Contacts of the helix formed by residues 152 - 162 (chain A) in PDB entry 1B43
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 GLY 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ASP* 3.5 11.2 - - - -
77A VAL* 3.5 23.6 - - - +
78A PHE 4.3 4.3 - - - -
79A ASP* 2.7 21.6 + - - +
148A ALA* 4.0 6.3 - - - -
150A SER 3.4 2.0 + - - -
151A GLU* 1.3 72.6 - - - +
153A GLU* 1.3 52.9 + - - +
155A GLN 3.1 0.3 + - - -
156A ALA* 2.8 37.6 + - - +
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Residues in contact with GLU 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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26A ASP* 3.3 25.7 + - - +
29A ASN* 4.8 0.7 - - - +
79A ASP* 4.4 0.2 + - - -
151A GLU* 4.1 4.9 - - + +
152A GLY* 1.3 76.5 - - - +
154A ALA* 1.3 58.0 - - - +
156A ALA* 4.0 4.0 - - - +
157A ALA* 3.3 22.2 + - - +
168A SER* 5.0 2.8 - - - -
169A ALA 4.6 1.7 - - - +
170A SER* 3.1 37.9 + - - -
172A ASP* 4.1 11.8 - - - +
174A ASP* 3.3 34.0 - - + +
175A SER* 3.3 34.8 + - - +
178A PHE* 3.9 9.0 - - + -
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Residues in contact with ALA 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 SER* 5.6 0.2 - - - -
151A GLU* 3.0 16.3 + - + +
153A GLU* 1.3 78.2 - - - +
155A GLN* 1.3 59.3 + - - +
157A ALA* 3.4 3.3 + - - +
158A TYR* 3.0 28.6 + - - +
178A PHE* 3.7 28.3 - - + +
277A PHE* 5.4 0.7 - - + -
281A PRO* 3.6 33.2 - - + +
282A PRO 4.6 5.8 - - - +
283A VAL* 4.0 4.4 - - - +
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Residues in contact with GLN 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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77A VAL* 3.6 17.7 - - + -
146A VAL* 3.9 6.3 - - + +
148A ALA* 3.5 26.0 - - + -
149A PRO* 4.0 2.3 - - + +
151A GLU 3.2 1.8 + - - +
152A GLY 3.1 5.1 + - - +
154A ALA* 1.3 77.8 - - - +
156A ALA* 1.3 60.1 + - - +
158A TYR* 3.4 5.7 + - - +
159A MET* 3.0 64.5 + - - +
282A PRO 5.2 1.1 + - - +
283A VAL* 3.6 9.2 - - + +
284A THR* 2.9 55.6 + - - +
287A TYR* 3.5 9.5 - - - -
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Residues in contact with ALA 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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24A ALA* 3.7 38.3 - - + +
26A ASP* 5.3 4.3 - - + +
77A VAL* 4.3 7.2 - - + +
152A GLY 2.8 21.6 + - - +
153A GLU* 4.0 7.6 - - - +
155A GLN* 1.3 72.4 - - - +
157A ALA* 1.3 63.0 + - - +
159A MET* 3.3 6.3 + - - +
160A ALA* 3.1 22.7 + - - +
168A SER* 3.8 15.6 - - - -
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Residues in contact with ALA 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 GLU 3.3 12.2 + - - +
154A ALA 3.5 9.0 - - - +
156A ALA* 1.3 79.3 - - - +
158A TYR* 1.3 57.3 + - - +
160A ALA* 3.1 5.6 + - - +
161A ALA* 2.9 28.0 + - - +
168A SER* 4.4 0.8 - - - -
175A SER* 3.4 26.5 - - - +
178A PHE* 3.7 14.6 - - + +
179A GLY 5.0 0.9 - - - -
180A ALA* 3.6 24.8 - - + +
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Residues in contact with TYR 158 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ALA 3.0 16.6 + - - +
155A GLN* 3.7 8.1 - - - +
156A ALA 3.3 0.2 - - - -
157A ALA* 1.3 77.6 - - - +
159A MET* 1.3 60.3 + - + +
161A ALA* 3.2 8.9 + - + +
162A LYS* 2.8 52.5 + - + +
178A PHE 5.1 1.5 + - - -
283A VAL* 3.8 37.7 - - + -
284A THR 3.5 24.5 - - - -
285A ASP* 2.7 35.0 + - - -
287A TYR* 4.6 1.1 - - - -
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Residues in contact with MET 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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24A ALA* 4.6 1.8 - - + -
75A VAL* 4.4 4.9 - - + -
77A VAL* 4.2 16.2 - - - -
146A VAL* 3.9 20.4 - - + -
155A GLN* 3.0 57.1 + - - +
156A ALA* 3.6 6.5 - - - +
158A TYR* 1.3 77.4 - - + +
160A ALA* 1.3 56.4 + - - +
162A LYS* 3.7 1.1 + - - +
163A GLY 3.1 4.2 + - - -
164A SER* 2.8 31.3 + - - -
165A VAL* 3.3 25.3 + - + -
287A TYR* 3.9 39.7 - - + +
289A LEU* 4.1 11.7 - - + -
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Residues in contact with ALA 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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156A ALA 3.1 12.6 + - - +
157A ALA* 3.1 9.4 + - - +
159A MET* 1.3 74.6 - - - +
161A ALA* 1.3 67.2 + - - +
163A GLY* 3.1 12.6 + - - -
165A VAL* 3.3 26.5 - - + +
166A TYR 4.3 0.4 - - - +
167A ALA* 4.0 18.2 - - - -
168A SER 4.3 1.8 - - - +
180A ALA* 4.9 0.2 - - - -
181A PRO* 3.6 24.3 - - + +
182A ARG* 4.5 6.9 + - - +
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Residues in contact with ALA 161 (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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157A ALA 2.9 12.7 + - - +
158A TYR* 3.6 14.1 - - + +
160A ALA* 1.3 78.0 - - - +
162A LYS* 1.3 63.5 + - - +
163A GLY* 3.2 1.0 + - - -
179A GLY 4.1 8.3 - - - +
181A PRO* 3.5 18.3 - - + +
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Residues in contact with LYS 162 (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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158A TYR* 2.8 35.5 + - + +
159A MET 3.8 5.4 - - - +
161A ALA* 1.3 75.3 - - - +
163A GLY* 1.3 59.5 + - - +
164A SER* 3.8 7.4 + - - +
285A ASP* 2.6 40.1 + - - +
287A TYR* 3.2 28.8 + - - +
276B GLU* 5.1 1.2 + - - -
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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
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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