Contacts of the helix formed by residues 355 - 374 (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 THR 355 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A VAL 4.3 6.3 - - - +
354A ALA* 1.3 77.2 - - - +
356A LYS* 1.3 64.5 + - - +
357A ASP* 3.6 7.6 + - - +
358A GLN* 3.2 38.6 + - - +
359A LEU* 3.1 20.8 + - - +
397A SER* 5.4 2.2 - - - -
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Residues in contact with LYS 356 (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 THR* 1.3 73.6 - - - +
357A ASP* 1.3 64.0 + - - +
359A LEU* 3.0 17.4 + - - +
360A PHE* 3.1 29.7 + - + -
393A ILE* 3.7 26.5 - - + +
394A ASP* 2.9 38.6 + - - +
395A THR 5.4 1.7 - - - -
397A SER* 3.8 27.4 - - - +
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Residues in contact with ASP 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A THR* 3.3 6.4 + - - +
356A LYS* 1.3 81.2 - - - +
358A GLN* 1.3 61.7 + - - +
360A PHE* 4.0 16.9 + - - +
361A PRO* 3.2 19.2 - - - +
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Residues in contact with GLN 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A VAL 4.3 2.1 - - - +
354A ALA* 3.5 14.6 - - + +
355A THR* 3.2 42.0 + - - +
356A LYS 3.2 0.2 - - - -
357A ASP* 1.3 80.1 - - + +
359A LEU* 1.3 60.2 + - - +
361A PRO* 3.4 12.3 - - - +
362A LEU* 3.6 21.6 - - + +
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Residues in contact with LEU 359 (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* 4.5 13.7 - - + +
355A THR 3.1 17.2 + - - +
356A LYS 3.0 6.0 + - - +
358A GLN* 1.3 77.9 - - - +
360A PHE* 1.3 64.9 + - - +
362A LEU* 3.2 4.3 + - + +
363A ALA* 2.9 21.8 + - - +
393A ILE* 3.8 20.9 - - + -
397A SER 3.6 23.8 - - - +
398A THR* 3.7 20.2 - - - +
399A TYR* 4.2 8.7 - - + -
580A GLY 3.9 15.0 - - - +
581A GLY* 3.8 28.0 - - - +
582A LEU* 4.5 3.4 - - + -
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Residues in contact with PHE 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LYS* 3.1 34.5 + - + -
357A ASP* 4.0 15.7 - - - +
359A LEU* 1.3 74.8 - - - +
361A PRO* 1.3 70.5 - - + +
363A ALA* 3.2 2.1 + - - +
364A LYS* 3.0 23.9 + - - +
390A ASN* 3.3 49.1 + - - +
393A ILE* 3.5 34.3 - - + -
394A ASP* 4.1 24.0 - - + -
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Residues in contact with PRO 361 (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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357A ASP 3.2 20.4 - - - +
358A GLN* 3.4 12.1 - - - +
360A PHE* 1.3 93.1 - - + +
362A LEU* 1.3 59.8 + - + +
364A LYS* 3.8 7.5 - - + +
365A GLU* 3.0 31.1 + - - +
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Residues in contact with LEU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A GLN* 3.6 19.3 - - + +
359A LEU* 3.2 9.8 + - + +
361A PRO* 1.3 81.1 - - + +
363A ALA* 1.3 63.6 + - - +
365A GLU* 3.6 20.3 + - - +
366A PHE* 3.2 16.5 + - - +
578A GLU* 5.2 4.5 - - - +
580A GLY* 3.7 12.1 - - - -
581A GLY* 3.8 30.7 - - - +
706A THR* 6.2 2.5 - - + -
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Residues in contact with ALA 363 (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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359A LEU 2.9 14.7 + - - +
360A PHE 3.7 3.8 - - - +
362A LEU* 1.3 74.7 - - - +
364A LYS* 1.3 61.5 + - - +
366A PHE* 3.1 3.6 + - - +
367A ILE* 2.8 34.6 + - - +
389A VAL* 3.9 18.2 - - + -
393A ILE* 4.0 4.7 - - + -
399A TYR* 3.5 42.0 - - + +
580A GLY* 3.7 1.3 + - - -
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Residues in contact with LYS 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A PHE 3.0 17.0 + - - +
361A PRO* 3.8 7.9 - - + +
363A ALA* 1.3 76.1 - - - +
365A GLU* 1.3 58.1 + - - +
367A ILE* 3.3 0.5 + - - +
368A ASP* 2.7 65.3 + - - +
386A LEU* 3.9 31.0 - - + -
389A VAL* 5.7 0.4 - - - +
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Residues in contact with GLU 365 (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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324A LYS 4.9 1.2 - - - +
326A THR* 3.6 26.6 - - - +
361A PRO 3.0 16.5 + - - +
362A LEU* 3.7 25.8 - - - +
364A LYS* 1.3 76.1 - - - +
366A PHE* 1.3 62.2 + - - +
368A ASP* 3.7 7.7 + - - +
369A GLN* 3.2 30.1 + - - +
706A THR* 4.0 15.3 - - + +
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Residues in contact with PHE 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LEU 3.2 2.7 + - - +
363A ALA 3.1 5.0 + - - +
365A GLU* 1.3 79.1 - - - +
367A ILE* 1.3 76.1 + - + +
369A GLN* 3.1 11.8 + - - +
370A TYR* 2.9 28.0 + - + +
399A TYR* 4.5 1.6 - - - -
401A LEU* 3.8 19.7 - - + -
405A GLU* 3.6 30.3 - - + -
408A TYR* 3.7 29.2 - + - -
409A GLY* 4.2 0.9 - - - -
579A ILE* 3.4 32.8 - - + -
580A GLY* 3.5 27.8 - - - -
706A THR* 6.6 0.4 - - + -
707A PRO* 3.8 21.5 - - + -
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Residues in contact with ILE 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ALA* 2.8 27.3 + - + +
366A PHE* 1.3 88.1 - - + +
368A ASP* 1.3 63.5 + - - +
370A TYR* 3.2 4.1 + - + +
371A TYR* 3.0 45.3 + - + -
382A HIS* 3.9 6.1 - - + -
385A ARG* 4.0 15.5 - - + +
386A LEU* 3.7 29.4 - - + +
389A VAL* 4.4 17.9 - - + -
399A TYR* 5.0 5.2 - - + -
405A GLU* 3.6 29.4 - - + +
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Residues in contact with ASP 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LYS* 2.7 50.7 + - - +
365A GLU* 3.7 7.2 - - - +
367A ILE* 1.3 75.8 - - - +
369A GLN* 1.3 57.5 + - - +
371A TYR* 3.4 0.5 + - - -
372A SER* 2.9 30.6 + - - -
377A PHE* 3.7 21.3 - - + -
382A HIS* 2.8 29.0 + - - -
386A LEU* 3.8 11.6 - - - +
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Residues in contact with GLN 369 (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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365A GLU* 3.2 23.3 + - - +
366A PHE* 3.1 12.0 + - - +
368A ASP* 1.3 79.4 - - - +
370A TYR* 1.3 62.4 + - - +
372A SER* 3.4 7.1 + - - -
373A SER* 3.1 17.3 + - - -
408A TYR* 3.0 30.8 + - - +
412A HIS* 4.4 7.4 - - - -
416A ASN* 5.4 0.3 + - - -
674A ARG* 5.3 3.1 + - - -
706A THR* 3.5 20.8 + - - +
707A PRO* 3.7 20.0 - - - +
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Residues in contact with TYR 370 (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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366A PHE* 2.9 20.0 + - + +
367A ILE* 3.2 9.4 + - - +
369A GLN* 1.3 77.0 - - - +
371A TYR* 1.3 87.5 + + - +
373A SER* 2.8 22.8 + - - -
374A ILE* 3.2 44.6 + - + +
404A THR* 3.2 36.7 + - - +
405A GLU* 4.2 20.2 - - + -
408A TYR* 3.6 47.7 + + + -
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Residues in contact with TYR 371 (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* 3.0 25.9 + - + +
368A ASP 4.1 0.4 - - - +
370A TYR* 1.3 96.9 - + - +
372A SER* 1.3 58.7 + - - +
374A ILE* 3.5 23.7 - - + +
375A LYS 3.4 2.4 + - - -
376A ARG* 2.9 42.7 + - + +
377A PHE* 3.2 3.3 + - - -
379A SER* 4.5 0.4 - - - -
381A ALA* 3.5 27.4 + - + +
382A HIS* 3.5 54.3 - + + +
385A ARG* 3.6 33.0 - - + +
405A GLU* 4.7 2.7 + - - -
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Residues in contact with SER 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ASP 2.9 19.3 + - - -
369A GLN* 3.6 8.7 - - - -
370A TYR 3.1 0.2 - - - -
371A TYR* 1.3 78.6 - - - +
373A SER* 1.3 62.0 + - - +
375A LYS* 3.3 21.0 + - - +
377A PHE* 3.9 24.5 - - - +
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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
----------------------------------------------------------
369A GLN 3.1 13.7 + - - -
370A TYR* 2.8 15.9 + - - -
372A SER* 1.3 79.5 - - - +
374A ILE* 1.3 64.2 + - - +
375A LYS* 3.2 15.3 + - - +
408A TYR* 3.3 33.1 - - - -
412A HIS* 5.6 1.3 - - - -
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Residues in contact with ILE 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A TYR* 3.5 41.5 - - + +
371A TYR* 3.5 38.4 - - + +
373A SER* 1.3 87.7 + - - +
375A LYS* 1.3 69.8 + - - +
376A ARG* 3.4 28.0 + - + +
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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
------------------------------------------------------------
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