Contacts of the helix formed by residues 336 - 352 (chain A) in PDB entry 1PET
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 GLU 336 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A ARG* 1.3 77.9 - - - +
337A ARG* 1.3 69.0 + - + +
339A GLU* 2.8 29.2 + - + +
340A MET* 3.1 16.9 + - + +
343C GLU* 4.0 15.8 - - - +
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Residues in contact with ARG 337 (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* 4.8 11.1 - - + +
333A ARG 4.8 12.0 + - - +
334A GLY* 5.8 0.7 - - - -
335A ARG 3.5 2.7 - - - +
336A GLU* 1.3 79.2 - - + +
338A PHE* 1.3 63.6 + - - +
340A MET* 2.9 35.4 + - + +
341A PHE* 3.3 12.7 + - + -
348B LEU* 3.1 65.4 + - + +
351B LYS* 4.4 18.2 - - - +
352B ASP* 5.2 7.1 + - - -
343C GLU* 4.7 15.3 + - - +
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Residues in contact with PHE 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ILE* 3.8 23.3 - - + +
334A GLY 5.3 0.9 - - - -
335A ARG* 3.6 14.3 + - - +
336A GLU 3.1 0.6 - - - -
337A ARG* 1.3 80.0 - - - +
339A GLU* 1.3 66.5 + - + +
341A PHE* 3.5 6.1 + - - +
342A ARG* 3.0 46.3 + - + +
328B PHE* 3.2 53.2 - + + -
329B THR 3.2 26.0 - - - -
330B LEU* 3.2 36.7 - - + +
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Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ARG* 3.0 31.0 + - + +
336A GLU* 2.8 18.2 + - + +
338A PHE* 1.3 80.2 - - + +
340A MET* 1.3 66.4 + - + +
342A ARG* 3.0 12.6 + - - +
343A GLU* 2.9 21.7 + - - +
340C MET* 5.0 0.4 - - - +
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Residues in contact with MET 340 (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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336A GLU* 3.5 19.3 - - + +
337A ARG* 2.9 20.2 + - + +
339A GLU* 1.3 77.7 - - + +
341A PHE* 1.3 60.3 + - + +
343A GLU* 2.9 11.1 + - - +
344A LEU* 2.6 26.9 + - - +
348B LEU* 4.9 2.0 - - + -
339C GLU 5.0 0.4 - - - +
340C MET* 4.1 33.7 - - + -
343C GLU* 3.3 50.7 - - + +
344C LEU* 3.6 28.3 - - + -
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Residues in contact with PHE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ILE* 3.9 9.9 - - + -
337A ARG 3.3 13.5 + - - -
338A PHE 3.8 2.5 - - - +
340A MET* 1.3 80.7 - - + +
342A ARG* 1.3 63.2 + - - +
343A GLU 3.2 0.2 + - - -
344A LEU* 3.2 8.7 + - + +
345A ASN* 3.0 25.5 + - - +
330B LEU* 3.4 22.7 - - + -
341B PHE* 3.1 34.0 - + + -
344B LEU* 3.0 46.7 - - + -
345B ASN* 3.0 38.8 - - - -
348B LEU* 3.9 11.4 - - + -
344C LEU* 3.4 18.2 - - + -
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Residues in contact with ARG 342 (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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338A PHE* 3.0 44.8 + - + +
339A GLU* 3.2 17.5 - - - +
341A PHE* 1.3 78.8 - - - +
343A GLU* 1.3 54.8 + - - +
345A ASN* 3.3 6.4 + - + +
346A GLU* 2.8 34.7 + - - +
330B LEU* 4.4 8.7 - - + +
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Residues in contact with GLU 343 (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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339A GLU 2.9 8.0 + - - +
340A MET 2.9 10.5 + - - +
342A ARG* 1.3 76.2 - - - +
344A LEU* 1.3 68.8 + - - +
346A GLU* 2.8 38.7 + - + +
347A ALA* 3.1 12.8 + - - +
336C GLU* 4.1 14.9 - - - +
337C ARG* 4.7 13.5 + - + +
340C MET* 3.4 33.8 - - + +
348D LEU* 4.6 13.3 - - + +
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Residues in contact with LEU 344 (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 MET* 2.6 37.0 - - + +
341A PHE* 3.6 7.2 - - + +
343A GLU* 1.3 76.6 - - - +
345A ASN* 1.3 60.2 + - - +
347A ALA* 3.7 4.4 + - - +
348A LEU* 3.3 26.9 + - - +
341B PHE* 3.0 29.6 - - + -
340C MET* 3.7 23.8 - - + -
341C PHE* 3.4 19.7 - - + -
344C LEU* 4.9 7.6 - - + -
344D LEU* 3.3 38.0 - - + +
347D ALA* 4.8 0.7 - - - +
348D LEU* 4.0 10.3 - - + -
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Residues in contact with ASN 345 (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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341A PHE 3.0 12.5 + - - +
342A ARG* 3.5 5.6 - - - +
344A LEU* 1.3 75.1 - - - +
346A GLU* 1.3 61.0 + - - +
347A ALA 3.3 0.2 - - - -
348A LEU* 3.9 9.4 - - - +
349A GLU* 3.0 34.7 + - + +
330B LEU* 3.3 21.3 - - + +
332B ILE* 3.0 45.4 - - - +
341B PHE* 3.0 33.4 - - - -
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Residues in contact with GLU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ARG* 2.8 18.2 + - - +
343A GLU* 2.8 34.5 + - + +
345A ASN* 1.3 80.1 - - - +
347A ALA* 1.3 57.7 + - - +
349A GLU* 3.6 5.7 + - - +
350A LEU* 3.1 23.7 + - - +
351D LYS* 5.9 7.4 - - + -
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Residues in contact with ALA 347 (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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343A GLU 3.1 5.2 + - - +
344A LEU 4.1 4.5 - - - +
346A GLU* 1.3 76.2 - - - +
348A LEU* 1.3 59.2 + - - +
350A LEU* 2.7 38.1 + - + +
351A LYS 2.9 9.5 + - - -
344D LEU 5.0 0.2 - - - +
347D ALA* 3.5 8.7 - - + +
348D LEU* 3.4 53.1 - - + +
350D LEU* 3.6 2.1 - - - +
351D LYS* 5.2 2.5 - - + -
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Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU 3.3 19.1 + - - +
345A ASN* 4.0 9.9 - - - +
347A ALA* 1.3 76.6 - - - +
349A GLU* 1.3 59.4 + - + +
351A LYS* 2.8 30.8 + - + +
352A ASP* 3.3 5.5 + - - +
332B ILE* 5.7 0.9 - - + -
337B ARG* 3.1 55.1 + - + +
340B MET* 4.9 0.9 - - + -
341B PHE* 3.9 23.1 - - + -
343D GLU* 4.6 13.5 - - + +
344D LEU* 4.1 11.0 - - + -
347D ALA* 3.4 21.1 - - + -
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Residues in contact with GLU 349 (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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345A ASN* 3.0 23.2 + - + +
346A GLU* 3.7 6.5 - - - +
348A LEU* 1.3 77.1 - - + +
350A LEU* 1.3 62.6 + - - +
352A ASP* 3.1 12.3 + - + +
353A ALA* 3.1 20.3 + - - +
331B GLN 5.7 0.9 - - - +
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Residues in contact with LEU 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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346A GLU 3.1 13.5 + - - +
347A ALA* 2.7 29.8 + - - +
349A GLU* 1.3 73.7 - - - +
351A LYS* 1.3 62.7 + - - +
353A ALA* 2.9 18.3 + - - -
354A GLN 3.1 8.7 + - - -
347D ALA 3.8 0.9 - - - +
350D LEU* 3.0 20.9 - - + -
351D LYS* 3.1 51.4 - - + +
354D GLN* 2.8 43.7 - - + +
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Residues in contact with LYS 351 (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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347A ALA 2.9 4.4 + - - -
348A LEU* 2.8 20.5 + - + +
350A LEU* 1.3 78.3 - - - +
352A ASP* 1.3 62.4 + - - +
354A GLN* 3.1 31.0 + - - +
337B ARG* 4.4 18.4 - - - +
346D GLU* 6.1 6.1 - - - -
347D ALA* 5.5 2.0 - - - +
350D LEU* 3.1 31.9 - - + -
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Residues in contact with ASP 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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348A LEU 3.3 4.6 + - - +
349A GLU* 3.1 15.1 + - + +
351A LYS* 1.3 80.9 - - - +
353A ALA* 1.3 57.7 + - - +
354A GLN 3.3 2.8 + - - -
355A ALA* 6.0 0.3 - - - +
333B ARG* 4.6 17.6 + - - +
337B ARG* 5.2 6.2 + - - -
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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