Contacts of the strand formed by residues 158 - 163 (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 SER 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A GLU 3.4 3.8 + - - -
157A ARG* 1.3 90.4 + - - +
159A VAL* 1.3 60.3 + - - +
171A LYS* 4.5 13.7 - - - +
172A MET 3.7 8.9 + - - -
173A LYS* 4.8 4.5 - - - +
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Residues in contact with VAL 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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157A ARG* 3.7 15.7 - - + +
158A SER* 1.3 80.9 + - - +
160A ASP* 1.3 66.6 + - - +
161A VAL* 3.6 16.6 + - + +
171A LYS* 3.3 5.5 - - - -
172A MET* 2.8 52.1 + - + +
173A LYS 3.9 11.2 - - - +
174A LEU* 3.9 26.9 - - + +
177A PHE* 4.7 1.3 - - + -
192A VAL* 4.6 9.6 - - + -
195A LEU* 4.8 18.6 - - + -
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Residues in contact with ASP 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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159A VAL* 1.3 73.0 - - - +
161A VAL* 1.3 62.9 + - - +
162A THR* 5.6 0.4 - - - -
169A ASP* 5.8 7.3 - - + +
170A CYS 3.5 8.0 - - - +
171A LYS* 4.5 8.3 - - - +
192A VAL* 3.7 21.3 - - - +
193A THR 4.7 2.1 + - - -
194A ASN* 2.8 40.6 + - + +
360A LEU* 5.0 8.8 - - - +
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Residues in contact with VAL 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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159A VAL* 3.9 7.9 - - + +
160A ASP* 1.3 81.6 - - - +
162A THR* 1.3 65.4 + - - +
163A ASP 3.6 1.6 + - - -
169A ASP* 3.7 2.2 - - - +
170A CYS* 2.7 43.8 + - - +
172A MET* 3.7 44.4 - - + -
177A PHE* 4.1 8.5 - - + -
190A LEU* 3.8 28.5 - - + -
191A ASN 3.4 9.2 - - - +
192A VAL* 3.9 15.5 - - + -
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Residues in contact with THR 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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160A ASP 4.2 0.7 - - - -
161A VAL* 1.3 73.4 - - - +
163A ASP* 1.3 73.5 + - - +
164A VAL* 3.4 10.9 + - + +
167A GLN* 5.0 9.2 - - - +
168A LYS 3.8 4.5 - - - +
169A ASP* 2.8 27.5 + - - +
190A LEU* 3.3 6.8 - - - -
191A ASN* 3.0 38.6 + - - -
193A THR* 4.8 10.5 + - - -
245A TYR 5.7 2.5 - - - +
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Residues in contact with ASP 163 (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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161A VAL 3.6 2.8 + - - -
162A THR* 1.3 71.0 - - - +
164A VAL* 1.3 58.4 + - - +
165A THR* 3.1 21.7 + - - -
166A LYS* 3.1 35.5 + - + +
167A GLN* 2.9 29.1 + - - -
168A LYS* 3.1 16.8 + - + +
170A CYS* 5.6 5.8 - - - -
188A ARG* 4.8 10.6 - - - +
189A VAL 4.1 2.9 + - - +
190A LEU* 3.5 23.4 - - + +
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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