Contacts of the helix formed by residues 324 - 334 (chain A) in PDB entry 2PU1
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 ASN 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A TYR 4.8 6.1 + - - -
321A THR 3.0 13.4 + - - +
322A VAL* 3.4 19.3 - - + +
323A THR* 1.3 76.2 - - - +
325A THR* 1.3 64.9 + - - +
326A GLU* 2.9 26.4 + - - +
327A ARG* 3.0 10.6 + - + +
328A ILE* 2.9 25.8 + - - +
346A GLN 5.6 0.8 + - - -
347A ILE* 3.5 24.4 - - + +
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Residues in contact with THR 325 (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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324A ASN* 1.3 72.9 + - - +
326A GLU* 1.3 65.9 + - - +
328A ILE* 3.7 3.7 - - - +
329A LYS* 2.9 42.3 + - - +
347A ILE* 5.3 1.4 - - - +
352A GLU 4.9 0.9 - - - +
355A ALA* 4.1 14.1 - - + +
356A SER* 3.6 31.1 + - - +
359A LEU* 3.8 24.9 - - + +
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Residues in contact with GLU 326 (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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324A ASN* 2.9 13.7 + - - +
325A THR* 1.3 83.4 + - - +
327A ARG* 1.3 62.1 + - + +
329A LYS* 3.4 35.5 + - - +
330A MET* 3.3 26.4 + - - +
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Residues in contact with ARG 327 (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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44A TYR* 3.3 39.1 + - + +
296A GLN 2.8 28.9 + - - -
297A ASP* 3.1 20.2 + - - -
299A PHE* 3.5 23.7 - - - -
320A LEU 2.8 26.9 + - - +
321A THR* 3.3 24.6 - - - +
322A VAL* 3.9 14.8 - - + -
324A ASN* 3.0 10.5 + - + +
326A GLU* 1.3 74.6 - - + +
328A ILE* 1.3 61.3 + - - +
330A MET* 3.1 25.8 + - - +
331A ALA* 2.9 27.3 + - - +
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Residues in contact with ILE 328 (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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321A THR* 4.0 26.7 - - + -
324A ASN 2.9 26.5 + - - +
325A THR* 3.7 6.1 - - + +
327A ARG* 1.3 76.9 - - - +
329A LYS* 1.3 55.6 + - - +
331A ALA* 3.2 2.2 + - - +
332A ILE* 2.8 46.0 + - + +
340A LEU* 4.0 7.2 - - + -
356A SER* 3.6 35.0 - - - +
359A LEU* 3.8 10.8 - - + -
360A CYS* 3.5 33.4 - - - -
365A TRP* 4.0 5.4 - - + -
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Residues in contact with LYS 329 (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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325A THR* 2.9 26.7 + - - +
326A GLU* 3.6 32.2 + - - +
327A ARG 3.2 0.2 - - - -
328A ILE* 1.3 77.1 - - - +
330A MET* 1.3 60.6 + - + +
332A ILE* 3.5 8.1 + - + +
333A GLU* 3.0 25.1 + - - +
359A LEU* 4.2 23.8 - - + -
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Residues in contact with MET 330 (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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299A PHE* 3.9 26.2 - - + -
326A GLU 3.3 16.1 + - - +
327A ARG* 3.1 31.9 + - - +
329A LYS* 1.3 78.5 - - + +
331A ALA* 1.3 62.0 + - - +
333A GLU* 3.4 8.6 + - - +
334A LYS* 3.1 50.6 + - - +
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Residues in contact with ALA 331 (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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299A PHE* 3.7 13.1 - - + -
320A LEU* 4.3 1.6 - - + -
321A THR* 4.0 12.6 - - + -
327A ARG 2.9 13.4 + - - +
328A ILE 3.6 7.4 - - - +
330A MET* 1.3 77.2 - - - +
332A ILE* 1.3 56.3 + - - +
334A LYS 3.3 0.9 + - - -
335A LYS* 3.0 8.1 + - - -
336A ALA* 2.8 36.2 + - + -
337A CYS* 4.1 9.2 + - - +
365A TRP* 3.7 23.2 - - + -
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Residues in contact with ILE 332 (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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328A ILE* 2.8 41.5 + - + +
329A LYS* 3.9 7.6 - - + +
331A ALA* 1.3 69.7 - - - +
333A GLU* 1.3 67.7 + - - +
335A LYS* 3.0 20.9 + - - +
359A LEU* 4.3 13.7 - - + +
360A CYS* 5.3 0.2 - - - -
363A ASN* 3.7 44.0 - - + +
365A TRP* 3.6 27.8 - - + +
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Residues in contact with GLU 333 (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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329A LYS 3.0 17.9 + - - +
330A MET* 3.6 6.5 - - - +
332A ILE* 1.3 79.3 - - - +
334A LYS* 1.3 88.6 + - - +
335A LYS* 3.7 3.8 + - - +
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Residues in contact with LYS 334 (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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299A PHE* 3.7 33.0 - - + +
303A ALA* 3.4 15.1 - - + +
330A MET* 3.1 51.8 + - - +
331A ALA 3.3 2.4 + - - +
332A ILE 3.1 0.2 - - - -
333A GLU* 1.3 97.2 - - - +
335A LYS* 1.3 71.0 + - - +
336A ALA* 3.1 9.5 + - + +
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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