Contacts of the helix formed by residues 145 - 154 (chain B) in PDB entry 3PU3
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 TYR 145 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A SER* 3.7 17.3 - - - -
102A GLU* 3.4 25.1 - - + -
103A ASP* 3.0 30.7 + - - -
21B EDO 3.1 33.4 - - - -
143B THR* 3.4 37.0 - - - +
144B PHE* 1.3 76.2 - - - +
146B VAL* 1.3 62.3 + - - +
147B SER* 3.2 10.8 - - - +
148B ASP* 2.8 31.2 + - - +
149B VAL* 3.0 15.3 + - - +
263B LYS* 3.8 22.2 - - - -
330B LEU* 4.5 2.2 - - - -
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B EDO 3.0 25.4 - - - +
145B TYR* 1.3 70.8 - - - +
147B SER* 1.3 67.4 + - - +
149B VAL* 3.1 12.5 + - + +
150B GLU* 3.0 20.4 + - - +
177B PHE* 5.6 2.7 - - + -
178B VAL* 4.3 17.0 - - + -
181B TYR* 3.9 31.9 - - + +
182B TYR* 3.7 9.2 - - + +
239B ILE* 3.9 31.4 - - + -
329B CYS 5.9 0.2 - - - +
330B LEU* 4.7 15.3 - - + -
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Residues in contact with SER 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A EDO 4.9 1.7 - - - -
100A SER* 4.3 2.8 + - - -
102A GLU* 3.1 34.4 - - - +
107A ARG* 3.3 28.7 - - - +
145B TYR* 3.8 3.1 - - - +
146B VAL* 1.3 77.6 - - - +
148B ASP* 1.3 64.2 + - - +
150B GLU* 3.3 12.3 + - - +
151B ASN* 3.0 30.7 + - - -
178B VAL* 4.9 1.1 - - - -
182B TYR* 3.1 11.0 + - - -
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Residues in contact with ASP 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A SER* 4.6 10.8 - - - -
143B THR 3.8 7.4 - - - +
144B PHE* 3.8 23.1 - - + -
145B TYR* 2.8 45.3 + - - +
147B SER* 1.3 77.7 + - - +
149B VAL* 1.3 63.9 + - - +
151B ASN* 3.1 14.4 + - - +
152B TYR* 3.0 35.6 + - + +
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Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PHE* 3.5 24.4 - - + -
145B TYR 3.0 9.9 + - - +
146B VAL* 3.1 17.5 + - + +
148B ASP* 1.3 76.1 - - - +
150B GLU* 1.3 66.3 + - - +
151B ASN 3.1 0.2 + - - -
153B VAL* 2.8 45.1 + - + +
174B LEU* 4.6 6.7 - - + -
195B LEU* 4.4 10.1 - - + -
202B MET* 4.0 8.7 - - - -
237B CYS* 4.2 28.3 - - - -
239B ILE* 4.7 7.6 - - + -
330B LEU* 4.3 9.2 - - + -
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ARG* 4.6 12.7 + - - -
308A LYS* 5.3 6.0 - - - +
311A GLN* 5.6 5.4 + - - -
146B VAL 3.0 7.0 + - - +
147B SER* 3.3 9.5 + - - +
149B VAL* 1.3 75.9 - - - +
151B ASN* 1.3 68.4 + - - +
154B GLY* 2.8 28.9 + - - -
155B PRO* 3.5 24.2 - - + +
174B LEU* 3.5 13.7 - - + -
175B LYS* 3.3 31.4 - - - +
178B VAL* 3.7 35.2 - - + +
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Residues in contact with ASN 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ILE* 3.2 32.2 - - + +
308A LYS* 3.3 35.6 + - - +
147B SER* 3.0 24.0 + - - +
148B ASP* 3.1 16.7 + - - +
150B GLU* 1.3 87.0 - - - +
152B TYR* 1.3 70.9 + - + +
154B GLY* 3.9 6.2 + - - -
155B PRO* 5.1 0.2 - - - +
201B ARG* 4.1 12.5 + - - -
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Residues in contact with TYR 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A EDO 5.6 1.2 + - - -
304A LYS* 4.9 10.8 + - - -
144B PHE* 4.1 20.4 - + - -
148B ASP* 3.0 29.4 + - + +
149B VAL 4.3 0.2 - - - +
151B ASN* 1.3 82.8 - - + +
153B VAL* 1.3 64.2 + - - +
200B THR* 3.8 0.2 - - - -
201B ARG* 3.3 66.0 + - + +
202B MET* 3.5 25.5 + - + +
205B PHE* 4.1 33.9 - + - -
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B VAL* 2.8 36.9 + - + +
152B TYR* 1.3 80.0 - - - +
154B GLY* 1.3 60.0 + - - +
157B ARG* 3.7 30.9 + - + +
174B LEU* 3.9 13.9 - - + -
195B LEU* 4.3 18.6 - - + -
197B PHE* 4.6 2.5 - - + -
200B THR* 4.0 27.4 - - + +
202B MET* 4.0 23.3 - - + -
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Residues in contact with GLY 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B GLU 2.8 10.9 + - - -
151B ASN 3.9 4.2 + - - -
152B TYR 3.4 1.8 - - - -
153B VAL* 1.3 78.0 - - - +
155B PRO* 1.3 68.9 - - - +
156B GLU 3.2 5.4 - - - -
157B ARG* 3.0 28.0 - - - +
174B LEU* 3.6 7.4 - - - +
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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