Contacts of the helix formed by residues 379 - 389 (chain A) in PDB entry 3L4U
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 TYR 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A ARG* 3.6 32.7 - - + +
336A ASP* 2.6 45.8 + - - +
338A THR* 3.8 17.3 - - + -
369A ILE* 3.8 18.3 - - + +
370A SER* 3.5 39.8 + - - -
372A ASN 3.7 17.9 - - - +
373A SER* 2.8 13.1 + - - +
377A LYS 5.0 0.2 - - - +
378A PRO* 1.3 71.8 - - - +
380A GLY* 1.3 64.0 + - - +
381A PRO* 3.5 22.9 - - + +
382A TYR* 3.2 10.2 + - + +
383A ASP* 3.1 23.7 + - - +
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Residues in contact with GLY 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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378A PRO* 3.9 4.7 + - - +
379A TYR* 1.3 71.7 - - - +
381A PRO* 1.4 65.5 - - - +
383A ASP* 3.2 7.9 + - - +
384A ARG* 2.8 57.6 + - - +
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Residues in contact with PRO 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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337A PHE* 3.8 28.5 - - + +
338A THR* 6.0 0.2 - - + -
369A ILE* 4.2 8.3 - - + -
379A TYR* 3.5 40.8 - - + +
380A GLY* 1.4 90.5 - - - +
382A TYR* 1.3 56.1 + - - +
384A ARG* 3.4 5.4 - - - +
385A GLY* 3.0 23.2 + - - -
391A TRP* 4.0 0.3 - - - -
423A TRP* 3.2 15.0 + - + -
427A GLU* 3.5 28.9 - - + +
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Residues in contact with TYR 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ILE* 3.8 7.9 - - + +
370A SER 3.3 24.9 - - - +
371A ASN* 3.6 32.3 + - + +
373A SER* 3.8 14.6 - - - -
379A TYR* 3.2 13.2 + - + +
381A PRO* 1.3 77.6 - - - +
383A ASP* 1.3 72.7 + - - +
385A GLY 3.3 0.3 + - - -
386A SER* 2.8 56.7 + - - -
391A TRP* 3.6 7.1 + + - -
400A PRO* 6.0 2.1 - - - +
411A VAL* 3.7 32.5 - - + +
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Residues in contact with ASP 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 SER* 2.7 33.9 + - - -
374A SER 5.2 0.3 - - - +
378A PRO* 3.7 18.2 - - - +
379A TYR 3.1 10.3 + - - +
380A GLY* 3.2 8.4 + - - +
382A TYR* 1.3 83.2 - - - +
384A ARG* 1.3 58.3 + - + +
386A SER* 3.4 4.4 + - - -
387A ASP* 3.0 36.7 + - - +
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Residues in contact with ARG 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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337A PHE* 6.0 0.2 - - - +
380A GLY* 2.8 41.5 + - - +
381A PRO* 3.4 4.8 - - - +
383A ASP* 1.3 70.8 - - + +
385A GLY* 1.3 65.4 + - - +
387A ASP* 3.5 12.1 + - - +
388A MET* 3.3 30.5 + - - +
423A TRP* 3.8 6.3 - - + -
426A LYS* 5.1 8.9 - - - +
427A GLU* 2.7 46.0 + - - +
430A LEU* 3.6 28.5 - - - +
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Residues in contact with GLY 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 PRO 3.0 11.5 + - - -
384A ARG* 1.3 78.5 - - - +
386A SER* 1.3 56.2 + - - +
388A MET 3.3 1.2 + - - -
389A LYS* 2.9 22.7 + - - -
390A ILE* 3.4 19.1 + - - +
391A TRP* 3.5 21.7 + - - -
423A TRP* 3.3 21.6 - - - +
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Residues in contact with SER 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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382A TYR* 2.8 46.1 + - - -
383A ASP* 3.7 5.8 - - - -
385A GLY* 1.3 69.9 - - - +
387A ASP* 1.3 66.3 + - - +
389A LYS* 3.1 24.1 + - - +
391A TRP* 3.0 23.3 + - - +
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Residues in contact with ASP 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 ASP* 3.0 22.6 + - - +
384A ARG* 3.5 18.0 - - - +
386A SER* 1.3 77.4 - - - +
388A MET* 1.3 63.3 + - + +
389A LYS* 3.6 12.5 + - - +
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Residues in contact with MET 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 ARG* 3.3 15.7 + - - +
385A GLY 3.3 4.7 + - - +
386A SER 3.2 0.4 - - - -
387A ASP* 1.3 78.4 - - + +
389A LYS* 1.3 72.0 + - - +
390A ILE* 3.3 16.7 + - + +
417A ASN* 5.5 0.3 + - - -
419A ASN* 3.8 33.2 + - + +
422A VAL* 4.1 19.7 - - + -
423A TRP* 3.6 26.0 - - - -
2B NAG 4.9 6.2 + - - -
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Residues in contact with LYS 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 GLY 2.9 6.6 + - - -
386A SER* 3.1 17.9 + - - +
387A ASP 3.9 8.5 + - - +
388A MET* 1.3 79.9 - - - +
390A ILE* 1.3 61.1 + - - +
391A TRP* 3.5 10.1 + - - +
417A ASN* 4.4 7.1 + - - -
1B NAG 3.6 46.7 + - - +
2B NAG 3.1 44.0 + - - +
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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