Contacts of the helix formed by residues 378 - 395 (chain A) in PDB entry 5UFL
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 378 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A GLN* 5.1 7.7 + - - -
373A VAL* 3.5 15.0 - - + +
376A ALA* 3.3 16.5 + - - +
377A ALA* 1.3 83.1 - - - +
379A CYS* 1.3 63.0 + - - +
380A SER* 3.3 4.5 - - - +
381A SER* 3.4 25.5 + - - +
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Residues in contact with CYS 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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373A VAL* 3.9 8.3 - - + -
374A ILE* 4.1 25.4 - - - -
377A ALA* 3.0 17.0 + - - -
378A ASN* 1.3 77.7 - - - +
380A SER* 1.3 58.3 + - - +
381A SER 3.4 0.2 + - - -
382A ALA* 3.4 4.4 + - - +
383A ASP* 3.0 28.5 + - - +
429A ASP* 3.3 39.3 - - - +
432A LEU* 4.6 9.0 - - + +
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Residues in contact with SER 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ASN* 3.3 2.4 - - - -
379A CYS* 1.3 75.7 - - - +
381A SER* 1.3 63.6 + - - +
383A ASP* 3.7 20.4 + - - +
384A ARG* 4.4 4.0 + - - +
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Residues in contact with SER 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PHE* 3.8 30.9 + - - +
373A VAL* 6.3 0.2 - - - -
378A ASN* 3.4 22.4 + - - +
379A CYS 3.2 0.6 - - - -
380A SER* 1.3 80.1 - - - +
382A ALA* 1.3 59.5 + - - +
383A ASP 3.7 0.2 + - - -
384A ARG* 4.3 9.9 + - - +
385A PHE* 4.9 1.2 + - - +
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Residues in contact with ALA 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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321A PHE* 4.0 35.6 - - + +
370A PHE* 4.1 17.0 - - + -
373A VAL* 4.2 15.5 - - + -
378A ASN 4.0 0.4 + - - -
379A CYS 3.4 7.8 + - - +
381A SER* 1.3 76.0 - - - +
383A ASP* 1.3 56.2 + - - +
384A ARG 3.2 2.9 - - - -
385A PHE* 2.8 27.8 + - - +
386A VAL* 3.0 14.4 + - + +
432A LEU* 5.7 2.2 - - + -
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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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379A CYS 3.0 16.2 + - - +
380A SER* 3.7 15.7 - - - +
381A SER 3.4 0.8 - - - -
382A ALA* 1.3 76.0 - - - +
384A ARG* 1.3 61.9 + - - +
386A VAL* 3.4 10.3 + - - +
387A THR* 3.6 12.5 + - - -
429A ASP* 5.4 0.2 - - - +
431A THR* 3.5 27.5 - - - +
432A LEU* 3.6 22.3 - - - +
435A HIS* 3.2 24.6 + - - -
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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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380A SER 4.4 3.4 + - - +
381A SER 4.3 8.8 + - - +
382A ALA 3.0 0.6 + - - -
383A ASP* 1.3 79.1 + - - +
385A PHE* 1.3 61.9 + - - +
387A THR* 3.5 18.2 + - - -
388A LEU* 3.9 4.2 + - - +
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Residues in contact with PHE 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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321A PHE* 3.4 33.0 - + + -
341A THR* 3.4 30.7 - - + -
345A LEU* 4.3 15.3 - - + -
366A PHE* 3.5 29.6 - + - -
370A PHE* 3.7 17.3 - + - -
381A SER 4.9 1.3 + - - +
382A ALA* 2.8 14.5 + - - +
384A ARG* 1.3 72.3 - - - +
386A VAL* 1.3 56.0 + - - +
387A THR 3.2 2.5 - - - -
388A LEU* 2.9 19.7 + - + +
389A LEU* 2.9 57.1 + - + +
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Residues in contact with VAL 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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370A PHE* 3.5 33.2 - - + -
382A ALA* 3.0 16.6 + - + +
383A ASP 3.8 8.5 - - - +
384A ARG 3.4 0.6 - - - -
385A PHE* 1.3 75.6 - - - +
387A THR* 1.3 60.5 + - - +
389A LEU* 4.4 7.0 - - + -
390A LEU* 3.1 48.8 + - + +
426A LEU* 4.2 13.2 - - + -
432A LEU* 3.7 31.9 - - + +
435A HIS* 4.4 8.7 - - + -
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Residues in contact with THR 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* 3.6 11.4 + - - -
384A ARG* 3.5 11.5 + - - -
385A PHE 3.2 0.2 - - - -
386A VAL* 1.3 78.2 - - - +
388A LEU* 1.3 61.1 + - - +
390A LEU* 4.7 2.0 - - - +
391A PRO* 3.3 22.3 - - - +
435A HIS* 3.8 19.8 + - + -
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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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338A LEU* 4.9 13.9 - - + -
341A THR* 5.4 2.0 - - - +
342A VAL* 4.7 14.1 - - + -
345A LEU* 4.3 24.0 - - + +
384A ARG 3.9 2.8 + - - +
385A PHE* 2.9 26.0 + - + +
387A THR* 1.3 79.8 - - - +
389A LEU* 1.3 61.6 + - - +
391A PRO* 4.0 6.2 - - - +
392A THR* 4.2 8.7 + - - -
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Residues in contact with LEU 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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345A LEU* 3.4 29.6 - - + -
348A LEU* 4.4 1.8 - - + -
366A PHE* 4.0 21.8 - - + -
370A PHE* 3.3 39.9 - - + -
385A PHE* 2.9 28.8 + - + +
386A VAL* 4.1 5.2 - - + +
388A LEU* 1.3 78.3 - - - +
390A LEU* 1.3 66.6 + - + +
391A PRO 3.4 1.1 - - - -
392A THR* 3.0 15.6 + - - -
393A ILE* 3.2 41.6 + - + -
422A VAL* 4.9 0.4 - - + -
426A LEU* 5.6 3.4 - - + -
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Residues in contact with LEU 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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386A VAL* 3.1 37.9 + - + +
387A THR* 4.7 1.6 - - - +
389A LEU* 1.3 79.4 - - + +
391A PRO* 1.4 65.2 - - + +
393A ILE* 3.1 8.2 + - + +
394A LEU* 2.8 37.3 + - + +
423A LEU* 3.4 33.7 - - + -
426A LEU* 3.8 12.1 - - + -
435A HIS* 3.7 35.9 - - + +
436A ILE* 3.8 14.1 - - + +
439A ILE* 4.6 11.9 - - + -
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Residues in contact with PRO 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 THR 3.3 21.1 - - - +
388A LEU 4.0 5.2 - - - +
389A LEU 3.5 3.1 - - - -
390A LEU* 1.4 92.9 - - + +
392A THR* 1.3 56.1 + - - +
394A LEU* 3.5 9.8 + - + +
395A ASP* 3.1 26.7 + - - +
439A ILE* 5.7 10.7 - - + -
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Residues in contact with THR 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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345A LEU* 4.0 26.1 - - + +
348A LEU* 4.0 29.8 - - + -
349A SER* 4.9 7.4 - - - +
388A LEU 4.2 7.1 + - - -
389A LEU 3.0 10.6 + - - -
391A PRO* 1.3 74.4 - - - +
393A ILE* 1.3 63.8 + - - +
395A ASP* 3.4 19.2 + - + +
396A GLN* 3.5 14.6 + - - +
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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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348A LEU* 4.3 9.4 - - + -
363A LEU* 4.5 5.8 - - + -
366A PHE* 5.1 2.5 - - + -
389A LEU* 3.2 42.7 + - + -
390A LEU* 3.1 13.2 + - + +
392A THR* 1.3 74.8 - - - +
394A LEU* 1.3 64.0 + - - +
396A GLN* 3.1 23.6 + - - +
397A LEU* 3.8 6.9 - - - +
419A ALA* 3.7 31.6 - - + +
422A VAL* 3.4 32.5 - - + -
423A LEU* 4.0 22.0 - - + -
426A LEU* 5.6 0.2 - - + -
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Residues in contact with LEU 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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390A LEU* 2.8 26.8 + - + +
391A PRO* 3.8 7.9 - - + +
393A ILE* 1.3 72.7 - - - +
395A ASP* 1.3 57.5 + - - +
397A LEU* 3.1 26.5 + - + +
423A LEU* 3.7 34.5 - - + -
436A ILE* 5.4 0.7 - - + -
439A ILE* 3.8 43.5 - - + +
440A LEU* 4.0 27.4 - - + -
444A LYS* 3.6 28.0 + - + -
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Residues in contact with ASP 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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391A PRO 3.1 14.8 + - - +
392A THR* 3.5 15.5 - - + +
393A ILE 3.2 0.4 - - - -
394A LEU* 1.3 75.6 - - - +
396A GLN* 1.3 65.1 + - - +
397A LEU 3.3 0.2 - - - -
398A GLN* 2.9 45.9 + - - +
412A LYS* 5.2 2.1 + - - -
444A LYS* 5.2 1.1 - - - +
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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