24.8 + - - -
147A CYS 5.4 0.4 + - - -
148A GLY 5.0 0.8 + - - -
149A LEU 3.6 0.6 - - - -
150A PHE* 1.3 79.7 - - - +
152A VAL* 1.3 59.6 + - - +
155A PRO* 3.1 26.3 - - - +
190A GLU* 3.6 41.7 + - - -
191A PHE* 4.4 4.6 - - - -
194A VAL* 4.1 21.6 - - - +
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Residues in contact with VAL 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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112A ARG* 3.6 54.7 - - + +
115A SER* 3.6 33.1 + - - +
116A HIS* 4.4 20.4 + - + +
123A LEU* 5.2 1.4 - - - +
127A PHE* 4.0 10.5 - - + -
149A LEU 3.3 17.7 - - - +
151A SER* 1.3 78.1 + - - +
153A CYS* 1.3 62.7 + - - +
154A TYR 3.6 0.2 - - - -
155A PRO* 3.9 7.0 - - - +
156A ARG* 5.0 10.6 + - - -
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Residues in contact with CYS 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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123A LEU* 4.1 18.7 - - + +
127A PHE* 3.5 31.9 - - + -
128A VAL* 4.9 6.5 - - + -
131A VAL* 4.4 9.9 - - - -
149A LEU 3.6 16.2 - - - -
150A PHE* 3.8 6.7 - - - -
152A VAL* 1.3 78.1 - - - +
154A TYR* 1.3 67.6 + - - +
155A PRO* 3.5 2.0 - - - -
156A ARG 3.9 2.5 + - - -
157A VAL* 3.3 27.9 + - + +
165A LEU* 4.0 19.7 - - - -
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Residues in contact with TYR 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 PHE 3.1 16.7 + - - +
153A CYS* 1.3 77.5 - - - +
155A PRO* 1.3 66.9 - - + +
157A VAL* 3.2 14.9 - - - +
162A LYS* 2.9 62.0 + - + +
165A LEU* 3.7 25.1 - - + -
166A ARG* 2.8 24.7 + - + -
191A PHE* 4.0 12.8 - + + -
194A VAL* 3.5 29.8 - - + -
195A LEU* 3.3 29.6 - - + +
196A GLU* 2.4 29.1 + - - -
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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