Contacts of the helix formed by residues 473 - 492 (chain A) in PDB entry 4FLZ
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 ASP 473 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A SER* 3.4 6.1 + - - +
472A LYS* 1.4 74.8 - - - +
474A PRO* 1.4 67.7 - - - +
475A VAL* 3.2 22.8 + - - +
476A GLU* 3.5 38.0 + - + +
477A LYS* 3.2 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A LYS 3.5 10.1 - - - +
473A ASP* 1.4 87.6 - - - +
475A VAL* 1.4 62.1 + - + +
477A LYS* 3.8 9.3 - - + +
478A LYS* 3.3 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A ASP* 3.2 14.6 + - - +
474A PRO* 1.4 77.5 - - + +
476A GLU* 1.4 64.5 + - - +
478A LYS* 3.3 8.7 + - - +
479A LEU* 3.3 19.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ARG* 5.2 2.9 - - - +
471A SER* 3.2 30.3 + - - +
473A ASP* 3.5 26.7 + - - +
475A VAL* 1.4 76.3 - - - +
477A LYS* 1.4 55.6 + - - +
479A LEU* 3.2 10.6 + - + +
480A LEU* 2.7 61.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A MET* 3.8 20.9 - - + +
471A SER* 5.0 11.0 - - - +
473A ASP 3.2 18.2 + - - +
474A PRO* 3.8 10.3 - - + +
476A GLU* 1.4 79.4 - - - +
478A LYS* 1.4 54.4 + - - +
480A LEU* 3.9 7.7 - - - +
481A ASP* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A PRO 3.3 12.8 + - - +
475A VAL* 3.4 11.0 - - - +
476A GLU 3.2 0.2 - - - -
477A LYS* 1.4 75.1 - - - +
479A LEU* 1.3 64.2 + - - +
481A ASP* 3.3 15.5 + - - +
482A TYR* 3.3 29.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A GLN* 3.6 32.5 - - + +
475A VAL* 3.3 10.3 + - + +
476A GLU* 3.2 13.3 + - + +
478A LYS* 1.3 77.3 - - - +
480A LEU* 1.4 69.6 + - + +
482A TYR* 3.2 14.2 + - + +
483A ARG* 3.2 53.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ILE* 3.3 27.6 - - + +
467A ARG* 4.2 33.4 - - + +
468A MET* 3.7 30.3 - - + +
471A SER* 5.3 0.4 - - - -
476A GLU* 2.7 51.9 + - + +
477A LYS* 4.0 1.3 - - - +
479A LEU* 1.4 75.5 - - + +
481A ASP* 1.3 60.0 + - - +
483A ARG* 3.2 18.5 + - - +
484A GLN* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A MET* 3.8 21.5 - - + +
477A LYS 3.0 19.5 + - - +
478A LYS* 3.5 9.0 - - - +
479A LEU 3.2 0.4 - - - -
480A LEU* 1.3 75.9 - - - +
482A TYR* 1.4 60.0 + - + +
484A GLN* 3.1 23.4 + - - +
485A ARG* 3.1 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A GLU 4.8 7.2 + - - -
328A PRO* 3.5 38.6 - - + +
329A MET* 3.5 23.7 - - + +
332A GLN* 3.8 17.9 - - + +
478A LYS* 3.3 28.5 + - + -
479A LEU* 3.2 16.0 + - + +
481A ASP* 1.4 79.1 - - - +
483A ARG* 1.3 58.4 + - - +
485A ARG* 3.8 26.9 - - - -
486A ALA* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A MET 5.2 1.0 + - - -
131A GLY* 4.8 16.0 + - - +
332A GLN* 3.0 27.5 + - + +
335A ARG* 3.2 48.3 - - - +
464A ILE* 4.1 17.3 - - + -
479A LEU* 3.2 41.0 + - - +
480A LEU* 3.2 23.8 + - - +
482A TYR* 1.3 74.1 - - - +
484A GLN* 1.4 62.7 + - - +
486A ALA* 3.4 7.1 + - - +
487A ILE* 3.2 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ARG* 2.8 73.0 + - + +
464A ILE* 3.8 21.0 - - + +
465A LYS* 3.5 17.4 - - + +
468A MET* 4.2 12.7 - - - +
480A LEU 3.0 12.2 + - - +
481A ASP* 3.1 37.0 + - - +
483A ARG* 1.4 72.6 - - - +
485A ARG* 1.4 71.0 + - - +
487A ILE* 3.4 1.6 + - - -
488A LYS 3.1 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A THR* 6.0 3.8 - - - +
329A MET* 3.7 26.8 - - + +
481A ASP* 3.1 41.7 + - - +
482A TYR* 3.8 32.3 - - - +
483A ARG 3.3 0.2 - - - -
484A GLN* 1.4 88.7 - - - +
486A ALA* 1.4 59.7 + - - +
488A LYS* 3.1 10.9 + - + +
489A ILE* 2.9 42.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A MET* 4.0 17.2 - - + -
332A GLN* 4.0 22.7 - - + +
333A LEU* 3.8 14.3 - - + +
336A LEU* 3.4 18.3 - - + +
482A TYR 3.0 18.8 + - - +
483A ARG* 3.6 6.1 - - - +
484A GLN 3.4 0.4 - - - -
485A ARG* 1.4 74.3 - - - +
487A ILE* 1.4 61.5 + - - +
489A ILE* 3.4 4.4 + - - +
490A LEU* 3.1 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A LEU* 3.9 26.2 - - + -
457A LEU* 3.4 37.2 - - + +
458A LEU* 4.8 1.3 - - + +
460A GLU* 3.9 20.2 - - + -
461A ARG* 3.8 22.2 - - + +
464A ILE* 3.5 32.1 - - + -
483A ARG* 3.2 11.3 + - + +
484A GLN 3.7 6.3 - - - +
485A ARG 3.3 0.4 - - - -
486A ALA* 1.4 72.9 - - - +
488A LYS* 1.4 55.6 + - - +
490A LEU* 3.2 2.5 + - - +
491A ALA* 2.7 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A SER* 3.8 16.1 + - - +
461A ARG* 3.6 36.9 - - - +
484A GLN 3.1 14.2 + - - +
485A ARG* 3.1 12.8 + - + +
487A ILE* 1.4 74.7 - - - +
489A ILE* 1.3 64.3 + - + +
491A ALA* 4.6 4.3 - - - -
492A ASN* 3.0 43.9 + - - +
576A GLU* 5.2 4.6 + - - -
578A GLU* 2.8 38.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ARG* 5.5 3.8 - - - +
329A MET* 3.4 33.7 - - + -
333A LEU* 4.2 19.7 - - + -
349A THR* 4.4 20.9 - - + -
352A LEU* 5.7 1.3 - - + -
485A ARG* 2.9 25.4 + - + +
486A ALA* 3.7 6.1 - - - +
487A ILE 3.3 0.2 - - - -
488A LYS* 1.3 78.8 - - + +
490A LEU* 1.3 56.1 + - - +
492A ASN* 3.6 4.2 + - - +
493A SER* 2.6 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LEU* 5.1 3.6 - - + -
336A LEU* 3.7 23.1 - - + -
337A VAL* 4.3 10.5 - - + -
352A LEU* 4.2 12.1 - - + -
353A VAL* 3.9 35.7 - - + +
356A PHE* 3.7 32.5 - - + -
457A LEU* 4.0 16.6 - - + -
486A ALA 3.1 16.7 + - - +
487A ILE* 3.8 3.1 - - - +
489A ILE* 1.3 77.5 - - - +
491A ALA* 1.4 61.9 - - - +
493A SER* 3.1 17.4 + - - -
494A TYR* 3.1 22.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A PRO* 3.6 16.5 - - + +
414A ILE* 5.8 0.2 - - - +
454A LEU* 3.8 19.7 - - + +
457A LEU* 4.7 5.8 - - + +
458A LEU* 4.0 21.3 - - + -
487A ILE* 2.7 24.3 + - + +
488A LYS* 4.1 4.5 - - - +
490A LEU* 1.4 70.4 - - - +
492A ASN* 1.4 61.2 + - - +
493A SER 3.2 4.6 + - - -
494A TYR* 3.4 27.2 + - - +
495A TYR 4.8 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ARG* 3.7 40.5 - - + +
408A SER* 3.2 26.8 + - - -
410A TYR* 6.5 0.2 - - - -
411A PRO* 3.5 20.8 - - - +
488A LYS* 3.0 34.3 + - - +
489A ILE* 4.0 3.4 - - - +
490A LEU 3.3 0.2 - - - -
491A ALA* 1.4 75.3 - - - +
493A SER* 1.4 58.6 + - - +
494A TYR 3.5 0.4 - - - -
495A TYR* 4.6 10.0 + - - +
496A GLY 5.0 1.4 + - - -
----------------------------------------------------------
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