Contacts of the helix formed by residues 373 - 385 (chain A) in PDB entry 1PG0
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 373 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A ASN* 3.7 18.1 + - - +
358A TYR* 3.5 7.8 + - - +
362A LYS* 4.7 2.7 - - - +
371A ASP* 3.4 20.8 + - - +
372A LEU* 1.3 71.9 - - - +
374A LEU* 1.3 58.7 + - - +
375A GLU* 3.1 13.9 + - - +
376A ASP* 2.9 39.6 + - + +
377A PHE* 2.8 28.8 + - - +
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Residues in contact with LEU 374 (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 VAL* 4.1 14.8 - - + -
329A ASN* 3.0 28.6 + - - +
339A THR* 5.1 1.3 - - + -
341A ILE* 4.9 7.0 - - + -
346A TRP* 4.9 10.8 - - + -
372A LEU* 3.3 29.5 + - + -
373A ASN* 1.3 69.4 - - - +
375A GLU* 1.3 64.5 + - + +
377A PHE* 3.3 22.2 + - + +
378A VAL* 3.5 11.8 + - - +
536A MET* 4.6 3.1 - - + -
539A VAL* 3.5 25.9 - - + +
542A LEU* 5.0 6.5 - - + -
543A VAL* 3.6 31.2 - - + -
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Residues in contact with GLU 375 (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 ASN* 4.6 1.6 + - - +
373A ASN* 3.1 10.3 + - - +
374A LEU* 1.3 78.3 - - + +
376A ASP* 1.3 64.2 + - - +
378A VAL* 3.4 11.1 + - - +
379A GLN* 3.5 27.3 + - - +
536A MET* 3.2 42.1 - - + +
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Residues in contact with ASP 376 (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 TYR* 2.6 30.3 + - - +
362A LYS* 4.1 8.1 + - - -
373A ASN* 2.9 25.3 + - + +
375A GLU* 1.3 76.4 - - - +
377A PHE* 1.3 54.5 + - - +
379A GLN* 3.3 18.0 + - - +
380A ARG* 2.8 49.0 + - - +
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Residues in contact with PHE 377 (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 TRP* 3.4 35.7 - + - -
350A PHE* 3.9 14.8 - + - -
354A SER* 3.5 42.2 - - - -
355A LEU* 4.1 1.3 - - - -
358A TYR* 3.5 30.4 - + + -
372A LEU* 4.3 13.5 - - + -
373A ASN 2.8 13.6 + - - +
374A LEU* 3.3 17.3 - - + +
375A GLU 3.2 0.2 - - - -
376A ASP* 1.3 76.6 - - - +
378A VAL* 1.3 70.4 + - + +
380A ARG* 3.8 0.7 - - - +
381A VAL* 3.0 35.8 + - + +
534A ILE* 3.5 21.5 - - + -
539A VAL* 4.5 6.1 - - + -
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Residues in contact with VAL 378 (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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350A PHE* 5.3 0.2 - - + -
374A LEU 4.1 3.1 - - - +
375A GLU 3.4 6.7 + - - +
376A ASP 3.4 0.4 - - - -
377A PHE* 1.3 78.2 - - + +
379A GLN* 1.3 66.2 + - + +
381A VAL* 4.0 0.9 - - - +
382A ASN* 3.1 35.4 + - - +
534A ILE* 3.3 45.5 - - + +
535A ASP* 3.9 17.9 - - - +
536A MET* 4.2 12.8 - - + +
539A VAL* 3.4 33.2 - - + -
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Residues in contact with GLN 379 (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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375A GLU* 3.5 24.2 + - - +
376A ASP* 3.3 22.9 + - - +
378A VAL* 1.3 78.6 - - + +
380A ARG* 1.3 57.2 + - - +
382A ASN* 4.1 3.3 - - - +
383A ALA* 2.9 33.7 + - - +
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Residues in contact with ARG 380 (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 TYR* 4.0 13.6 + - + -
358A TYR* 4.1 16.4 - - + -
361A ALA* 4.6 23.4 + - + +
362A LYS* 6.1 2.8 - - - +
376A ASP* 2.8 42.2 + - - +
377A PHE 3.8 2.9 - - - +
379A GLN* 1.3 71.3 - - - +
381A VAL* 1.3 61.2 + - + +
383A ALA* 4.6 2.7 - - - -
384A ASP* 2.6 75.8 + - - +
441A VAL* 5.1 4.4 - - - +
442A ARG* 5.6 11.7 - - - +
445A MET* 5.1 3.8 - - - +
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Residues in contact with VAL 381 (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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354A SER* 4.1 13.7 - - - +
357A TYR* 4.8 9.2 - - + -
358A TYR* 5.3 1.3 - - + -
377A PHE* 3.0 46.5 + - + +
380A ARG* 1.3 76.5 - - + +
382A ASN* 1.3 64.7 + - - +
385A ILE* 3.1 35.9 + - + +
386A VAL* 3.4 2.1 + - + +
531A TYR* 3.9 33.2 - - + +
534A ILE* 4.0 21.1 - - + -
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Residues in contact with ASN 382 (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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378A VAL* 3.1 27.1 + - - +
379A GLN* 4.1 3.0 - - - +
381A VAL* 1.3 77.6 - - - +
383A ALA* 1.3 53.7 + - - +
386A VAL* 3.3 9.5 - - - +
387A ASN* 2.7 40.1 + - - +
533A ARG* 3.1 43.8 - - - +
534A ILE* 2.8 50.6 + - - +
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Residues in contact with ALA 383 (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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379A GLN 2.9 21.1 + - - +
380A ARG* 4.0 3.4 - - - +
382A ASN* 1.3 78.7 - - - +
384A ASP* 1.3 65.5 + - - +
387A ASN* 3.2 21.3 - - - +
388A LYS* 3.1 26.7 + - - +
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Residues in contact with ASP 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A TYR* 2.7 29.4 + - + +
380A ARG* 2.6 56.0 + - - +
383A ALA* 1.3 82.8 - - - +
385A ILE* 1.3 62.4 + - - +
388A LYS* 3.1 29.0 + - - +
389A VAL* 3.0 28.2 + - - +
445A MET* 3.8 13.6 - - - +
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Residues in contact with ILE 385 (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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354A SER* 6.3 0.9 - - - -
357A TYR* 3.6 50.7 - - + -
381A VAL* 3.1 23.5 + - + +
384A ASP* 1.3 77.8 - - - +
386A VAL* 1.3 59.2 + - + +
389A VAL* 3.7 4.3 - - + +
390A VAL* 2.8 35.9 + - + +
445A MET* 4.7 5.2 - - + -
491A LEU* 5.1 3.8 - - + -
495A LEU* 3.7 20.0 - - + -
498A LEU* 3.9 15.5 - - + -
531A TYR* 3.8 37.0 - - + -
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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