Contacts of the helix formed by residues 149 - 159 (chain A) in PDB entry 3OJW
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 ALA 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A GLY* 4.2 2.2 - - - -
114A PRO* 4.4 8.7 - - + -
137A MET* 3.6 30.7 - - + -
145A PRO* 4.3 10.3 - - + -
146A THR* 3.0 22.5 + - - +
148A ASN* 1.3 78.6 + - - +
150A GLN* 1.3 59.6 + - - +
151A ASP 3.3 2.5 - - - -
152A PHE* 3.2 7.9 + - + +
153A TYR* 2.9 29.1 + - - +
184A MET* 5.6 0.2 - - - -
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Residues in contact with GLN 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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145A PRO* 4.2 19.8 + - + -
146A THR 3.3 7.9 + - - +
147A CYS* 3.3 23.3 + - - +
148A ASN 3.5 0.2 - - - -
149A ALA* 1.3 77.9 - - - +
151A ASP* 1.3 62.6 + - - +
153A TYR* 3.3 3.0 + - + +
154A ASP* 2.8 39.8 + - - +
514A CYS* 3.4 16.9 - - - -
515A LYS* 2.6 47.7 + - - +
516A SER* 4.9 1.4 - - - +
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Residues in contact with ASP 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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114A PRO 6.0 1.1 - - - +
115A GLU* 4.6 23.9 - - - +
117A TYR 6.0 1.6 - - - +
148A ASN 5.0 2.5 + - - +
149A ALA 3.3 0.6 - - - -
150A GLN* 1.3 77.8 - - - +
152A PHE* 1.3 61.4 + - - +
154A ASP* 3.8 10.8 - - - +
155A TRP* 2.9 30.9 + - - +
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Residues in contact with PHE 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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114A PRO* 4.5 16.6 - - + +
119A LEU* 3.4 42.0 - - + -
122A LEU* 4.5 3.6 - - + -
135A PHE* 3.6 41.1 - + - -
137A MET* 4.1 18.8 - - + -
148A ASN 5.5 0.4 + - - +
149A ALA* 3.2 11.9 + - + +
151A ASP* 1.3 77.7 - - - +
153A TYR* 1.3 58.6 + - + +
155A TRP* 3.4 9.7 + + - +
156A LEU* 2.9 63.2 + - + +
184A MET* 6.4 0.2 - - - -
188A VAL* 4.0 18.4 - - + -
192A LEU* 5.0 1.8 - - + -
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Residues in contact with TYR 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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143A GLY 5.1 3.0 + - - -
144A ASP* 5.1 7.3 + - - -
145A PRO* 3.7 30.7 - - + -
149A ALA 2.9 16.4 + - - +
150A GLN* 3.5 4.7 - - + +
152A PHE* 1.3 75.1 - - + +
154A ASP* 1.3 72.0 + - - +
156A LEU* 3.1 18.4 + - + +
157A GLN* 3.1 48.3 + - - +
184A MET* 3.7 27.8 - - + +
187A TYR* 3.6 39.6 - + + -
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Residues in contact with ASP 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 GLN* 2.8 31.2 + - - +
151A ASP* 3.8 11.4 - - - +
153A TYR* 1.3 77.7 - - - +
155A TRP* 1.3 64.6 + - - +
157A GLN* 3.1 28.3 + - - +
158A GLU* 3.2 13.9 + - - +
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Residues in contact with TRP 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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118A ASP* 5.3 3.8 - - - -
119A LEU* 3.9 16.6 - - + -
120A ALA* 3.5 41.0 - - + +
122A LEU* 4.4 8.1 - - + -
151A ASP 2.9 18.5 + - - +
152A PHE* 3.6 18.4 - + - +
154A ASP* 1.3 77.4 - - - +
156A LEU* 1.3 97.7 + - + +
158A GLU* 3.1 7.3 + - + +
159A THR* 2.9 56.2 + - + +
161A VAL* 3.6 22.9 - - + -
163A LEU* 4.9 6.1 - - + -
195A LEU* 4.9 0.9 - - + -
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Residues in contact with LEU 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 PHE* 2.9 53.8 + - + +
153A TYR* 3.1 10.7 + - - +
155A TRP* 1.3 97.5 - - + +
157A GLN* 1.3 61.4 + - - +
159A THR* 3.6 7.0 - - - +
187A TYR* 3.6 25.8 - - + +
188A VAL* 4.1 19.1 - - + -
191A ARG* 2.9 42.4 + - + -
192A LEU* 4.4 9.6 - - + -
195A LEU* 4.1 12.1 - - + -
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Residues in contact with GLN 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 TYR* 3.1 56.6 + - - +
154A ASP* 3.1 17.4 + - - +
156A LEU* 1.3 76.7 - - - +
158A GLU* 1.3 61.4 + - - +
159A THR 4.7 0.4 - - - +
187A TYR* 3.3 22.7 - - + +
191A ARG* 4.6 6.0 + - - +
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Residues in contact with GLU 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 ASP 3.2 10.9 + - - +
155A TRP* 3.1 12.1 + - + +
157A GLN* 1.3 80.1 - - - +
159A THR* 1.3 64.3 + - - +
160A ASP* 4.0 2.4 + - - +
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Residues in contact with THR 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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155A TRP* 2.9 56.8 + - + +
156A LEU* 3.6 13.2 - - - +
157A GLN 4.7 0.2 - - - +
158A GLU* 1.3 82.5 - - - +
160A ASP* 1.3 64.9 + - - +
161A VAL* 3.2 21.2 + - + +
191A ARG* 2.7 31.4 + - - -
195A LEU* 4.0 16.8 - - + -
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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