Contacts of the helix formed by residues 372 - 382 (chain A) in PDB entry 4B9N
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 ASP 372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A PHE* 1.3 84.4 - - + +
373A SER* 1.3 66.3 + - - +
374A LYS* 3.2 9.4 + - - +
375A ARG* 3.2 42.6 + - + +
376A ALA* 3.7 4.7 + - - +
393A ASP* 3.0 15.8 + - - -
395A LEU* 3.6 30.7 - - + +
2D FRU 2.7 37.6 + - - +
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Residues in contact with SER 373 (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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370A MET* 4.0 25.6 - - - -
371A PHE 3.5 1.0 - - - -
372A ASP* 1.3 73.6 - - - +
374A LYS* 1.3 57.9 + - - +
376A ALA* 3.2 2.3 + - - +
377A ALA* 2.8 31.5 + - - +
387A LEU* 4.1 2.2 - - - +
390A VAL* 3.8 32.1 - - - +
393A ASP* 2.8 25.0 + - - +
482A SER* 4.0 9.7 + - - -
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Residues in contact with LYS 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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327A TYR* 2.9 21.5 + - - +
372A ASP* 3.1 8.0 + - - +
373A SER* 1.3 78.7 + - - +
375A ARG* 1.3 60.3 + - - +
377A ALA* 4.2 5.4 - - - -
378A VAL* 2.9 30.3 + - - +
393A ASP* 4.5 0.4 + - - -
482A SER* 3.6 32.7 + - - +
485A LEU* 3.8 17.5 - - + -
486A ALA* 3.7 21.8 - - + +
489A GLU* 2.7 24.8 + - - +
605A ILE* 4.4 1.4 - - - +
606A PHE 2.7 28.9 + - - -
608A GLN* 4.3 12.3 - - - +
2D FRU 5.1 5.3 - - - -
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Residues in contact with ARG 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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320A VAL 5.2 2.5 - - - +
322A VAL* 3.0 38.6 + - + +
323A VAL 4.7 0.2 + - - -
324A GLU 2.7 27.1 + - - -
325A GLU* 3.0 24.0 + - - +
327A TYR* 3.7 30.2 - - + +
372A ASP* 3.2 36.2 + - - +
374A LYS* 1.3 79.5 - - - +
376A ALA* 1.3 62.1 + - + +
379A ALA* 3.1 23.7 + - - +
1881A SO4 3.6 23.3 + - - -
1D GLC 3.5 13.7 + - - -
2D FRU 3.0 20.8 + - - -
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Residues in contact with ALA 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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320A VAL* 3.7 40.6 - - + +
322A VAL* 4.8 0.4 - - - -
370A MET* 3.8 19.3 - - + -
372A ASP 3.7 3.6 + - - +
373A SER 3.2 8.5 + - - +
375A ARG* 1.3 78.3 - - + +
377A ALA* 1.3 61.7 + - - +
379A ALA* 3.2 5.3 + - - +
380A LEU* 2.8 36.8 + - + +
387A LEU* 4.3 4.3 - - + -
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Residues in contact with ALA 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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373A SER* 2.8 21.9 + - - +
374A LYS* 3.7 7.9 - - - +
376A ALA* 1.3 72.4 - - - +
378A VAL* 1.3 58.0 + - - +
380A LEU* 3.3 3.0 + - - +
381A LYS* 2.8 37.0 + - - +
385A ILE 4.6 1.0 - - - +
387A LEU* 4.0 28.9 + - + +
483A SER* 6.5 0.4 - - - -
486A ALA* 4.5 11.9 - - + -
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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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327A TYR* 3.6 18.2 - - + +
328A HIS* 3.5 30.1 - - + +
374A LYS* 2.9 22.0 + - + +
377A ALA* 1.3 72.0 - - - +
379A ALA* 1.3 67.4 + - - +
381A LYS* 3.0 17.0 + - + +
382A TRP* 3.1 22.6 + - + +
486A ALA* 3.7 34.1 - - + +
489A GLU* 3.8 17.5 - - + +
490A PHE* 4.9 5.2 - - + -
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Residues in contact with ALA 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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322A VAL* 3.5 25.6 - - + -
327A TYR 4.0 18.1 + - - +
329A ASP 5.3 0.2 - - - +
330A ALA 4.4 8.6 - - - +
332A ILE* 4.3 12.3 - - + -
375A ARG 3.1 20.3 + - - +
376A ALA 3.7 3.4 - - - +
378A VAL* 1.3 77.6 - - - +
380A LEU* 1.3 60.1 + - - +
382A TRP* 3.5 13.6 + - - +
383A LYS* 3.6 18.9 + - - +
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Residues in contact with LEU 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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320A VAL* 4.3 16.8 - - + -
332A ILE* 3.6 25.8 - - + -
352A LEU* 3.8 27.1 - - + -
361A LEU* 4.6 13.7 - - + -
376A ALA 2.8 23.8 + - - +
377A ALA* 3.6 4.0 - - - +
379A ALA* 1.3 75.6 - - - +
381A LYS* 1.3 59.0 + - - +
383A LYS* 2.9 19.5 + - + +
384A GLY 3.1 0.2 + - - -
385A ILE* 2.9 45.4 + - + +
387A LEU* 4.1 28.3 - - + -
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Residues in contact with LYS 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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377A ALA* 2.8 21.9 + - - +
378A VAL* 3.3 12.1 - - - +
380A LEU* 1.3 75.3 - - - +
382A TRP* 1.3 57.5 + - - +
384A GLY* 2.9 19.8 + - - +
385A ILE 3.5 10.3 + - - +
386A GLU* 5.7 8.5 - - - +
486A ALA* 4.1 32.8 - - - +
487A GLU* 3.8 21.3 + - - +
490A PHE* 3.6 52.4 - - + -
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Residues in contact with TRP 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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328A HIS* 3.1 30.4 + - + -
329A ASP* 3.2 63.7 - - + +
378A VAL* 3.1 34.2 + - + +
379A ALA* 3.7 8.5 - - - +
380A LEU 3.2 0.6 - - - -
381A LYS* 1.3 75.7 - - - +
383A LYS* 1.3 60.0 + - + +
384A GLY 3.3 1.1 - - - -
490A PHE* 3.6 25.5 - + - -
596A ARG* 4.1 14.4 - - - -
598A ASP* 4.3 11.7 - - - -
599A THR* 4.6 8.1 - - + -
603A HIS* 4.0 38.1 - + - -
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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