Contacts of the helix formed by residues 365 - 383 (chain A) in PDB entry 5F0L
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 ARG 365 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A ALA 4.9 0.7 - - - +
362A TYR* 3.1 20.9 + - + +
363A PRO 4.2 1.5 - - - +
364A ASP* 1.3 92.7 + - - +
366A VAL* 1.3 63.8 + - - +
367A ASP* 3.1 33.5 + - - +
368A TYR* 2.9 65.4 + - + +
369A VAL* 4.1 6.4 + - - +
509A EDO 3.0 38.2 + - - -
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Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PRO 4.4 3.8 - - - +
364A ASP 3.2 12.9 + - - +
365A ARG* 1.3 68.1 - - - +
367A ASP* 1.3 65.8 + - - +
368A TYR 3.1 2.2 - - - -
369A VAL* 3.0 15.2 + - - +
370A ASP* 3.2 8.7 + - - -
409A TYR* 3.4 28.3 - - + +
414A THR* 4.1 23.8 - - - +
417A LYS* 6.0 4.3 - - + -
418A LEU* 3.5 28.0 - - + +
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Residues in contact with ASP 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ARG* 3.1 52.9 + - - +
366A VAL* 1.3 74.7 + - - +
368A TYR* 1.3 66.2 + - - -
370A ASP* 3.5 8.5 + - - +
371A LYS* 3.0 26.4 + - - +
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Residues in contact with TYR 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LYS* 5.9 2.8 - - - +
325A PHE* 3.4 40.4 - + + +
326A ASP* 4.1 12.9 + - - -
358A ALA* 4.0 14.1 - - + -
362A TYR* 3.8 36.4 - + + -
365A ARG* 2.9 69.2 + - + +
366A VAL 3.1 0.6 - - - -
367A ASP* 1.3 85.9 + - - +
369A VAL* 1.3 65.1 + - - +
371A LYS* 3.0 17.0 + - + +
372A VAL* 3.1 17.9 + - - +
509A EDO 4.6 5.0 + - - -
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Residues in contact with VAL 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ILE* 4.4 11.6 - - + +
358A ALA* 4.4 14.8 - - + +
359A MET* 3.7 32.3 - - + +
365A ARG 4.5 5.6 - - - +
366A VAL 3.0 9.6 + - - +
368A TYR* 1.3 75.7 - - - +
370A ASP* 1.3 60.9 + - - +
372A VAL* 3.5 9.1 + - - +
373A LEU* 3.3 35.4 + - + +
405A PRO* 4.3 20.4 - - + -
409A TYR* 3.9 14.6 - - - +
418A LEU* 4.4 11.7 - - + -
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Residues in contact with ASP 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A VAL 3.2 7.6 + - - +
367A ASP* 3.8 11.0 - - - +
368A TYR 3.2 0.2 - - - -
369A VAL* 1.3 76.9 - - - +
371A LYS* 1.3 52.7 + - - +
372A VAL 3.3 0.2 - - - -
373A LEU* 3.4 4.3 + - - +
374A GLU* 2.7 35.3 + - - +
418A LEU* 3.4 24.7 - - + +
419A LYS* 3.1 18.3 + - - +
420A HIS* 2.8 51.8 + - - +
421A PHE 4.1 1.0 + - - -
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Residues in contact with LYS 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A PHE* 4.4 17.0 - - + -
367A ASP 3.0 13.7 + - - +
368A TYR* 3.0 13.9 + - + +
370A ASP* 1.3 73.0 - - - +
372A VAL* 1.3 57.4 + - - +
374A GLU* 3.4 34.0 - - - +
375A THR* 2.6 49.8 + - - +
378A GLU* 5.2 3.1 - - - -
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Residues in contact with VAL 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A PHE* 3.5 31.0 - - + -
351A GLN* 3.4 43.0 - - + +
354A LEU* 4.0 16.6 - - + +
355A ILE* 3.5 27.4 - - + +
358A ALA* 5.4 0.2 - - + -
368A TYR 3.1 8.5 + - - +
369A VAL* 3.8 2.5 - - - +
371A LYS* 1.3 74.6 - - - +
373A LEU* 1.3 52.4 - - - +
375A THR* 3.2 6.3 + - - -
376A THR* 2.6 42.8 + - - +
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Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ILE* 4.2 6.1 - - + -
369A VAL* 3.3 31.6 + - + +
370A ASP* 3.6 13.2 - - - +
372A VAL* 1.3 77.2 - - - +
374A GLU* 1.3 58.6 + - - +
376A THR* 3.3 7.8 + - - -
377A VAL* 3.0 32.6 + - - +
401A LEU* 3.3 33.2 - - + -
402A LEU* 3.8 10.3 - - + -
405A PRO* 5.2 3.8 - - + -
418A LEU* 4.1 16.6 - - + -
420A HIS* 3.9 15.0 - - + +
421A PHE* 4.3 14.6 - - + -
424A LEU* 3.4 17.2 - - + +
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Residues in contact with GLU 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ASP* 2.7 21.2 + - - +
371A LYS* 3.4 34.4 - - - +
373A LEU* 1.3 72.9 - - - +
375A THR* 1.3 58.9 + - - +
377A VAL* 3.4 5.9 + - + +
378A GLU* 3.1 45.4 + - - +
420A HIS* 3.6 44.2 + - + +
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Residues in contact with THR 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A GLN* 4.1 12.6 - - - +
354A LEU* 6.4 0.2 - - + -
371A LYS* 2.6 35.7 + - - +
372A VAL* 3.5 7.6 - - - -
374A GLU* 1.3 75.4 - - - +
376A THR* 1.3 59.2 + - - +
378A GLU* 3.3 18.8 + - + +
379A ILE* 2.9 38.4 + - + +
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Residues in contact with THR 376 (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 VAL* 5.1 3.4 - - + -
351A GLN* 3.7 23.3 - - + +
372A VAL 2.6 30.1 + - - -
373A LEU* 3.5 9.9 - - - -
375A THR* 1.3 73.1 - - - +
377A VAL* 1.3 56.9 + - - +
379A ILE* 3.0 13.4 + - + +
380A PHE* 2.9 58.9 + - + -
398A LEU* 4.4 1.8 - - + -
401A LEU* 4.0 22.2 - - + +
424A LEU* 3.9 10.5 - - + -
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Residues in contact with VAL 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LEU 3.0 16.2 + - - +
374A GLU* 3.5 11.2 - - + +
375A THR 3.3 0.2 - - - -
376A THR* 1.3 74.8 - - - +
378A GLU* 1.3 54.7 + - + +
380A PHE* 3.2 5.2 + - - +
381A ASN* 2.7 43.7 + - + +
420A HIS* 4.2 13.0 - - + +
423A PRO* 4.2 25.1 - - + +
424A LEU* 3.4 30.2 - - + +
427A TYR* 3.9 16.2 + - + +
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Residues in contact with GLU 378 (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 LYS* 5.2 3.3 - - - -
374A GLU* 3.1 42.3 + - + +
375A THR* 3.3 21.8 + - + +
377A VAL* 1.3 80.7 - - + +
379A ILE* 1.3 53.6 + - + +
381A ASN* 3.6 6.9 - - - +
382A LYS* 2.7 37.5 + - - +
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Residues in contact with ILE 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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336A ILE* 6.1 1.1 - - + -
347A VAL* 4.0 27.6 - - + -
348A VAL* 5.3 7.4 - - + -
351A GLN* 3.9 35.9 - - + +
375A THR* 2.9 27.7 + - + +
376A THR* 3.2 9.6 - - + +
378A GLU* 1.3 73.7 - - + +
380A PHE* 1.3 67.5 + - + +
382A LYS* 3.3 6.0 + - - +
383A LEU* 3.0 45.1 + - + +
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Residues in contact with PHE 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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348A VAL* 4.0 18.2 - - + -
376A THR* 2.9 49.3 + - + -
377A VAL 3.6 6.1 - - - +
379A ILE* 1.3 76.2 - - + +
381A ASN* 1.3 53.8 + - - +
383A LEU* 2.7 27.3 - - + +
385A LEU* 3.4 29.6 - - + +
388A ILE* 3.5 16.8 - - + -
394A VAL* 3.5 33.7 - - + -
398A LEU* 3.7 31.9 - - + -
424A LEU* 4.2 6.7 - - + -
427A TYR* 3.8 32.7 - + + -
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Residues in contact with ASN 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 VAL* 2.7 27.0 + - - +
378A GLU* 3.6 8.5 - - - +
380A PHE* 1.3 71.2 - - - +
382A LYS* 1.3 64.7 + - - +
383A LEU 3.5 6.8 - - - +
384A ASN* 4.8 1.9 - - - -
427A TYR* 3.6 21.2 + - - +
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Residues in contact with LYS 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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378A GLU 2.7 23.4 + - - +
379A ILE* 3.7 6.5 - - - +
381A ASN* 1.3 73.8 - - - +
383A LEU* 1.3 64.7 + - + +
384A ASN* 3.2 5.0 + - - +
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Residues in contact with LEU 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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344A SER* 3.6 29.6 - - - +
347A VAL* 6.3 1.3 - - + -
379A ILE* 3.0 35.1 + - + +
380A PHE* 2.7 22.5 - - + +
381A ASN 3.5 4.1 - - - +
382A LYS* 1.3 77.3 - - + +
384A ASN* 1.3 55.3 + - - +
385A LEU* 2.7 43.0 + - + -
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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
------------------------------------------------------------
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