Contacts of the helix formed by residues 408 - 427 (chain A) in PDB entry 5HI7
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 HIS 408 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A VAL* 3.2 26.9 - - + +
216A PHE 3.0 24.7 + - - -
217A ASN* 3.7 29.5 - - + +
222A LEU* 4.0 11.4 - - + +
404A HIS* 3.7 27.4 - + + +
405A GLY 3.0 12.1 + - - +
406A ARG 3.9 5.0 - - - +
407A GLU* 1.3 78.4 - - - +
409A SER* 1.3 66.9 + - - +
410A LEU* 3.0 43.2 + - + +
411A ILE* 3.1 18.4 + - - +
412A GLU* 4.0 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASN* 3.0 33.6 + - - +
407A GLU 3.9 0.8 + - - -
408A HIS* 1.3 73.6 + - - +
410A LEU* 1.3 64.4 + - - +
412A GLU* 3.0 20.8 + - - +
413A ASP* 3.3 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ALA* 5.8 5.2 - - + -
371A VAL* 4.1 20.6 - - + -
374A MET* 4.0 21.5 - - + -
400A MET* 3.5 27.4 - - + -
404A HIS* 4.2 7.0 - - + +
408A HIS* 3.0 23.3 + - + +
409A SER* 1.3 80.5 + - - +
411A ILE* 1.3 55.9 + - - +
413A ASP* 3.3 18.0 + - + +
414A LEU* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A PHE* 4.2 20.4 - - + -
400A MET* 3.6 38.6 - - + +
401A ARG* 3.9 7.0 - - - +
404A HIS* 4.0 7.0 - - + -
405A GLY 3.2 38.6 - - - +
406A ARG* 4.3 13.0 - - + +
408A HIS 3.1 4.1 + - - +
409A SER 3.1 0.6 - - - -
410A LEU* 1.3 75.3 - - - +
412A GLU* 1.3 59.7 + - - +
414A LEU* 3.2 7.5 + - + +
415A ILE* 2.9 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A HIS 4.0 1.4 + - - +
409A SER* 3.0 15.2 + - - +
411A ILE* 1.3 80.2 - - - +
413A ASP* 1.3 64.9 + - - +
415A ILE* 3.4 11.6 + - - +
416A LEU* 3.2 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A MET* 4.4 9.9 - - + -
409A SER* 3.3 15.8 + - - +
410A LEU* 3.3 22.9 + - + +
411A ILE 3.3 0.2 - - - -
412A GLU* 1.3 79.5 - - - +
414A LEU* 1.3 61.5 + - - +
416A LEU* 3.2 15.7 + - - +
417A LEU* 3.0 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A MET* 3.9 23.1 - - + +
393A LEU* 3.8 42.0 - - + +
396A ALA* 3.8 10.1 - - + +
397A PHE* 3.5 46.7 - - + +
400A MET* 4.2 13.7 - - - -
410A LEU 2.9 16.7 + - - +
411A ILE* 3.6 11.2 - - + +
413A ASP* 1.3 75.2 - - - +
415A ILE* 1.3 59.6 + - - +
417A LEU* 3.1 3.3 + - - +
418A LEU* 2.9 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A PHE* 3.8 24.0 - - + -
411A ILE* 2.9 39.6 + - + +
412A GLU* 3.7 8.7 - - - +
414A LEU* 1.3 75.0 - - - +
416A LEU* 1.3 60.5 + - + +
418A LEU* 3.3 11.4 + - + +
419A GLU* 3.0 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A GLU* 3.2 16.6 + - + +
413A ASP* 3.2 17.7 + - - +
415A ILE* 1.3 80.0 - - + +
417A LEU* 1.3 59.2 + - + +
419A GLU* 3.4 19.4 + - + +
420A GLU* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A MET* 3.8 28.9 - - + -
378A LYS* 3.9 39.5 - - + +
381A LEU* 4.0 19.7 - - + +
382A HIS* 5.3 3.8 - - + +
393A LEU* 3.9 28.6 - - + +
413A ASP* 3.0 16.8 + - + +
414A LEU* 3.1 6.7 + - - +
416A LEU* 1.3 76.3 - - + +
418A LEU* 1.3 59.1 + - - +
420A GLU* 3.3 12.1 + - - +
421A CYS* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A MET* 4.0 17.4 - - + +
393A LEU* 3.5 30.3 - - + +
394A ARG* 3.7 27.6 - - + +
397A PHE* 4.0 38.1 - - + -
414A LEU* 2.9 18.2 + - + +
415A ILE* 3.6 12.6 - - + +
417A LEU* 1.3 76.4 - - - +
419A GLU* 1.3 56.7 + - + +
421A CYS* 3.3 4.7 + - - +
422A ASP* 2.8 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ILE* 3.0 38.4 + - + +
416A LEU* 3.9 18.2 - - + +
418A LEU* 1.3 77.8 - - + +
420A GLU* 1.3 61.3 + - - +
422A ASP* 3.6 6.5 + - - +
423A ALA* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A LEU* 4.0 26.3 - - + +
382A HIS* 4.8 11.5 + - - -
416A LEU 3.0 17.3 + - - +
417A LEU* 3.7 12.5 - - - +
419A GLU* 1.3 74.1 - - - +
421A CYS* 1.3 64.5 + - - +
423A ALA* 3.2 8.0 + - - +
424A ASN* 3.1 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A LEU* 4.0 19.5 - - + +
386A PHE* 3.3 32.3 - - - -
389A ALA* 3.9 12.1 - - - -
390A MET* 3.5 29.4 - - - -
393A LEU* 4.0 6.5 - - + -
417A LEU 2.9 18.6 + - - +
418A LEU 3.8 3.1 - - - +
420A GLU* 1.3 77.1 - - - +
422A ASP* 1.3 63.4 + - - +
424A ASN* 3.2 5.0 + - - +
425A ILE* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A MET* 3.9 22.0 - - + +
418A LEU 2.8 18.5 + - - +
419A GLU* 3.9 7.3 - - - +
421A CYS* 1.3 76.6 - - - +
423A ALA* 1.3 63.0 + - - +
425A ILE* 3.2 8.7 + - - +
426A ARG* 2.9 58.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A GLU 3.1 16.2 + - - +
420A GLU* 3.6 7.9 - - - +
422A ASP* 1.3 76.9 + - - +
424A ASN* 1.3 64.2 + - - +
426A ARG* 3.4 28.6 + - - +
427A ALA* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A LEU* 4.3 3.6 - - - +
386A PHE* 3.5 48.0 - - + -
420A GLU* 3.1 41.2 + - - +
421A CYS 3.6 6.7 - - - +
422A ASP 3.2 0.2 - - - -
423A ALA* 1.3 77.7 - - - +
425A ILE* 1.3 63.9 + - - +
427A ALA* 3.2 14.5 + - - +
428A SER* 3.1 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A PHE* 3.6 30.3 - - + +
387A PRO* 4.2 8.3 - - + -
390A MET* 3.6 37.0 - - + -
421A CYS 3.1 14.9 + - - +
422A ASP* 3.2 9.6 + - - +
424A ASN* 1.3 75.5 - - - +
426A ARG* 1.3 67.3 + - + +
428A SER* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A GLU 5.4 0.2 + - - -
422A ASP* 2.9 44.5 + - - +
423A ALA* 3.4 28.9 + - - +
424A ASN 3.3 0.2 - - - -
425A ILE* 1.3 79.3 - - + +
427A ALA* 1.3 59.6 + - - +
428A SER 3.1 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ALA 3.1 14.3 + - - +
424A ASN* 3.5 13.9 - - - +
425A ILE 3.2 1.0 - - - -
426A ARG* 1.3 75.6 - - - +
428A SER* 1.3 59.4 + - - +
----------------------------------------------------------
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