Contacts of the helix formed by residues 469 - 477 (chain A) in PDB entry 3AR2
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 ASN 469 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A SER* 3.3 34.2 + - - +
424A SER* 3.8 8.3 - - - -
425A LEU* 2.6 44.6 + - - +
446A THR* 4.1 6.4 - - - +
450A GLU* 2.9 12.4 - - - +
465A VAL 4.7 2.6 + - - -
466A GLU 3.3 4.1 + - - +
468A ALA* 1.3 83.2 - - - +
470A ALA* 1.3 64.3 + - - +
472A ASN* 3.3 3.4 + - + +
473A SER* 2.9 26.5 + - - +
476A ARG* 4.1 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A GLU* 3.1 8.0 + - - +
457A THR* 5.5 3.6 - - + -
459A VAL* 4.1 12.8 - - + -
462A LEU* 3.7 29.6 - - + -
466A GLU 3.4 10.4 + - - +
467A ARG* 4.4 4.0 - - - +
469A ASN* 1.3 80.4 - - - +
471A CYS* 1.3 58.5 + - - +
473A SER* 3.2 5.4 + - - -
474A VAL* 3.1 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A VAL* 3.8 19.5 - - + +
450A GLU* 3.0 27.9 + - - +
453A ASN* 3.6 40.6 - - - +
454A VAL 5.6 0.7 - - - +
457A THR* 4.8 3.1 - - - -
459A VAL* 4.0 17.7 - - - -
467A ARG* 4.1 0.4 - - - -
470A ALA* 1.3 69.8 - - - +
472A ASN* 1.3 65.4 + - - +
474A VAL* 3.4 11.4 + - - +
475A ILE* 3.2 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ALA* 3.2 26.3 - - + +
421A ASN* 5.1 1.2 - - - +
446A THR* 3.0 50.1 + - - +
449A VAL* 3.1 23.8 - - - +
450A GLU* 3.0 14.6 + - - -
469A ASN* 3.5 12.0 - - + +
471A CYS* 1.3 76.0 - - - +
473A SER* 1.3 63.2 + - - +
475A ILE* 3.1 6.8 + - - +
476A ARG* 3.1 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LYS* 4.3 26.2 + - - +
136A SER* 4.9 1.6 + - - -
469A ASN* 2.9 19.6 + - - +
470A ALA* 3.4 9.8 - - - -
472A ASN* 1.3 72.3 - - - +
474A VAL* 1.3 66.7 + - - +
476A ARG* 2.9 33.0 + - - +
477A GLN* 3.0 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A PHE* 3.8 26.0 - - + -
457A THR* 3.5 36.6 - - + +
470A ALA 3.1 16.4 + - - +
471A CYS* 3.5 11.7 - - - +
472A ASN 3.2 0.4 - - - -
473A SER* 1.3 76.6 - - - +
475A ILE* 1.3 63.7 + - - +
477A GLN* 3.3 25.0 + - - +
478A LEU* 3.7 9.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ALA* 3.8 31.0 - - + +
415A THR* 3.9 30.1 - - + +
418A ALA* 4.0 13.2 - - + -
419A LEU* 4.0 19.9 - - + +
449A VAL* 4.8 6.5 - - + -
454A VAL* 4.4 11.0 - - + -
455A PHE* 3.8 23.1 - - + -
471A CYS* 3.2 12.3 + - + +
472A ASN 3.1 8.1 + - - +
474A VAL* 1.3 74.5 - - - +
476A ARG* 1.3 65.5 + - - +
478A LEU* 3.1 23.1 + - + +
479A MET* 3.6 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A SER* 4.1 17.6 + - - -
418A ALA* 5.2 9.9 + - + +
419A LEU* 4.1 19.5 - - + -
424A SER* 5.7 3.4 - - - -
469A ASN* 4.1 8.5 + - - +
472A ASN* 3.1 29.1 + - - +
473A SER* 2.9 45.3 + - - +
475A ILE* 1.3 70.6 - - + +
477A GLN* 1.3 60.1 + - + +
478A LEU 2.8 8.8 + - - -
479A MET 2.6 26.7 + - - +
481A LYS* 6.4 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LYS* 4.1 20.8 - - - +
473A SER* 3.0 23.5 + - - +
474A VAL* 3.6 17.3 - - - +
475A ILE 3.2 0.8 - - - -
476A ARG* 1.3 75.9 - - + +
478A LEU* 1.3 57.1 + - - +
479A MET 3.6 0.2 - - - -
501A ALA* 3.3 19.4 - - - +
505A ARG* 4.4 5.2 + - - +
----------------------------------------------------------
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