Contacts of the helix formed by residues 379 - 387 (chain A) in PDB entry 3PDC
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 PHE 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ZYI 4.7 15.9 - - + -
372A SER 4.7 2.2 - - - -
373A ILE* 3.5 43.2 - - + +
376A ASN* 3.3 33.6 + - + +
378A VAL* 1.3 78.0 - - + +
380A ASP* 1.3 62.6 + - - +
381A TYR* 3.0 20.0 - + - -
382A GLN* 2.9 48.3 + - - +
383A LEU 3.7 0.5 + - - -
497A VAL* 4.1 20.2 - - + -
498A LEU* 5.2 1.3 - - + -
502A MET* 3.9 31.6 - - + -
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Residues in contact with ASP 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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373A ILE 4.5 1.3 + - - -
376A ASN 4.4 1.2 + - - -
377A PRO 3.7 16.1 + - - +
378A VAL 2.9 2.6 + - - +
379A PHE* 1.3 77.0 - - - +
381A TYR* 1.3 62.5 + - - +
383A LEU* 3.3 30.7 + - + +
384A TYR* 3.3 9.7 + - - +
419A HIS 4.4 6.1 - - - +
420A LYS* 3.9 11.3 - - + +
421A VAL* 3.2 26.5 + - + +
422A CYS* 3.2 30.2 + - - +
423A GLU 4.9 0.2 + - - -
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Residues in contact with TYR 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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1A ZYI 2.9 58.7 + + - -
378A VAL* 2.9 27.4 + - + +
379A PHE* 3.0 22.4 - + - -
380A ASP* 1.3 79.1 + - - +
382A GLN* 1.3 78.2 + - + +
384A TYR* 3.0 19.7 - - - +
385A PHE* 3.1 38.6 + + + -
418A MET* 4.0 17.7 - - + -
421A VAL* 3.7 32.3 - - + +
427A LEU* 4.5 4.5 - - + -
465A TYR* 4.2 0.9 - + - -
497A VAL* 3.3 23.4 - - + +
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Residues in contact with GLN 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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1A ZYI 3.2 18.2 - - - +
334A TRP* 5.5 0.2 - - - -
373A ILE* 3.3 37.5 - - + +
379A PHE* 2.9 34.6 + - - +
381A TYR* 1.3 107.9 + - + +
383A LEU* 1.3 60.8 + - - +
384A TYR 3.0 1.8 - - - -
385A PHE* 2.8 24.6 + - - +
386A GLN* 3.0 22.4 + - - +
465A TYR* 3.8 18.6 - - + -
468A MET* 5.1 5.8 - - + +
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Residues in contact with LEU 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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373A ILE* 3.7 28.3 - - + +
374A LYS* 3.6 44.6 - - + -
379A PHE 4.3 1.1 - - - +
380A ASP* 3.3 28.2 + - - +
382A GLN* 1.3 76.9 - - + +
384A TYR* 1.3 60.1 + - - +
385A PHE 3.4 0.3 + - - -
386A GLN* 3.4 29.8 + - + +
387A GLU* 4.2 3.5 + - - +
422A CYS* 4.6 4.7 - - - -
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Residues in contact with TYR 384 (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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380A ASP 3.3 4.5 + - - +
381A TYR* 3.0 12.8 - - - +
383A LEU* 1.3 81.7 - - - +
385A PHE* 1.3 74.2 + + - +
387A GLU* 4.2 10.6 + - - +
390A VAL* 3.5 31.5 + - + +
391A ALA* 3.6 32.3 - - + +
394A GLU* 2.7 33.1 + - - +
421A VAL* 3.7 29.4 - - + -
422A CYS* 3.6 28.0 - - - -
425A GLY* 5.0 2.2 - - - -
426A GLY* 3.7 17.5 - - - -
427A LEU* 4.3 2.9 - - + -
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Residues in contact with PHE 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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1A ZYI 4.4 11.4 - + + -
265A PHE* 3.8 30.3 - + - -
381A TYR* 3.1 38.4 + + + -
382A GLN* 2.8 11.6 + - - +
384A TYR* 1.3 94.5 - + - +
386A GLN* 1.3 64.4 + - - +
387A GLU 3.2 7.3 + - - +
391A ALA* 3.7 25.3 - - + +
395A LEU* 4.5 7.4 - - + -
427A LEU* 4.9 7.9 - - + -
462A LEU* 3.7 19.3 - - + +
465A TYR* 3.8 35.9 - + + -
466A ARG* 3.2 19.8 + - - -
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Residues in contact with GLN 386 (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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373A ILE* 6.1 1.8 - - - +
382A GLN* 3.0 26.9 + - - +
383A LEU* 3.4 25.5 + - + +
385A PHE* 1.3 75.4 - - - +
387A GLU* 1.3 63.8 + - - +
388A PRO* 3.1 11.1 - - - +
465A TYR* 2.9 35.5 + - - +
466A ARG* 3.2 29.4 + - - +
468A MET* 5.1 9.7 + - - +
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Residues in contact with GLU 387 (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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383A LEU 4.2 4.4 + - - +
384A TYR 4.2 5.8 + - - +
385A PHE 3.2 5.8 + - - +
386A GLN* 1.3 75.8 - - - +
388A PRO* 1.3 79.1 - - - +
389A GLY 3.5 0.7 + - - -
390A VAL* 3.3 40.6 + - + +
391A ALA 4.4 1.4 + - - -
466A ARG* 3.1 9.9 + - - -
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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