Contacts of the helix formed by residues 358 - 375 (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 CYS 358 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PRO* 3.3 20.9 - - - -
296A SER 4.5 0.7 - - - -
297A SER* 3.2 28.9 - - - -
300A LEU* 3.7 14.5 - - + +
347A TRP* 3.5 47.1 - - + +
350A GLN* 5.8 0.7 - - + -
357A ASN* 1.3 76.6 - - - +
359A SER* 1.3 55.4 + - - +
361A LEU* 3.2 1.8 + - - -
362A ALA* 2.7 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A TRP 2.6 29.9 + - - -
348A LEU* 3.5 9.1 - - - +
350A GLN* 4.1 5.4 + - - +
351A PRO 5.3 0.2 + - - -
357A ASN 3.4 0.8 + - - +
358A CYS* 1.3 78.2 - - - +
360A VAL* 1.3 57.3 + - - +
363A LEU* 3.1 36.4 + - - +
396A GLN* 5.1 0.4 - - - -
411A LYS* 5.0 2.6 + - - -
415A ARG* 3.1 48.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ASN* 3.4 15.2 + - - +
358A CYS 3.3 0.4 - - - -
359A SER* 1.3 74.6 - - - +
361A LEU* 1.3 58.9 + - + +
363A LEU* 3.4 9.7 + - - +
364A GLU* 2.9 43.9 + - - +
411A LYS* 4.0 25.8 - - + +
414A GLU* 4.1 26.0 - - + +
415A ARG* 4.3 23.3 - - + +
418A LYS* 3.7 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A SER* 3.6 35.4 - - - +
300A LEU* 3.8 16.3 - - + +
301A GLU* 4.0 18.8 - - + -
304A LEU* 3.4 27.6 - - + +
357A ASN* 3.3 38.1 + - - +
358A CYS* 3.2 6.4 + - - +
360A VAL* 1.3 74.9 - - + +
362A ALA* 1.3 59.0 + - - +
364A GLU* 3.4 14.1 + - - +
365A LEU* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LEU* 4.3 7.3 - - + +
344A LEU* 3.9 28.9 - - + +
347A TRP* 4.2 6.7 - - + -
348A LEU* 3.7 20.0 - - + -
358A CYS 2.7 21.2 + - - +
361A LEU* 1.3 70.8 - - - +
363A LEU* 1.3 59.9 + - - +
365A LEU* 3.2 8.8 + - - +
366A PHE* 3.0 35.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 3.6 28.7 - - + +
359A SER 3.1 23.4 + - - +
360A VAL* 3.7 4.3 - - - +
361A LEU 3.4 0.2 - - - -
362A ALA* 1.3 74.6 - - - +
364A GLU* 1.3 63.3 + - - +
366A PHE* 3.4 5.9 + - + -
367A LYS* 3.2 18.7 + - - +
393A ILE* 4.5 9.9 - - + -
396A GLN* 4.7 9.4 - - + +
415A ARG* 3.3 40.2 - - + +
418A LYS* 3.7 16.4 - - + -
419A ALA* 3.8 26.2 - - + +
422A VAL* 3.2 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 3.7 22.7 - - + +
360A VAL* 2.9 35.2 + - - +
361A LEU* 3.5 17.5 - - - +
362A ALA 3.3 0.2 - - - -
363A LEU* 1.3 73.9 - - - +
365A LEU* 1.3 62.3 + - - +
367A LYS* 3.3 11.9 + - + +
368A GLU* 3.1 24.9 + - - +
418A LYS* 3.6 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LEU* 3.7 31.4 - - + +
303A LEU* 3.8 26.7 - - + +
304A LEU* 3.6 15.7 - - + +
307A CYS* 3.7 28.7 - - - -
316A LEU* 4.0 15.3 - - + -
320A MET* 5.3 3.4 - - + -
344A LEU* 4.0 19.5 - - + -
361A LEU 2.9 11.2 + - - +
362A ALA* 3.2 9.2 + - - +
364A GLU* 1.3 74.3 - - - +
366A PHE* 1.3 64.4 + - - +
368A GLU* 3.1 4.6 + - - +
369A ILE* 3.0 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A THR* 4.3 7.4 - - + -
344A LEU* 3.5 45.8 - - + -
345A LEU* 4.4 1.6 - - + -
348A LEU* 4.2 17.0 - - + -
362A ALA 3.0 28.7 + - - -
363A LEU* 3.7 11.9 - - + +
364A GLU 3.4 0.2 - - - -
365A LEU* 1.3 74.0 - - - +
367A LYS* 1.3 63.4 + - - +
368A GLU 3.3 0.2 + - - -
369A ILE* 3.4 18.1 - - + +
370A PHE* 3.0 49.9 + + + -
385A PHE* 3.5 26.7 - + - -
389A LEU* 4.0 25.4 - - + -
393A ILE* 5.1 0.7 - - + -
422A VAL* 4.1 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A LEU 3.2 12.8 + - - +
364A GLU* 3.4 14.4 - - + +
366A PHE* 1.3 76.3 - - - +
368A GLU* 1.3 64.7 + - - +
370A PHE* 4.2 0.3 - - - +
371A GLU* 2.9 51.8 + - - +
418A LYS* 6.4 0.4 - - + -
421A GLU* 3.0 41.9 + - + +
422A VAL* 3.9 11.7 - - + +
425A THR* 3.6 30.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 4.1 12.7 - - + +
307A CYS* 3.6 37.6 - - + +
313A ARG* 3.3 35.8 + - - -
364A GLU* 3.1 14.1 + - - +
365A LEU 3.1 7.9 + - - +
367A LYS* 1.3 85.2 - - - +
369A ILE* 1.3 58.6 + - - +
371A GLU* 3.3 10.9 + - - +
372A ASP* 2.8 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A CYS* 5.0 1.8 - - - -
313A ARG* 5.3 0.2 - - - -
316A LEU* 4.5 10.3 - - + -
317A THR* 3.4 31.5 - - + +
320A MET* 3.9 35.9 - - + -
321A PHE* 3.5 28.7 - - + -
344A LEU* 5.1 1.3 - - + -
365A LEU* 3.0 21.6 + - + +
366A PHE* 3.4 34.1 - - + +
368A GLU* 1.3 76.7 - - + +
370A PHE* 1.3 62.1 + - + +
372A ASP 3.3 0.5 + - - -
373A VAL* 2.9 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PHE* 4.1 17.5 - + - -
366A PHE* 3.0 40.6 + + + +
369A ILE* 1.3 74.6 - - + +
371A GLU* 1.3 66.4 + - - +
372A ASP 3.2 0.2 - - - -
373A VAL* 3.8 5.1 - - + +
374A ILE* 3.0 34.7 + - + +
382A ALA* 4.1 13.0 - - + -
385A PHE* 3.7 17.0 - + - -
386A VAL* 3.5 27.1 - - + -
389A LEU* 3.3 34.8 - - + -
422A VAL* 4.3 5.6 - - + -
425A THR* 4.0 7.4 - - - +
426A LEU* 3.4 32.3 - - + -
432A LEU* 5.2 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ARG* 3.2 23.6 + - - +
367A LYS* 2.9 43.8 + - - +
368A GLU* 3.5 11.7 - - - +
370A PHE* 1.3 76.6 - - - +
372A ASP* 1.3 59.9 + - - +
374A ILE* 4.3 4.4 - - - +
375A ASP* 3.3 27.2 + - - +
425A THR* 4.3 16.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A THR* 4.4 0.5 - - - +
313A ARG* 3.1 37.5 + - - +
314A HIS* 2.9 44.8 + - - +
317A THR* 3.2 38.2 + - - +
368A GLU 2.8 8.4 + - - +
369A ILE 3.4 3.4 - - - +
370A PHE 3.2 0.2 - - - -
371A GLU* 1.3 73.9 - - - +
373A VAL* 1.3 68.3 + - - +
375A ASP* 3.2 12.1 + - - +
376A ALA* 3.4 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A THR* 3.3 26.2 - - + -
321A PHE* 3.5 24.9 - - + -
369A ILE 2.9 16.7 + - - +
370A PHE* 3.8 9.4 - - + +
372A ASP* 1.3 71.9 - - - +
374A ILE* 1.3 65.9 + - + +
376A ALA* 3.1 11.6 + - - +
377A ALA 2.6 23.2 - - - +
378A ASN* 3.5 26.0 - - + +
379A CYS* 3.9 14.6 - - - -
381A SER* 6.3 0.4 - - - -
382A ALA* 4.2 12.8 - - + +
432A LEU* 5.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A PHE* 3.0 28.4 + - + +
371A GLU* 4.3 4.0 - - - +
373A VAL* 1.3 79.2 - - + +
375A ASP* 1.3 57.8 + - - +
376A ALA 3.3 3.6 + - - -
377A ALA* 3.9 7.4 + - - +
379A CYS* 4.1 15.5 - - - -
425A THR* 3.1 32.8 - - - +
426A LEU* 4.2 9.2 - - - -
428A GLY* 4.3 21.5 - - - +
429A ASP* 4.3 17.5 - - + +
432A LEU* 4.3 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ARG* 4.9 9.0 + - - +
314A HIS* 5.8 3.1 - - + -
371A GLU* 3.3 19.8 + - - +
372A ASP* 3.2 7.8 + - - +
374A ILE* 1.3 77.5 - - + +
376A ALA* 1.3 60.2 + - - +
377A ALA 3.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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