Contacts of the helix formed by residues 453 - 469 (chain A) in PDB entry 4I28
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 SER 453 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ARG* 3.5 28.0 - - - +
452A GLY* 1.3 74.3 + - - -
454A ARG* 1.3 67.0 + - - +
456A PHE* 3.1 8.1 + - - +
457A GLU* 3.0 19.4 + - - +
508A ARG 3.1 22.4 + - - -
509A ASN* 4.6 1.6 - - - -
510A ALA 2.5 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A GLU* 3.9 21.6 + - - -
192A MET* 4.0 14.9 - - - -
452A GLY* 4.2 0.4 - - - -
453A SER* 1.3 73.5 - - - +
455A GLN* 1.3 59.6 + - + +
457A GLU* 3.4 8.1 + - - +
458A ARG* 3.0 68.1 + - - +
4C A 5.4 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ALA* 4.4 0.2 - - - -
157A ARG* 5.5 0.2 - - - +
189A LEU* 5.3 1.4 - - - +
192A MET* 4.2 13.5 - - - +
193A ARG* 3.8 34.2 - - - +
196A SER* 3.4 28.1 - - - +
453A SER* 3.2 1.4 + - - -
454A ARG* 1.3 77.4 - - + +
456A PHE* 1.3 67.3 + - - +
458A ARG* 2.6 44.5 + - - +
459A ASP* 3.0 45.5 + - - +
510A ALA* 3.3 20.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ALA* 3.4 35.0 - - + -
155A CYS* 3.5 16.2 - - + +
157A ARG 4.6 0.9 - - - -
159A THR* 6.1 0.2 - - - -
448A LEU* 4.9 0.9 - - + -
452A GLY 3.9 0.4 - - - -
453A SER* 3.1 24.1 + - - +
455A GLN* 1.3 79.5 - - - +
457A GLU* 1.4 69.5 + - - +
459A ASP* 3.4 1.7 + - - +
460A LEU* 3.0 47.1 + - + +
495A PHE* 3.8 21.5 - + - -
503A ILE* 3.9 16.2 - - + -
507A GLU 4.9 0.4 - - - -
508A ARG* 3.6 54.3 - - + +
510A ALA* 4.0 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A LEU* 2.9 31.9 - - - +
449A GLY* 3.3 27.3 - - - +
452A GLY* 3.3 23.4 - - - +
453A SER 3.0 15.4 + - - +
454A ARG* 3.6 9.4 - - - +
456A PHE* 1.4 79.6 - - - +
458A ARG* 1.4 66.3 + - - +
460A LEU* 3.4 17.2 - - - +
461A ARG* 3.2 33.8 + - + +
474A ASN* 5.0 1.9 + - - +
508A ARG* 5.3 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 4.9 12.5 - - - +
192A MET* 3.5 30.2 - - - +
193A ARG* 6.2 0.2 - - - +
454A ARG* 3.0 57.3 + - - +
455A GLN* 2.6 40.2 + - - +
457A GLU* 1.4 76.8 - - - +
459A ASP* 1.4 60.9 + - - +
461A ARG* 3.5 7.0 + - - +
462A ARG* 3.1 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLN 3.8 2.9 - - - +
153A TYR* 3.6 6.9 - - + -
154A ALA* 2.7 43.8 + - + +
155A CYS* 3.8 6.1 - - - +
157A ARG* 4.2 2.6 + - - -
193A ARG* 4.6 2.4 + - - -
455A GLN* 3.0 37.2 + - - +
456A PHE 4.1 1.1 - - - +
458A ARG* 1.4 75.1 - - - +
460A LEU* 1.3 56.1 + - - +
462A ARG* 3.0 36.0 + - - +
463A TYR* 2.8 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A CYS* 3.7 22.3 - - + -
448A LEU* 3.9 23.8 - - + -
456A PHE* 3.0 41.5 + - + +
457A GLU* 3.4 30.5 - - - +
459A ASP* 1.3 74.2 - - - +
461A ARG* 1.4 58.2 + - + +
463A TYR* 3.7 2.9 - - - +
464A ALA* 2.9 29.5 + - - +
472A LEU* 4.2 12.3 - - + +
495A PHE* 4.6 9.2 - - + -
498A LEU* 4.2 15.0 - - + +
500A LEU* 4.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A SER* 3.2 32.7 + - - -
457A GLU* 3.2 20.8 + - + +
458A ARG* 3.9 7.4 - - - +
460A LEU* 1.4 77.9 - - + +
462A ARG* 1.4 60.0 + - - +
464A ALA* 3.5 6.5 + - - +
465A THR* 2.9 33.9 + - - -
472A LEU* 3.1 43.7 + - + +
473A ASP* 4.2 12.9 - - - +
474A ASN* 5.9 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLN* 3.3 40.8 + - - +
153A TYR* 3.5 25.3 + - + +
193A ARG* 3.8 43.7 - - - +
458A ARG 3.1 16.2 + - - +
459A ASP* 3.0 29.3 + - - +
461A ARG* 1.4 74.5 - - - +
463A TYR* 1.3 59.8 + - - +
465A THR* 3.3 2.0 + - - -
466A HIS* 2.9 57.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A TYR* 3.6 28.4 - + + -
155A CYS* 3.6 14.1 - - - -
156A GLN* 3.6 30.4 + - - -
459A ASP 2.8 21.1 + - - +
460A LEU 3.7 2.9 - - - +
462A ARG* 1.3 72.8 - - - +
464A ALA* 1.3 59.7 + - - +
467A GLU* 2.8 60.2 + - + +
468A ARG* 3.5 17.0 + - + -
498A LEU* 3.4 29.9 + - + -
499A GLY* 4.2 7.1 + - - -
500A LEU* 3.6 29.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LEU 2.9 19.9 + - - +
461A ARG 3.7 4.9 - - - +
463A TYR* 1.3 75.9 - - - +
465A THR* 1.4 53.0 + - - +
468A ARG* 3.3 8.0 + - - +
469A LYS 3.0 9.9 + - - -
470A MET* 2.7 39.6 + - + +
472A LEU* 4.1 19.1 - - + +
498A LEU* 3.6 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ARG 2.9 18.7 + - - -
462A ARG* 3.7 4.2 - - - -
463A TYR 3.3 0.2 - - - -
464A ALA* 1.4 74.5 - - - +
466A HIS* 1.3 81.4 + - + +
469A LYS* 3.2 26.0 + - - +
470A MET 3.4 13.3 + - - +
471A MET* 5.1 5.1 - - + +
472A LEU 5.5 0.5 + - - -
480A ARG* 5.6 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 466 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A TYR* 3.9 13.5 - - - +
462A ARG* 2.9 48.7 + - + +
465A THR* 1.3 92.0 - - + +
467A GLU* 1.4 64.2 - - - +
469A LYS* 5.2 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLN* 5.1 2.4 - - - +
153A TYR* 2.7 34.6 + - + +
463A TYR* 2.8 57.6 + - + +
466A HIS* 1.4 78.9 - - - +
468A ARG* 1.3 62.3 + - - +
469A LYS* 3.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A TYR* 3.5 24.9 + - + -
464A ALA* 3.3 13.4 + - - +
467A GLU* 1.3 81.9 - - - +
469A LYS* 1.4 72.9 + - - +
470A MET* 3.2 35.4 + - + +
479A ASP* 5.1 1.7 - - - +
481A THR* 5.0 2.6 + - - -
496A ALA 4.6 1.4 + - - -
497A HIS 2.8 25.2 + - - -
498A LEU* 2.8 35.4 + - - +
499A GLY* 3.6 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ALA 3.0 2.4 + - - -
465A THR 3.2 17.2 + - - +
466A HIS 5.6 4.0 - - - +
467A GLU 5.6 1.1 - - - -
468A ARG* 1.4 78.4 - - - +
470A MET* 1.3 59.1 - - - +
479A ASP* 4.5 0.3 - - - +
480A ARG* 3.2 51.8 + - + +
481A THR* 4.2 20.3 + - - +
----------------------------------------------------------
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