Contacts of the helix formed by residues 200 - 206 (chain A) in PDB entry 3PU8
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 THR 200 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A TYR 3.8 9.2 - - - -
153A VAL* 4.0 20.0 - - + +
157A ARG* 3.2 30.7 - - - +
197A PHE* 2.9 26.0 + - + +
198A SER 3.3 0.7 + - - +
199A ASP* 1.3 82.3 - - - +
201A ARG* 1.3 64.2 + - - +
202A MET* 3.1 20.8 + - - +
203A SER* 3.1 18.2 + - - -
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Residues in contact with ARG 201 (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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151A ASN* 3.0 30.3 + - - +
152A TYR* 3.4 43.5 + - + +
200A THR* 1.3 75.5 - - - +
202A MET* 1.3 60.4 + - - +
203A SER 3.1 1.3 + - - -
204A SER* 3.2 19.2 + - - -
205A PHE* 4.0 7.7 - - - -
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Residues in contact with MET 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PHE* 3.8 29.4 - - + -
149A VAL* 4.0 18.4 - - + +
152A TYR* 3.4 17.2 + - + +
153A VAL* 3.7 16.8 - - + -
197A PHE* 3.4 46.1 - - + -
200A THR* 3.1 11.2 + - - +
201A ARG* 1.3 77.3 - - - +
203A SER* 1.3 64.1 + - - +
204A SER 3.2 0.4 - - - -
205A PHE* 3.0 36.2 + - + +
206A VAL* 5.7 0.7 - - + -
237A CYS* 3.9 18.8 - - + -
332A PHE* 4.3 5.8 - - + -
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Residues in contact with SER 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 3.5 17.2 - - - -
198A SER* 3.4 24.2 + - - -
200A THR* 3.1 18.5 + - - -
202A MET* 1.3 79.7 - - - +
204A SER* 1.3 62.1 + - - +
205A PHE 3.1 1.2 + - - -
206A VAL* 3.1 9.4 + - - +
235A LYS* 2.8 44.1 + - - +
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Residues in contact with SER 204 (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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138A ALA* 6.0 0.5 - - - +
200A THR 4.7 0.2 + - - -
201A ARG 3.2 15.7 + - - -
203A SER* 1.3 77.7 - - - +
205A PHE* 1.3 71.8 + - - +
206A VAL 3.3 2.2 + - - -
207A GLU* 4.8 11.3 - - - +
235A LYS* 5.0 0.7 - - - +
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Residues in contact with PHE 205 (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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138A ALA* 3.5 5.1 - - - +
139A VAL* 3.5 9.0 - - - -
140A PRO* 3.5 30.5 - - + +
144A PHE* 4.5 9.0 - + - -
152A TYR* 3.5 52.3 - + - -
201A ARG 4.0 9.2 - - - -
202A MET* 3.0 34.7 + - + +
204A SER* 1.3 86.2 - - - +
206A VAL* 1.3 64.6 + - + +
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Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ALA 3.0 8.7 - - - +
139A VAL* 4.5 4.3 - - + -
140A PRO* 4.1 15.3 - - + -
197A PHE* 3.6 36.8 - - + -
202A MET* 5.7 0.7 - - + -
203A SER 3.1 3.2 + - - +
204A SER 3.3 0.6 - - - -
205A PHE* 1.3 89.2 - - + +
207A GLU* 1.3 71.2 + - - +
235A LYS* 3.0 37.7 + - + -
258A TRP* 4.0 26.9 - - + -
332A PHE* 4.1 17.0 - - + -
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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