Contacts of the helix formed by residues 466 - 481 (chain A) in PDB entry 2XOA
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 466 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A GLN* 1.3 75.6 + - - +
467A LYS* 1.3 64.9 + - - +
468A LEU* 3.0 4.3 - - - +
469A ARG* 3.2 54.4 + - - +
470A SER* 3.8 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A PRO* 4.0 30.5 - - + +
465A GLN* 3.2 16.3 - - + +
466A SER* 1.3 80.8 - - - +
468A LEU* 1.3 61.7 + - - +
470A SER* 3.5 11.4 + - - +
471A LEU* 3.1 24.1 + - - +
474A ARG* 4.8 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A PRO* 5.5 2.2 - - + -
455A PRO* 3.6 27.6 - - + -
465A GLN* 3.1 49.1 - - - +
466A SER* 3.0 1.8 - - - -
467A LYS* 1.3 77.0 - - - +
469A ARG* 1.3 60.7 + - - +
471A LEU* 3.8 10.0 - - + +
472A ARG* 3.1 50.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A SER* 3.2 40.3 + - - +
467A LYS 3.2 0.4 - - - -
468A LEU* 1.3 75.9 - - - +
470A SER* 1.3 68.1 + - - +
471A LEU 3.2 0.3 + - - -
472A ARG* 3.2 28.2 + - - +
473A ASN* 2.9 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A GLU* 3.3 32.8 + - - -
466A SER 3.8 6.9 + - - -
467A LYS* 3.5 11.1 + - - +
469A ARG* 1.3 75.7 - - - +
471A LEU* 1.3 54.1 + - - +
473A ASN* 2.9 4.4 + - - +
474A ARG* 2.6 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A PHE* 3.6 29.4 - - + +
453A GLU 3.7 5.6 - - - +
454A PRO* 3.7 33.2 - - + -
455A PRO* 4.2 9.0 - - + -
467A LYS 3.1 14.5 + - - +
468A LEU* 3.8 11.4 - - + +
469A ARG 3.2 0.2 - - - -
470A SER* 1.3 79.0 - - - +
472A ARG* 1.3 55.3 + - - +
474A ARG* 3.3 18.4 + - - +
475A GLN* 2.7 66.5 + - + +
531A ARG* 5.6 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A LEU* 3.1 43.3 + - - +
469A ARG* 3.6 24.8 - - - +
471A LEU* 1.3 79.3 - - + +
473A ASN* 1.3 56.8 + - - +
475A GLN* 3.4 14.3 + - - +
476A SER* 2.9 28.6 + - - -
532A GLY* 3.8 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A THR* 5.0 4.3 - - - +
396A GLU* 3.4 22.6 + - - +
397A GLU* 5.4 5.5 - - - +
469A ARG 2.9 16.8 + - - +
470A SER* 3.5 3.6 - - - +
472A ARG* 1.3 75.0 - - - +
474A ARG* 1.3 58.3 + - - +
476A SER* 3.0 9.6 + - - -
477A LEU* 2.9 48.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A GLU* 3.7 31.2 + - + +
400A ALA* 5.1 3.8 - - + -
451A TYR* 2.6 80.1 + - + +
452A PHE* 3.8 9.9 - - + -
453A GLU 5.2 2.4 + - - -
467A LYS 4.8 1.8 + - - -
470A SER* 2.6 32.9 + - - +
471A LEU* 3.5 31.0 - - - +
473A ASN* 1.3 67.9 - - - +
475A GLN* 1.3 64.6 + - - +
477A LEU* 3.4 9.5 + - + +
478A PHE* 3.2 29.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A PHE* 3.8 18.8 - - + -
471A LEU* 2.7 44.6 + - + +
472A ARG* 3.4 20.5 - - - +
474A ARG* 1.3 73.3 - - - +
476A SER* 1.3 57.2 + - - +
478A PHE* 3.5 1.6 + - - +
479A GLN* 2.9 40.2 + - - +
528A SER 2.7 24.3 + - - +
529A LEU* 3.5 24.9 + - - +
530A ILE 4.0 0.9 - - - -
531A ARG* 2.9 28.3 + - - +
532A GLY 4.9 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A HIS* 5.2 5.2 + - - -
472A ARG 2.9 18.3 + - - -
473A ASN* 3.0 12.5 + - - -
475A GLN* 1.3 76.1 - - - +
477A LEU* 1.3 60.8 + - - +
479A GLN* 3.1 8.7 + - - +
480A GLU* 2.8 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A THR 3.6 24.0 - - - +
255A HIS* 4.0 4.5 - - + -
256A ALA* 3.7 25.7 + - + +
397A GLU* 4.1 28.5 - - + +
400A ALA* 3.7 24.2 - - + -
404A ILE* 3.7 15.6 - - + +
473A ASN* 2.9 32.2 + - - +
474A ARG* 3.7 12.3 - - + +
476A SER* 1.3 76.9 - - - +
478A PHE* 1.3 62.1 + - + +
480A GLU* 3.5 5.1 + - - +
481A GLU* 3.2 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ALA* 4.1 10.8 - - + -
403A MET* 4.0 20.2 - - + -
404A ILE* 3.8 31.6 - - + -
407A THR* 4.6 4.5 - - - -
448A LEU* 4.0 28.5 - - + -
451A TYR* 3.7 31.2 - + - -
452A PHE* 3.6 13.9 - + - -
474A ARG 3.2 19.0 + - - +
475A GLN 3.9 3.1 - - - +
477A LEU* 1.3 77.3 - - + +
479A GLN* 1.3 65.9 + - - +
481A GLU 3.0 9.5 + - - -
483A MET* 3.1 54.2 + - + +
529A LEU* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A GLN* 2.9 31.6 + - - +
476A SER* 3.6 6.6 - - - +
478A PHE* 1.3 75.9 - - - +
480A GLU* 1.3 61.2 + - + +
482A GLY* 2.9 21.0 + - - -
483A MET* 4.2 3.3 + - - +
484A LEU* 3.6 35.3 + - + +
529A LEU* 2.9 33.5 + - + +
530A ILE* 4.6 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ALA* 5.0 6.6 - - - +
236A ALA* 4.7 9.4 + - - +
255A HIS* 3.5 52.7 + - + +
256A ALA 5.9 0.2 - - - +
257A ARG* 5.4 3.0 - - - -
476A SER* 2.8 32.2 + - - +
477A LEU* 4.0 4.0 - - - +
479A GLN* 1.3 73.9 - - + +
481A GLU* 1.3 66.8 + - + +
482A GLY 3.3 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ALA* 3.8 15.0 + - - +
242A ARG* 2.5 41.7 + - - -
256A ALA* 4.2 11.0 - - + +
257A ARG* 3.3 21.2 + - - +
286A THR* 2.8 25.7 + - + +
404A ILE* 3.7 31.7 - - + +
477A LEU 3.2 14.8 + - - +
478A PHE 3.0 5.9 + - - +
480A GLU* 1.3 82.9 - - + +
482A GLY* 1.3 60.7 + - - +
483A MET* 3.3 13.8 + - + +
----------------------------------------------------------
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