Contacts of the helix formed by residues 349 - 363 (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 THR 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A ASP* 3.6 31.1 - - + +
93A LEU* 3.9 15.7 - - + +
109A ILE* 3.6 20.2 - - + -
110A LEU* 4.1 5.1 - - - +
113A SER* 3.7 4.0 - - - +
344A ILE 4.7 0.7 - - - +
347A ILE* 3.6 4.5 - - - +
348A GLY* 1.3 83.1 - - - +
350A ILE* 1.3 65.9 + - - +
351A SER* 3.7 1.9 + - - -
352A GLU* 2.8 42.7 + - - +
353A ALA* 3.0 23.9 + - - +
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Residues in contact with ILE 350 (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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85A GLN* 3.9 14.8 - - + +
110A LEU* 4.1 3.8 - - + -
113A SER* 2.8 38.4 + - - +
114A MET* 3.9 13.7 - - + +
132A LEU* 4.3 8.3 - - + -
135A LEU* 4.9 0.2 - - + -
344A ILE* 3.9 21.8 - - + -
349A THR* 1.3 69.8 - - - +
351A SER* 1.3 59.5 + - - +
353A ALA* 3.2 2.8 + - + +
354A ILE* 2.8 53.0 + - + +
380A TYR* 3.4 43.5 - - + +
384A LEU* 5.5 3.1 - - + -
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Residues in contact with SER 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLN* 3.6 9.5 - - - +
86A GLU* 3.5 27.6 - - - +
89A ASP* 2.6 36.6 + - - +
349A THR* 3.3 1.1 - - - -
350A ILE* 1.3 76.8 - - - +
352A GLU* 1.3 60.7 + - - +
354A ILE* 3.4 7.1 + - - +
355A ALA* 3.0 29.0 + - - +
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Residues in contact with GLU 352 (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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93A LEU* 3.7 21.5 - - + +
101A LYS* 2.9 35.8 + - - -
325A THR* 4.9 1.0 - - - +
347A ILE* 3.6 30.4 - - + +
349A THR* 2.8 28.3 + - - +
351A SER* 1.3 79.7 - - - +
353A ALA* 1.3 57.0 + - - +
355A ALA* 3.3 8.4 + - + +
356A SER* 2.9 31.9 + - - -
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Residues in contact with ALA 353 (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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323A THR* 4.3 5.8 - - + -
342A LEU* 3.8 18.5 - - + +
344A ILE* 3.9 27.6 - - + -
347A ILE* 3.9 16.0 - - + +
349A THR 3.0 17.6 + - - +
350A ILE* 3.7 5.4 - - + +
352A GLU* 1.3 76.0 - - - +
354A ILE* 1.3 65.2 + - + +
356A SER* 3.2 4.5 + - - -
357A SER* 3.0 22.2 + - - -
384A LEU* 5.4 2.2 - - + -
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Residues in contact with ILE 354 (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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85A GLN* 5.9 0.2 - - + -
132A LEU* 4.6 12.8 - - + +
135A LEU* 3.9 32.5 - - + +
136A ALA* 3.8 18.6 - - + -
342A LEU* 5.6 0.4 - - - -
350A ILE* 2.8 41.3 + - + +
351A SER* 3.8 6.3 - - - +
353A ALA* 1.3 77.3 - - + +
355A ALA* 1.3 61.1 + - - +
357A SER* 3.2 7.5 + - - -
358A LYS* 2.9 44.5 + - + +
384A LEU* 4.8 9.6 - - + -
388A LEU* 4.7 13.0 - - + -
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Residues in contact with ALA 355 (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* 4.1 12.4 - - + +
351A SER 3.0 14.7 + - - +
352A GLU* 3.3 12.3 + - + +
354A ILE* 1.3 75.9 - - - +
356A SER* 1.3 64.2 + - - +
358A LYS* 3.5 8.4 + - - +
359A LEU* 3.0 25.6 + - - +
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Residues in contact with SER 356 (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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323A THR* 2.8 32.3 + - - -
325A THR* 3.6 21.6 + - - +
328A ILE* 3.6 15.7 - - - -
340A LEU* 4.0 11.2 - - - -
347A ILE* 5.3 0.2 - - - +
352A GLU 2.9 15.3 + - - -
353A ALA 3.2 8.5 + - - -
355A ALA* 1.3 74.9 - - - +
357A SER* 1.3 62.5 + - - +
359A LEU* 3.3 2.7 + - - +
360A CYS* 3.0 28.6 + - - -
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Residues in contact with SER 357 (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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340A LEU* 4.2 2.4 - - - +
342A LEU* 3.7 23.8 - - - -
353A ALA 3.0 7.5 + - - -
354A ILE 3.2 8.0 + - - -
356A SER* 1.3 75.8 - - - +
358A LYS* 1.3 57.5 - - - +
360A CYS* 3.4 1.4 + - - +
361A MET* 2.9 55.9 + - - +
367A VAL* 3.9 11.4 - - - +
388A LEU* 3.6 23.6 - - - +
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Residues in contact with LYS 358 (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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135A LEU 5.0 2.2 - - - +
136A ALA* 2.9 36.6 + - + +
137A GLY* 4.5 5.7 + - - -
354A ILE* 2.9 36.5 + - + +
355A ALA* 3.9 6.7 - - - +
357A SER* 1.3 77.8 - - - +
359A LEU* 1.3 57.0 + - - +
361A MET* 4.0 4.7 - - - +
362A GLU* 3.0 54.8 + - - +
388A LEU* 6.1 0.7 - - + -
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Residues in contact with LEU 359 (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* 3.8 35.9 - - + +
328A ILE* 3.8 26.0 - - + -
329A LYS* 4.2 19.3 - - + -
332A ILE* 4.3 6.3 - - + -
355A ALA 3.0 17.2 + - - +
356A SER 3.7 2.7 - - - +
358A LYS* 1.3 75.9 - - - +
360A CYS* 1.3 64.6 + - - +
362A GLU* 3.5 10.8 + - - +
363A ASN* 2.8 48.5 + - - +
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Residues in contact with CYS 360 (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* 3.5 24.2 - - - -
332A ILE* 5.3 0.4 - - - -
340A LEU* 3.6 24.5 - - + -
356A SER 3.0 21.7 + - - +
357A SER 3.8 3.1 - - - +
359A LEU* 1.3 76.1 - - - +
361A MET* 1.3 60.0 + - - +
363A ASN* 3.1 10.9 + - - -
364A GLY 3.3 0.5 + - - -
365A TRP* 3.0 63.8 + - + +
367A VAL* 4.2 6.3 - - + -
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Residues in contact with MET 361 (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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357A SER* 2.9 40.2 + - - +
358A LYS* 4.0 5.4 - - - +
360A CYS* 1.3 71.6 - - - +
362A GLU* 1.3 59.3 + - + +
364A GLY* 3.0 18.2 + - - -
365A TRP 3.7 12.7 - - - +
366A SER* 5.7 0.2 - - - -
367A VAL* 3.9 16.2 - - + +
388A LEU* 3.5 26.0 - - + +
389A GLY 4.9 0.4 - - - -
390A SER* 3.7 28.5 - - - -
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Residues in contact with GLU 362 (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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358A LYS* 3.0 48.8 + - - +
359A LEU* 3.9 15.0 - - - +
361A MET* 1.3 77.0 - - + +
363A ASN* 1.3 62.6 + - - +
364A GLY 3.3 1.2 + - - -
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Residues in contact with ASN 363 (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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332A ILE* 3.7 38.3 - - + +
359A LEU* 2.8 38.6 + - - +
360A CYS 3.1 5.5 + - - +
362A GLU* 1.3 80.8 + - - +
364A GLY* 1.3 59.1 + - - +
365A TRP* 3.4 13.5 + - + +
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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