Contacts of the helix formed by residues 380 - 391 (chain A) in PDB entry 5WWT
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 380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A TYR* 4.6 0.3 - - - -
372A THR* 2.6 25.3 + - - -
374A THR* 3.2 25.1 + - - +
375A ILE 3.8 1.2 - - - -
376A THR 3.2 12.6 + - - +
377A LEU 3.0 2.4 + - - -
379A GLU* 1.3 83.0 - - - +
381A GLU* 1.3 78.7 + - - +
382A GLU 3.2 0.9 - - - -
383A GLN* 3.0 16.1 + - - +
384A VAL* 3.1 13.2 + - - +
423A ARG* 3.0 22.4 - - - +
459A PHE* 3.3 36.3 - - + +
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Residues in contact with GLU 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 LEU* 3.3 16.5 + - + +
380A ASN* 1.3 79.3 - - - +
382A GLU* 1.3 57.9 + - - +
384A VAL* 3.0 8.2 + - - +
385A ALA* 2.9 24.8 + - - +
407A GLY* 3.5 4.7 - - - -
408A MET 2.8 31.9 + - - +
411A ALA* 3.5 22.2 - - + +
413A LEU* 4.1 4.2 - - + +
418A LEU* 4.4 4.7 - - + -
421A LEU* 3.9 19.5 - - + -
423A ARG* 2.6 46.6 + - - -
459A PHE* 3.6 13.4 - - - -
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Residues in contact with GLU 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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348A GLN* 3.5 15.2 + - - +
352A ARG* 4.9 4.6 + - - +
377A LEU* 3.1 25.7 + - + +
378A ALA* 3.4 29.6 + - - +
381A GLU* 1.3 77.4 - - - +
383A GLN* 1.3 60.5 + - - +
385A ALA* 3.4 4.1 + - + +
386A TRP* 2.9 28.9 + - - +
410A GLY 5.3 4.3 - - - +
411A ALA* 3.6 17.2 - - + +
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Residues in contact with GLN 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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348A GLN* 3.2 32.8 + - - +
351A GLN* 2.8 26.9 + - - +
352A ARG* 2.9 35.5 + - - +
355A PHE* 5.3 5.3 - - + -
370A TYR* 3.8 15.7 - - + +
378A ALA 3.2 18.7 + - - +
379A GLU 3.3 19.5 - - - +
380A ASN 3.0 8.3 + - - +
382A GLU* 1.3 72.8 - - - +
384A VAL* 1.3 61.4 + - - +
386A TRP* 3.6 7.9 - - + -
387A ALA* 2.9 30.3 + - - +
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Residues in contact with VAL 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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355A PHE* 6.2 0.4 - - - -
370A TYR* 5.1 3.8 - - + -
380A ASN 3.1 13.2 + - - +
381A GLU* 3.0 10.6 + - - +
383A GLN* 1.3 75.8 - - - +
385A ALA* 1.3 59.9 - - - +
387A ALA* 3.3 2.3 + - - +
388A LEU* 2.9 44.1 + - + +
396A LEU* 4.2 11.9 - - + -
413A LEU* 4.2 13.2 - - + -
421A LEU* 4.2 5.4 - - + -
459A PHE* 3.7 26.7 - - + -
461A ALA* 3.9 15.7 - - + -
463A PHE* 3.9 21.3 - - + -
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Residues in contact with ALA 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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381A GLU 2.9 10.3 + - - +
382A GLU* 3.7 8.5 - - + +
384A VAL* 1.3 77.5 - - - +
386A TRP* 1.3 57.2 + - - +
388A LEU* 3.2 5.4 + - - +
389A THR* 2.9 34.8 + - - +
411A ALA* 3.9 18.2 - - + +
413A LEU* 3.7 24.7 - - + -
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Residues in contact with TRP 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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352A ARG* 3.4 80.8 - - + +
355A PHE* 3.9 30.3 - + + -
356A THR* 3.8 10.1 - - - -
382A GLU 2.9 18.3 + - - +
383A GLN* 3.6 15.0 - - + +
385A ALA* 1.3 75.5 - - - +
387A ALA* 1.3 75.1 + - - +
389A THR* 3.2 5.9 + - + -
390A LYS* 2.9 60.0 + - + +
391A PHE* 3.9 7.2 - + - -
2C A 4.1 10.0 - - - +
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Residues in contact with ALA 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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355A PHE* 3.5 37.5 - - + -
383A GLN 2.9 20.5 + - - +
384A VAL 3.6 4.7 - - - +
386A TRP* 1.3 85.7 - - + +
388A LEU* 1.3 59.1 + - - +
391A PHE* 2.9 41.1 + - - +
394A LEU* 4.6 3.2 - - + +
463A PHE* 4.4 7.2 - - + -
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Residues in contact with LEU 388 (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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384A VAL* 2.9 34.9 + - + +
385A ALA* 3.7 4.7 - - - +
387A ALA* 1.3 76.9 - - - +
389A THR* 1.3 61.0 + - - +
391A PHE 3.4 13.0 - - - +
392A PRO* 4.3 4.9 - - - +
394A LEU* 4.0 17.4 - - + +
395A GLN* 4.2 1.6 - - + -
396A LEU* 3.9 28.7 - - + +
413A LEU* 4.7 5.4 - - + -
417A GLN* 3.5 29.8 - - - +
463A PHE* 3.8 22.4 - - + -
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Residues in contact with THR 389 (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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385A ALA* 2.9 20.1 + - - +
386A TRP* 3.6 7.1 - - - -
387A ALA 3.1 0.2 - - - -
388A LEU* 1.3 79.3 - - - +
390A LYS* 1.3 68.0 + - + +
391A PHE 3.5 0.3 + - - -
392A PRO* 4.2 10.9 - - - +
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Residues in contact with LYS 390 (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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356A THR* 4.3 16.2 - - - -
386A TRP* 2.9 52.7 + - + +
389A THR* 1.3 76.2 - - + +
391A PHE* 1.3 83.0 + - + +
392A PRO* 3.3 10.7 - - - +
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Residues in contact with PHE 391 (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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355A PHE* 3.8 19.1 - + - -
356A THR* 3.5 41.1 - - + -
359A VAL* 3.7 29.2 - - + -
360A GLN* 5.9 2.0 - - + -
386A TRP* 3.9 15.7 - + - -
387A ALA* 2.9 28.3 + - - +
388A LEU 3.4 10.1 - - - +
390A LYS* 1.3 98.2 - - + +
392A PRO* 1.3 65.2 - - - +
393A CYS* 3.2 9.3 + - - -
394A LEU* 3.5 31.6 + - + +
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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