Contacts of the helix formed by residues 461 - 472 (chain A) in PDB entry 2YPT
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 PRO 461 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ARG* 5.4 3.6 - - - -
446A PRO 5.1 9.2 - - - +
448A SER* 5.4 7.4 - - - -
453A SER* 4.5 24.0 - - - +
457A TYR* 4.8 12.5 - - + -
459A HIS 3.8 1.5 - - - +
460A PRO* 1.4 90.3 - - + +
462A LEU* 1.3 66.7 + - - +
463A LEU* 4.5 6.1 - - + +
464A GLU* 3.1 27.2 + - + +
465A ARG* 3.0 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 4.8 10.8 - - + -
435A LEU* 3.4 45.8 - - + +
436A ILE* 4.2 10.8 - - + +
439A ASN* 3.6 37.5 - - + +
446A PRO* 5.1 17.5 + - + -
460A PRO 3.7 1.2 + - - -
461A PRO* 1.3 70.0 - - - +
463A LEU* 1.4 59.1 + - + +
465A ARG* 3.2 8.5 + - - +
466A LEU* 2.9 51.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLU* 4.4 26.2 - - + +
55A LEU* 4.5 16.2 - - + +
446A PRO* 3.4 42.2 - - + +
447A VAL* 5.3 2.9 - - + -
461A PRO* 3.3 4.0 - - + -
462A LEU* 1.4 78.8 - - + +
464A GLU* 1.3 57.5 + - + +
466A LEU* 4.1 11.2 - - + +
467A GLN* 3.0 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A PHE* 3.7 27.6 - - + -
461A PRO* 3.1 34.4 + - + +
463A LEU* 1.3 77.6 - - + +
465A ARG* 1.4 62.5 + - - +
467A GLN* 3.7 10.6 + - - +
468A ALA* 3.4 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A HIS* 3.7 9.1 + - - -
415A GLU* 3.7 14.8 + - - -
416A PHE* 4.1 8.3 - - + -
419A ASP* 3.1 38.2 + - - +
435A LEU* 3.5 38.1 - - + +
459A HIS* 3.7 29.5 - - - +
460A PRO* 3.5 42.3 + - + -
461A PRO 3.0 8.5 + - - +
462A LEU* 3.6 10.5 - - - +
464A GLU* 1.4 73.2 - - - +
466A LEU* 1.4 63.6 + - - +
468A ALA* 3.6 4.0 + - - +
469A LEU* 3.4 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 466 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 5.2 6.5 - - + -
432A TYR* 3.3 68.0 - - + +
435A LEU* 4.3 14.1 - - + -
436A ILE* 3.7 28.3 - - + -
462A LEU* 2.9 41.4 + - + +
463A LEU* 4.1 11.0 - - + +
465A ARG* 1.4 72.9 - - - +
467A GLN* 1.4 59.6 + - + +
469A LEU* 3.3 3.5 + - + -
470A LYS* 3.0 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A LEU* 3.0 33.7 + - + +
464A GLU* 4.0 10.0 - - - +
465A ARG 3.4 0.4 - - - -
466A LEU* 1.4 72.8 - - + +
468A ALA* 1.4 56.1 + - - +
470A LYS* 3.4 8.2 + - + +
471A THR* 2.7 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A PHE* 4.1 21.5 - - + -
419A ASP* 6.1 3.4 - - + -
464A GLU 3.4 15.3 + - - +
465A ARG 3.8 6.1 - - - +
466A LEU 3.3 0.6 - - - -
467A GLN* 1.4 77.4 - - - +
469A LEU* 1.3 58.5 + - + +
471A THR* 3.7 6.5 + - - -
472A MET* 3.3 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ASP* 3.8 36.3 - - + +
422A ALA* 5.3 0.2 - - + -
423A LYS* 4.4 4.7 - - + +
428A ALA* 4.0 37.0 - - + +
431A LEU* 4.5 12.1 - - + -
432A TYR* 4.3 27.1 - - + +
435A LEU* 4.2 21.3 - - + -
465A ARG 3.4 17.0 + - - +
466A LEU* 3.3 9.1 + - - +
468A ALA* 1.3 78.7 - - + +
470A LYS* 1.4 62.3 + - - +
471A THR 3.3 0.4 - - - -
472A MET* 3.5 20.8 + - - +
50D HIS* 3.9 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A TYR* 3.7 27.4 - - + +
466A LEU 3.0 12.0 + - - +
467A GLN* 3.7 9.9 - - + +
469A LEU* 1.4 74.1 - - - +
471A THR* 1.4 65.0 + - - +
472A MET 4.5 2.4 - - - +
49D THR 4.6 4.9 - - - +
50D HIS* 3.6 36.4 + - + +
51D VAL* 5.3 9.1 - - + +
61D SER* 4.2 19.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A GLN 2.7 22.5 + - - -
468A ALA* 3.8 8.4 - - - -
470A LYS* 1.4 78.1 - - - +
472A MET* 1.4 63.7 + - - +
61D SER* 4.3 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A ALA* 6.0 2.2 - - - -
423A LYS* 3.8 29.4 - - + -
428A ALA* 5.3 4.7 - - - -
468A ALA 3.3 15.6 + - - +
469A LEU* 3.5 14.6 + - - +
470A LYS 3.5 3.3 - - - +
471A THR* 1.4 83.3 - - - +
50D HIS* 6.2 0.4 - - - -
----------------------------------------------------------
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