Contacts of the helix formed by residues 379 - 397 (chain A) in PDB entry 5UO5
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 SER 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376A ARG* 2.6 44.4 + - - +
377A PHE 3.2 2.0 + - - -
378A GLY* 1.3 81.8 - - - +
380A LYS* 1.3 65.0 + - - +
381A ALA* 3.6 8.2 + - - +
382A HIS* 3.1 16.0 + - - +
383A MET* 3.0 22.5 + - - +
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Residues in contact with LYS 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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379A SER* 1.3 73.7 - - - +
381A ALA* 1.3 57.8 + - - +
383A MET* 3.4 5.6 + - - +
384A GLU* 2.7 66.0 + - + +
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Residues in contact with ALA 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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371A TYR* 3.5 18.9 + - + +
376A ARG* 5.9 1.3 - - + -
379A SER* 3.2 9.4 + - - +
380A LYS* 1.3 75.3 - - - +
382A HIS* 1.3 61.3 + - - +
384A GLU* 3.9 10.8 - - - +
385A ARG* 3.0 30.7 + - - +
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Residues in contact with HIS 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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367A ILE* 3.9 4.7 - - + -
368A ASP* 2.8 37.3 + - - -
371A TYR* 3.5 34.0 - + + -
376A ARG 3.6 6.7 - - - +
377A PHE* 3.6 28.8 - + - -
378A GLY 2.9 19.3 + - - -
379A SER* 3.1 20.9 + - - +
381A ALA* 1.3 78.2 - - - +
383A MET* 1.3 73.1 + - + +
385A ARG* 3.2 3.8 + - - +
386A LEU* 3.0 33.5 + - + +
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Residues in contact with MET 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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377A PHE* 6.1 0.9 - - + -
378A GLY* 3.6 22.4 - - - +
379A SER 3.0 14.1 + - - +
380A LYS* 3.9 5.8 - - - +
382A HIS* 1.3 115.2 - - + +
384A GLU* 1.3 62.9 + - + +
386A LEU* 3.4 16.8 + - + +
387A GLU* 3.1 25.8 + - - +
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Residues in contact with GLU 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 LYS* 2.7 61.3 + - + +
381A ALA* 3.9 10.2 - - - +
383A MET* 1.3 76.6 - - + +
385A ARG* 1.3 58.1 - - - +
387A GLU* 3.3 7.3 + - - +
388A GLU* 3.0 30.0 + - - +
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Residues in contact with ARG 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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367A ILE* 4.0 11.5 - - + +
371A TYR* 3.6 23.3 - - + +
381A ALA 3.0 19.1 + - - +
382A HIS 3.5 4.5 - - - +
384A GLU* 1.3 74.9 - - - +
386A LEU* 1.3 64.0 + - - +
388A GLU* 3.0 35.1 + - - +
389A VAL* 3.0 57.4 + - - +
392A GLU* 4.4 5.3 + - - -
399A TYR* 4.2 4.6 - - - -
400A GLN 3.0 26.3 + - - -
401A LEU* 3.9 1.0 - - - +
402A LYS* 3.8 23.5 - - - +
405A GLU* 2.6 42.8 + - - +
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Residues in contact with LEU 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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364A LYS* 3.9 36.6 - - + -
367A ILE* 3.7 28.9 - - + -
368A ASP* 3.8 7.6 - - - +
382A HIS* 3.0 38.5 + - + +
383A MET* 3.7 23.3 - - + +
384A GLU 3.3 0.2 - - - -
385A ARG* 1.3 76.5 - - - +
387A GLU* 1.3 56.2 + - - +
389A VAL* 3.8 5.3 - - + +
390A ASN* 3.0 31.3 + - - +
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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 MET 3.1 15.6 + - - +
384A GLU* 3.3 11.0 + - - +
386A LEU* 1.3 77.4 - - - +
388A GLU* 1.3 56.3 + - - +
390A ASN* 3.3 8.3 + - - +
391A LYS* 2.9 32.2 + - - +
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Residues in contact with GLU 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 GLU 3.0 15.5 + - - +
385A ARG* 3.0 32.8 + - - +
386A LEU 3.3 0.2 - - - -
387A GLU* 1.3 73.9 - - - +
389A VAL* 1.3 61.0 + - - +
391A LYS* 3.5 6.1 + - - +
392A GLU* 3.0 38.1 + - + +
402A LYS* 3.4 21.4 + - - -
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Residues in contact with VAL 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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363A ALA* 3.9 14.6 - - + -
367A ILE* 4.4 12.1 - - + -
385A ARG* 3.0 55.1 + - - +
386A LEU* 3.8 6.3 - - + +
388A GLU* 1.3 75.8 - - - +
390A ASN* 1.3 58.7 + - - +
392A GLU* 3.2 7.2 + - - +
393A ILE* 2.9 45.9 + - + +
399A TYR* 3.9 26.2 - - + -
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Residues in contact with ASN 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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360A PHE* 3.3 40.4 + - - +
386A LEU 3.0 19.4 + - - +
387A GLU* 3.6 9.6 - - - +
389A VAL* 1.3 79.3 - - - +
391A LYS* 1.3 57.7 + - - +
393A ILE 3.4 0.7 + - - -
394A ASP* 2.9 29.8 + - - +
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Residues in contact with LYS 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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387A GLU* 2.9 21.6 + - - +
388A GLU* 3.8 6.7 - - - +
390A ASN* 1.3 77.7 - - - +
392A GLU* 1.3 61.3 + - - +
394A ASP* 3.2 5.7 + - + +
395A THR* 3.0 46.6 + - + +
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Residues in contact with GLU 392 (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 ARG* 4.4 11.3 + - - -
388A GLU* 3.0 24.0 + - + +
389A VAL* 3.4 8.8 - - - +
391A LYS* 1.3 78.2 - - - +
393A ILE* 1.3 54.5 + - - +
395A THR* 3.4 6.0 + - - +
396A THR* 2.8 46.3 + - + +
398A THR 3.3 8.5 - - - +
399A TYR* 3.5 14.7 - - + +
400A GLN* 3.4 36.9 + - - +
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Residues in contact with ILE 393 (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 LYS* 3.7 23.6 - - + +
359A LEU* 3.8 31.0 - - + -
360A PHE* 3.5 42.6 - - + -
363A ALA* 4.0 10.1 - - + -
389A VAL* 2.9 35.1 + - + +
392A GLU* 1.3 75.0 - - - +
394A ASP* 1.3 58.5 + - - +
397A SER* 2.8 28.4 + - - -
398A THR 3.4 9.9 - - - +
399A TYR* 3.8 19.5 - - + -
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Residues in contact with ASP 394 (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 LYS* 2.9 36.2 + - - +
360A PHE* 4.1 16.7 - - + -
390A ASN* 2.9 21.0 + - - +
391A LYS* 3.7 7.0 - - - +
392A GLU 3.2 0.2 - - - -
393A ILE* 1.3 79.8 - - - +
395A THR* 1.3 61.3 + - + +
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Residues in contact with THR 395 (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 LYS* 5.4 1.8 - - - -
391A LYS* 3.0 44.8 + - + +
392A GLU* 3.4 6.6 + - - +
394A ASP* 1.3 84.0 - - + +
396A THR* 1.3 74.1 + - - +
397A SER 3.7 0.2 - - - -
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Residues in contact with THR 396 (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 LYS* 5.3 0.2 - - - -
392A GLU* 2.8 29.1 + - + +
395A THR* 1.3 89.6 - - - +
397A SER* 1.3 70.8 + - - +
398A THR* 2.9 33.9 + - - +
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Residues in contact with SER 397 (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 ALA 4.7 8.3 - - - +
355A THR 5.9 0.2 - - - -
356A LYS* 3.8 31.7 - - - +
359A LEU* 3.6 14.3 - - - +
393A ILE* 2.8 21.0 + - - +
395A THR 3.7 0.8 - - - -
396A THR* 1.3 90.5 + - - +
398A THR* 1.3 60.6 + - - +
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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