Contacts of the helix formed by residues 336 - 352 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B GLU* 4.0 15.6 - - - +
335D ARG* 1.3 76.6 - - - +
337D ARG* 1.3 70.3 + - + +
339D GLU* 2.8 32.8 + - + +
340D MET* 3.1 13.1 + - + +
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Residues in contact with ARG 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B GLU* 4.7 14.4 + - - +
348C LEU* 3.1 66.9 + - + +
351C LYS* 4.4 16.6 - - - +
352C ASP* 5.1 7.7 + - - -
332D ILE* 4.9 11.8 - - + +
333D ARG 4.8 12.0 + - - +
334D GLY* 5.8 0.7 - - - -
335D ARG 3.4 2.1 - - - +
336D GLU* 1.3 80.0 - - + +
338D PHE* 1.3 64.0 + - - +
340D MET* 2.9 36.6 + - + +
341D PHE* 3.2 12.5 + - + -
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Residues in contact with PHE 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C PHE* 3.2 53.6 - + + -
329C THR 3.3 26.7 - - - -
330C LEU* 3.2 37.0 - - + +
332D ILE* 3.8 23.8 - - + +
334D GLY 5.3 0.9 - - - -
335D ARG* 3.5 13.8 + - - +
336D GLU 3.1 0.4 - - - -
337D ARG* 1.3 79.7 - - - +
339D GLU* 1.3 67.4 + - + +
341D PHE* 3.5 6.4 + - - +
342D ARG* 3.0 45.0 + - + +
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Residues in contact with GLU 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B MET* 5.0 0.8 - - - +
335D ARG* 3.0 31.3 + - - +
336D GLU* 2.8 18.0 + - + +
338D PHE* 1.3 80.0 - - + +
340D MET* 1.3 66.2 + - + +
342D ARG* 3.0 12.7 + - - +
343D GLU* 2.9 21.7 + - - +
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Residues in contact with MET 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B GLU 5.4 0.4 - - - -
340B MET* 4.1 33.9 - - + -
343B GLU* 3.4 51.4 - - + +
344B LEU* 3.7 26.2 - - + -
348C LEU* 4.8 2.0 - - + -
336D GLU* 3.5 19.3 - - + +
337D ARG* 2.9 22.2 + - + +
339D GLU* 1.3 77.0 - - + +
341D PHE* 1.3 58.6 + - + +
343D GLU* 2.9 11.1 + - - +
344D LEU* 2.7 28.2 + - + +
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Residues in contact with PHE 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 3.5 19.7 - - + -
330C LEU* 3.4 22.0 - - + -
341C PHE* 3.1 33.4 - + + -
344C LEU* 3.0 47.1 - - + -
345C ASN* 3.0 39.7 - - - -
348C LEU* 3.9 12.1 - - + -
332D ILE* 3.8 9.9 - - + -
337D ARG 3.2 13.4 + - - -
338D PHE 3.9 2.2 - - - +
340D MET* 1.3 80.2 - - + +
342D ARG* 1.3 62.8 + - - +
344D LEU* 3.3 8.3 + - + +
345D ASN* 3.0 26.5 + - - +
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Residues in contact with ARG 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C LEU* 4.3 8.9 - - + +
338D PHE* 3.0 43.1 + - + +
339D GLU* 3.0 17.2 + - - +
341D PHE* 1.3 78.4 - - - +
343D GLU* 1.3 55.1 + - - +
345D ASN* 3.3 6.6 + - + +
346D GLU* 2.7 36.4 + - - +
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Residues in contact with GLU 343 (chain D).
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* 4.6 9.2 - - + +
336B GLU* 4.0 15.6 - - - +
337B ARG* 4.7 17.9 + - + +
340B MET* 3.3 35.5 - - + +
339D GLU 2.9 7.3 + - - +
340D MET 2.9 11.2 + - - +
342D ARG* 1.3 75.3 - - - +
344D LEU* 1.3 68.2 + - - +
346D GLU* 2.8 39.3 + - + +
347D ALA* 3.1 13.0 + - - +
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Residues in contact with LEU 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 3.3 37.7 - - + +
347A ALA* 5.0 0.3 - - - +
348A LEU* 4.1 10.5 - - + -
340B MET* 3.7 24.5 - - + -
341B PHE* 3.4 20.2 - - + -
344B LEU* 5.0 6.7 - - + -
341C PHE* 3.0 29.8 - - + -
340D MET* 2.7 35.9 + - + +
341D PHE* 3.7 7.2 - - + +
343D GLU* 1.3 76.2 - - - +
345D ASN* 1.3 58.4 + - - +
347D ALA* 3.7 4.5 + - - +
348D LEU* 3.3 27.5 + - - +
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Residues in contact with ASN 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C LEU* 3.3 21.4 - - + +
332C ILE* 3.0 46.3 - - - +
341C PHE* 3.0 34.1 - - - -
341D PHE 3.0 13.6 + - - +
342D ARG* 3.5 5.2 - - + +
344D LEU* 1.3 76.4 - - - +
346D GLU* 1.3 61.1 + - - +
348D LEU* 3.9 8.1 - - - +
349D GLU* 3.0 35.5 + - + +
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Residues in contact with GLU 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LYS* 6.1 6.1 - - - -
342D ARG* 2.7 18.1 + - - +
343D GLU* 2.8 34.6 + - + +
345D ASN* 1.3 80.2 - - - +
347D ALA* 1.3 61.7 + - - +
349D GLU* 3.6 5.9 + - - +
350D LEU* 3.1 19.9 + - - +
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Residues in contact with ALA 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A LEU 4.8 0.2 - - - +
347A ALA* 3.5 8.3 - - + +
348A LEU* 3.4 52.9 - - + +
350A LEU* 3.8 1.9 - - - +
351A LYS* 5.5 2.7 - - + -
343D GLU 3.1 8.1 + - - +
344D LEU 4.2 2.9 - - - +
346D GLU* 1.3 76.6 - - - +
348D LEU* 1.3 67.4 + - - +
350D LEU* 2.7 34.6 + - + +
351D LYS 3.0 2.3 + - - -
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Residues in contact with LEU 348 (chain D).
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* 4.6 15.0 - - + +
344A LEU* 4.0 11.4 - - + -
347A ALA* 3.4 20.8 - - + +
332C ILE* 5.7 0.9 - - + -
337C ARG* 3.1 53.8 + - + +
340C MET* 4.8 0.9 - - + -
341C PHE* 3.9 23.6 - - + -
344D LEU 3.3 19.4 + - - +
345D ASN* 4.0 9.4 - - - +
346D GLU 3.5 0.2 - - - -
347D ALA* 1.3 76.6 - - - +
349D GLU* 1.3 64.2 + - - +
351D LYS* 2.8 25.1 + - + +
352D ASP* 3.4 4.9 + - - +
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Residues in contact with GLU 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C GLN 5.7 0.9 - - - +
345D ASN* 3.0 22.8 + - + +
346D GLU* 3.8 6.5 - - - +
348D LEU* 1.3 76.6 - - + +
350D LEU* 1.3 62.9 + - - +
352D ASP* 3.0 20.4 + - + +
353D ALA* 3.1 12.7 + - - +
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Residues in contact with LEU 350 (chain D).
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 3.6 3.8 - - - +
350A LEU* 3.0 25.1 - - + -
351A LYS* 3.1 50.0 - - + +
354A GLN* 2.9 33.2 - - + +
346D GLU 3.1 13.5 + - - +
347D ALA* 2.7 28.9 + - - +
349D GLU* 1.3 73.3 - - - +
351D LYS* 1.3 62.4 + - - +
353D ALA* 2.9 18.4 + - - -
354D GLN 3.1 8.7 + - - -
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Residues in contact with LYS 351 (chain D).
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* 5.9 7.9 - - - -
347A ALA* 5.4 5.2 - - + -
350A LEU* 3.1 32.3 - - + -
337C ARG* 4.4 18.1 - - - +
347D ALA 3.0 4.6 + - - -
348D LEU* 2.8 18.9 + - + +
350D LEU* 1.3 77.9 - - - +
352D ASP* 1.3 60.2 + - - +
354D GLN* 3.1 29.8 + - - +
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Residues in contact with ASP 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C ARG* 4.7 16.4 + - - +
337C ARG* 5.1 7.8 + - - -
348D LEU 3.4 5.0 + - - +
349D GLU* 3.0 14.8 + - + +
351D LYS* 1.3 79.2 - - - +
353D ALA* 1.3 57.0 + - - +
354D GLN 3.3 2.6 + - - -
355D ALA* 6.0 0.5 - - - +
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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