Contacts of the helix formed by residues 145 - 154 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A PRO 3.7 10.1 - - - -
143A THR* 3.4 36.8 + - - +
144A PHE* 1.3 80.2 - - - +
146A VAL* 1.3 67.9 + - - +
147A SER* 3.1 9.0 - - - +
148A ASP* 2.9 28.1 + - - +
149A VAL* 3.2 12.6 + - - +
182A TYR* 3.7 12.8 - - - +
263A LYS* 4.2 25.6 - - + +
330A LEU* 4.4 4.7 - - - -
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A TYR* 1.3 75.0 - - - +
147A SER* 1.3 63.3 + - - +
149A VAL* 3.0 20.1 + - + +
150A GLU* 3.1 11.4 + - - +
177A PHE* 5.5 0.9 - - + -
178A VAL* 4.1 18.8 - - + -
181A TYR* 3.3 50.2 - - + +
182A TYR* 3.5 14.7 + - + +
239A ILE* 3.8 32.8 - - + -
330A LEU* 4.6 12.3 - - + +
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Residues in contact with SER 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A TYR* 3.9 12.1 - - - +
146A VAL* 1.3 78.1 - - - +
148A ASP* 1.3 62.5 + - - +
150A GLU* 3.4 17.1 - - - +
151A ASN* 3.1 34.6 + - - +
178A VAL* 5.0 0.9 - - - -
182A TYR* 3.1 30.2 + - - -
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Residues in contact with ASP 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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143A THR 4.0 3.8 - - - +
144A PHE* 3.6 29.8 - - + -
145A TYR* 2.9 36.2 + - - +
147A SER* 1.3 80.4 + - - +
149A VAL* 1.3 61.2 + - - +
151A ASN* 2.9 15.6 + - - +
152A TYR* 2.8 42.1 + - + -
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Residues in contact with VAL 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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144A PHE* 3.5 23.8 - - + -
145A TYR 3.2 7.8 + - - +
146A VAL* 3.0 13.7 + - - +
148A ASP* 1.3 75.6 - - - +
150A GLU* 1.3 56.0 + - - +
153A VAL* 2.7 57.2 + - + +
174A LEU* 4.6 4.9 - - + -
195A LEU* 4.4 9.2 - - + -
202A MET* 3.8 15.0 - - - -
237A CYS* 4.0 26.7 - - - -
239A ILE* 4.5 10.1 - - + -
330A LEU* 4.5 9.0 - - + -
332A PHE* 5.5 0.4 - - + -
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Residues in contact with GLU 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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46A EDO 6.0 0.9 - - - -
146A VAL 3.1 6.3 + - - +
147A SER* 3.4 15.9 - - - +
149A VAL* 1.3 78.3 - - - +
151A ASN* 1.3 62.6 + - - +
154A GLY* 2.9 32.4 + - - -
155A PRO* 3.5 25.2 - - + +
174A LEU* 3.5 13.2 - - + +
175A LYS* 3.1 30.9 - - - +
178A VAL* 3.1 40.0 - - + +
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Residues in contact with ASN 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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147A SER* 3.1 23.3 + - - +
148A ASP* 2.9 20.1 + - - +
150A GLU* 1.3 87.5 - - - +
152A TYR* 1.3 69.5 + - + +
154A GLY* 4.3 2.3 + - - -
155A PRO* 5.2 3.5 - - - +
201A ARG* 4.0 9.9 + - - -
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Residues in contact with TYR 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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144A PHE* 3.9 26.9 - + - -
148A ASP* 2.8 40.0 + - + +
149A VAL 4.3 0.4 - - - +
151A ASN* 1.3 76.8 - - + +
153A VAL* 1.3 67.4 + - - +
201A ARG* 3.0 48.2 + - + +
202A MET* 3.6 27.4 - - + +
205A PHE* 3.4 35.5 - + - -
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Residues in contact with VAL 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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37A EDO 4.9 9.2 - - - -
149A VAL* 2.7 40.4 + - + +
152A TYR* 1.3 73.7 - - - +
154A GLY* 1.3 56.9 + - - +
157A ARG* 3.6 34.5 - - + +
159A VAL* 5.8 0.2 - - + -
174A LEU* 3.8 17.5 - - + -
195A LEU* 4.3 12.6 - - + -
197A PHE* 4.3 8.3 - - + -
200A THR* 4.0 25.2 - - + +
201A ARG* 4.2 4.2 + - - -
202A MET* 3.9 22.2 - - + -
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Residues in contact with GLY 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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37A EDO 6.4 0.4 - - - -
150A GLU 2.9 11.1 + - - -
151A ASN 4.7 2.2 - - - -
152A TYR 3.5 1.7 - - - -
153A VAL* 1.3 77.7 - - - +
155A PRO* 1.3 74.9 - - - +
156A GLU 3.0 4.8 + - - -
157A ARG* 3.1 20.8 + - - +
174A LEU* 3.6 9.7 - - - +
201A ARG* 4.7 6.1 - - - -
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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