Contacts of the helix formed by residues 450 - 464 (chain A) in PDB entry 3OOY
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 450 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ILE 6.0 0.4 - - - -
317A THR* 3.8 6.7 - - - +
448A PRO 3.5 0.2 - - - -
449A SER* 1.3 77.1 - - - +
451A GLY* 1.3 73.9 + - - +
452A VAL* 2.8 15.5 + - - -
453A ALA* 3.8 6.5 - - + +
454A THR* 2.6 36.5 + - - -
478A ALA 4.4 4.5 - - - -
479A ILE* 2.8 19.0 - - - +
480A ILE* 2.7 35.0 + - + -
481A TYR* 2.9 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A TYR* 3.4 18.6 - - - -
315A ILE* 4.1 10.7 + - - +
317A THR* 4.4 1.8 - - - +
320A ALA* 3.6 24.7 - - - +
450A ASP* 1.3 81.1 + - - +
452A VAL* 1.3 55.2 + - - -
454A THR* 3.5 2.3 + - - -
455A GLU* 3.1 22.5 + - - +
479A ILE* 3.6 13.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A PRO* 4.3 15.2 - - + +
309A TYR* 3.9 13.0 - - + -
450A ASP* 2.8 18.1 + - - +
451A GLY* 1.3 70.4 - - - +
453A ALA* 1.3 62.9 + - - +
455A GLU* 3.2 5.3 + - - +
456A LYS* 3.1 26.1 + - + +
479A ILE* 3.9 9.2 - - + -
481A TYR* 3.5 33.4 - - + +
482A ASN 3.7 18.2 - - - +
483A ASN* 3.6 22.7 - - - +
485A GLU* 5.0 1.3 - - + +
487A PHE* 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A PRO* 3.7 3.1 - - + -
449A SER 4.0 17.3 - - - +
450A ASP* 3.6 18.3 + - + +
451A GLY 3.5 0.4 - - - -
452A VAL* 1.3 78.3 - - - +
454A THR* 1.3 56.8 + - - +
456A LYS* 3.4 1.6 + - - -
457A ALA* 2.9 24.6 + - - +
481A TYR* 4.2 4.9 - - + -
487A PHE* 3.9 31.6 - - + -
533A ASP* 5.2 0.7 - - - +
535A PHE* 3.3 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A THR* 3.3 26.1 - - - +
320A ALA* 3.8 5.4 - - - -
321A TYR* 3.4 41.3 - - + +
448A PRO* 3.4 19.0 - - + +
450A ASP 2.6 23.1 + - - -
451A GLY 3.5 6.3 - - - -
452A VAL 3.2 0.2 - - - -
453A ALA* 1.3 73.4 - - - +
455A GLU* 1.3 65.4 + - - +
457A ALA* 3.2 2.8 + - - +
458A VAL* 3.0 25.7 + - + +
470A ILE* 5.1 2.0 - - + -
472A THR* 4.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A MET* 3.7 24.8 - - + +
305A SER 4.0 2.8 - - - +
306A LEU 3.8 0.5 - - - -
307A PRO* 3.3 31.8 - - + +
308A SER 4.8 0.7 + - - -
309A TYR* 3.6 21.9 + - + +
320A ALA 5.3 0.2 + - - -
324A ALA* 3.7 19.9 - - + +
327A LYS* 2.8 39.3 + - - +
451A GLY 3.1 13.5 + - - +
452A VAL 3.2 8.2 + - - +
454A THR* 1.3 75.8 - - - +
456A LYS* 1.3 64.0 + - + +
458A VAL* 3.3 4.2 + - - +
459A GLU* 3.2 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A MET* 6.4 0.4 - - + -
306A LEU* 4.6 15.2 - - - +
307A PRO* 4.5 21.2 - - + +
452A VAL* 3.1 20.7 + - + +
453A ALA 3.8 4.5 - - - +
455A GLU* 1.3 77.7 - - + +
457A ALA* 1.3 63.8 + - - +
459A GLU* 3.4 22.1 + - - +
460A LEU* 3.0 30.9 + - + +
483A ASN 4.6 3.4 - - - -
484A ASN 5.9 0.2 - - - -
485A GLU 3.4 23.9 + - - -
486A ASP* 5.3 4.8 + - - +
487A PHE* 3.7 38.4 - - + +
535A PHE* 4.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A PHE* 3.7 40.9 - - + -
448A PRO* 4.6 3.1 - - + -
453A ALA 2.9 18.4 + - - +
454A THR* 3.2 8.2 + - - +
456A LYS* 1.3 72.1 - - - +
458A VAL* 1.3 60.9 - - - +
460A LEU* 3.8 0.7 - - - +
461A ALA* 2.9 32.7 + - - +
470A ILE* 4.1 13.7 - - + -
535A PHE* 4.0 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A MET* 4.0 14.1 - - + -
321A TYR* 3.7 29.2 - - + +
324A ALA* 4.0 13.7 - - + -
325A LEU* 4.3 18.4 - - + +
328A LEU* 4.1 10.8 - - + -
385A PHE* 3.7 20.2 - - + -
454A THR* 3.0 18.1 + - + +
455A GLU 3.6 7.0 - - - +
456A LYS 3.3 0.2 - - - -
457A ALA* 1.3 77.5 - - - +
459A GLU* 1.3 62.2 + - - +
461A ALA* 3.7 0.2 - - - +
462A ALA* 3.2 19.2 + - - +
470A ILE* 3.8 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ILE 4.0 13.9 - - - +
302A ARG* 3.4 15.3 - - - +
303A MET* 2.7 51.2 + - + +
328A LEU* 4.5 6.7 - - + -
455A GLU 3.2 13.4 + - - +
456A LYS* 3.8 28.8 + - - +
457A ALA 3.3 0.2 - - - -
458A VAL* 1.3 77.1 - - - +
460A LEU* 1.3 62.6 + - - +
462A ALA* 3.3 8.5 + - - +
463A ASN* 3.0 25.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
446A PHE* 4.0 12.3 - - + -
456A LYS* 3.0 22.1 + - + +
457A ALA 3.9 2.2 - - - +
459A GLU* 1.3 78.6 - - + +
461A ALA* 1.3 56.6 + - - +
463A ASN* 3.0 9.2 + - + +
464A THR* 2.8 35.0 + - - +
487A PHE* 3.8 20.4 - - + +
488A GLN* 4.1 24.5 - - - +
489A VAL* 4.1 15.0 - - + +
535A PHE* 3.8 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A PHE* 4.4 2.2 - - + -
411A ASN* 2.8 32.3 + - + +
446A PHE* 3.9 9.1 - - + -
457A ALA 2.9 19.8 + - - +
458A VAL 3.7 4.3 - - - +
460A LEU* 1.3 75.8 - - - +
462A ALA* 1.3 62.1 + - - +
463A ASN 3.3 0.3 + - - -
464A THR 3.4 15.2 + - - +
468A CYS* 3.8 25.3 - - + -
470A ILE* 4.3 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ILE* 5.1 6.4 - - + +
328A LEU* 3.8 22.2 - - + -
335A ILE* 4.5 2.9 - - + -
383A VAL* 4.0 26.5 - - + +
385A PHE* 4.0 14.6 - - + -
411A ASN* 4.3 0.6 + - - +
458A VAL 3.2 10.2 + - - +
459A GLU 3.5 10.3 - - - +
460A LEU 3.2 0.2 - - - -
461A ALA* 1.3 78.3 - - - +
463A ASN* 1.3 67.9 + - - +
464A THR 3.9 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ALA 4.7 0.3 - - - +
300A ASN* 3.5 28.2 - - - +
301A ILE* 2.8 51.9 + - - +
302A ARG* 5.9 0.2 - - - +
459A GLU* 3.0 24.2 + - - +
460A LEU* 3.0 10.2 + - + +
462A ALA* 1.3 82.9 - - - +
464A THR* 1.3 58.1 - - - +
465A LYS* 4.0 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ASN* 4.8 4.9 - - - +
411A ASN* 5.1 0.3 - - - +
444A THR* 3.7 23.1 - - + +
446A PHE* 4.8 0.6 - - - -
460A LEU* 2.8 22.4 + - - +
461A ALA 3.4 10.6 + - - +
462A ALA 4.8 1.4 - - - +
463A ASN* 1.3 78.9 - - - +
465A LYS* 1.3 77.3 + - - +
466A GLY 3.6 6.1 + - - +
468A CYS* 3.8 17.4 - - - -
489A VAL* 4.0 18.9 - - + +
----------------------------------------------------------
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