Contacts of the helix formed by residues 423 - 437 (chain A) in PDB entry 5IXC
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 423 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LEU* 5.3 4.2 - - - +
421A PRO* 4.8 6.5 - - + +
422A THR* 1.3 83.1 - - - +
424A PHE* 1.3 67.2 - - - +
425A VAL* 3.1 16.6 - - - +
426A ASP* 2.4 44.6 + - - +
427A LEU* 3.6 4.5 + - - +
533A LEU* 6.4 1.8 - - + -
601A ARG* 6.1 3.4 - - + +
602A SER* 4.6 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A THR* 1.3 71.9 - - - +
425A VAL* 1.3 59.0 + - - +
427A LEU* 2.9 34.7 + - + -
428A TRP* 2.8 29.9 + - + +
531A PHE* 4.1 35.4 - + + -
532A SER 5.4 1.6 - - - +
535A LEU* 3.2 53.2 - - + -
585A LEU* 5.2 0.4 - - + -
901A 7FA 4.0 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A THR* 3.1 26.4 + - - +
424A PHE* 1.3 77.9 - - - +
426A ASP* 1.3 63.7 + - - +
428A TRP* 3.4 7.2 + - + +
429A ALA 2.9 23.2 + - - -
522A PHE 5.8 0.2 - - - +
525A ALA* 3.3 46.8 - - + +
526A ILE* 4.0 22.0 - - + +
529A ASN* 4.1 23.6 - - + +
531A PHE* 6.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LEU* 4.3 14.6 - - + -
415A ARG* 2.9 35.4 + - - -
421A PRO 4.1 9.4 - - - +
422A THR* 5.0 1.8 - - - -
423A THR* 2.4 41.3 + - - +
425A VAL* 1.3 82.7 - - - +
427A LEU* 1.3 64.0 + - - +
429A ALA* 3.3 19.9 - - - +
430A LEU* 3.4 15.2 + - - +
522A PHE* 3.7 14.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A TYR* 4.3 19.3 - - + -
412A LEU* 4.6 11.6 - - + +
423A THR 3.6 3.4 + - - +
424A PHE* 2.9 35.3 + - + +
426A ASP* 1.3 75.9 - - - +
428A TRP* 1.3 65.5 + - - +
430A LEU* 2.9 18.0 + - + -
431A VAL* 3.0 31.7 + - + +
585A LEU* 4.2 22.7 - - + -
589A PHE* 4.0 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A TRP* 4.6 1.8 - + - -
424A PHE* 2.8 18.7 + - + +
425A VAL* 3.4 10.3 - - + +
427A LEU* 1.3 72.5 - - - +
429A ALA* 1.3 56.1 + - - +
431A VAL* 3.3 38.6 - - + -
432A LEU* 2.9 67.8 + - + +
435A MET* 4.7 4.9 - - - -
525A ALA* 3.6 33.5 + - + +
528A SER 3.4 28.8 + - - -
529A ASN* 3.8 12.0 - - - +
530A ILE* 5.1 2.5 - - + -
531A PHE* 3.7 34.1 - + + -
771A MET* 5.3 0.2 - - - -
901A 7FA 3.9 50.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A VAL 2.9 13.9 + - - +
426A ASP 3.3 12.1 - - - +
428A TRP* 1.3 76.5 - - - +
430A LEU* 1.3 56.4 + - - +
432A LEU* 3.9 2.4 - - - +
433A GLU* 3.0 29.6 + - - +
521A CYS* 3.4 27.6 - - - +
522A PHE* 3.4 26.9 - - + -
525A ALA* 3.6 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A TYR* 3.5 50.6 - - + +
411A GLU* 3.8 16.8 - - + +
412A LEU* 3.6 31.6 - - + -
426A ASP 3.5 8.7 - - - +
427A LEU* 2.9 9.4 + - - +
429A ALA* 1.3 74.5 - - - +
431A VAL* 1.3 64.5 + - - +
433A GLU* 3.3 8.2 + - - +
434A SER* 3.0 23.0 + - - -
519A ARG* 3.4 29.8 - - - +
522A PHE* 3.9 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A VAL* 4.2 11.4 - - + -
400A PHE* 4.9 14.4 - - + -
408A TYR* 4.0 19.1 - - + -
424A PHE* 6.4 0.2 - - + -
427A LEU* 3.0 33.0 + - + +
428A TRP* 3.3 35.7 - - + +
430A LEU* 1.3 75.5 - - - +
432A LEU* 1.3 62.8 + - - +
434A SER* 3.1 3.6 + - - -
435A MET* 2.8 40.2 + - - +
585A LEU* 5.0 6.3 - - + -
901A 7FA 4.8 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A TRP* 3.7 51.4 - - + +
428A TRP* 2.9 46.6 + - + +
429A ALA 3.9 2.9 - - - +
431A VAL* 1.3 78.8 - - - +
433A GLU* 1.3 57.7 + - - +
435A MET* 3.2 8.9 + - + +
436A LEU* 3.0 48.3 + - + +
521A CYS* 5.2 1.8 - - + +
524A GLU* 4.2 21.5 - - + +
525A ALA* 4.6 1.8 - - - +
528A SER* 3.9 9.4 - - - +
771A MET* 4.8 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ALA 3.0 18.7 + - - +
430A LEU* 3.5 9.5 - - - +
431A VAL 3.2 0.2 - - - -
432A LEU* 1.3 77.4 - - - +
434A SER* 1.3 55.8 + - - +
436A LEU* 4.6 1.3 - - - -
437A HIS* 2.8 51.4 + - + +
439A GLN 3.8 10.1 - - - +
440A VAL* 3.6 10.1 + - - -
441A MET* 2.8 25.4 + - + +
519A ARG* 2.8 41.7 + - - -
521A CYS* 3.5 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LYS* 4.9 8.3 - - - -
399A VAL* 3.4 13.2 - - - +
404A ARG* 3.7 21.8 + - - -
408A TYR* 3.0 31.0 + - - -
430A LEU 3.0 8.3 + - - -
431A VAL 3.4 5.8 - - - -
433A GLU* 1.3 77.9 - - - +
435A MET* 1.3 55.3 + - - +
437A HIS 2.3 23.6 - - - +
438A GLY* 4.5 3.3 + - - -
439A GLN* 4.9 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A HIS* 4.0 8.0 - - - +
392A LEU* 5.5 1.2 - - - +
394A LYS* 6.0 1.0 - - - +
396A LYS* 3.6 53.0 + - + -
399A VAL* 4.1 17.3 - - + -
400A PHE* 5.5 4.5 - - + -
428A TRP* 4.7 9.6 - - - -
431A VAL* 2.8 37.2 + - - +
432A LEU* 3.7 10.1 - - + +
434A SER* 1.3 72.9 - - - +
436A LEU* 1.3 61.9 + - - +
437A HIS 4.1 0.6 - - - +
771A MET* 3.2 52.0 - - + +
901A 7FA 4.8 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A MET* 4.1 20.0 - - + -
365A TRP* 4.1 40.2 - - + +
387A TYR* 3.7 5.0 - - - -
388A ALA* 6.0 0.2 - - - -
391A HIS* 3.6 20.3 - - - +
392A LEU* 6.1 0.7 - - + -
432A LEU* 3.0 32.3 + - + +
433A GLU* 5.5 0.9 - - - -
435A MET* 1.3 80.5 - - - +
437A HIS* 1.3 89.4 + - + +
524A GLU* 3.6 25.6 - - - +
771A MET* 4.9 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A HIS* 3.8 28.3 - + + -
387A TYR* 2.7 26.8 + + - +
391A HIS* 3.7 13.6 - - - -
394A LYS* 5.1 1.6 - - - -
433A GLU* 2.8 26.2 + - + +
434A SER 2.3 32.9 - - - +
435A MET 4.1 0.3 - - - -
436A LEU* 1.3 103.7 + - + +
438A GLY* 1.3 58.2 + - - +
439A GLN* 3.2 17.7 - - + +
441A MET* 3.3 31.7 - - + +
520A ILE* 6.3 0.6 - - - +
521A CYS* 6.1 0.4 - - + -
524A GLU* 5.1 7.0 + - - -
----------------------------------------------------------
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