Contacts of the helix formed by residues 472 - 485 (chain A) in PDB entry 3A1B
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 ARG 472 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A LYS* 1.3 63.3 + - - +
474A GLN* 3.4 7.4 - - - +
475A LEU* 3.2 40.1 + - - +
476A ARG* 3.0 33.5 + - - +
497A CYS* 3.0 40.3 + - + +
499A SER* 3.8 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ARG* 1.3 75.0 - - - +
474A GLN* 1.3 68.6 + - - +
476A ARG* 3.1 6.6 + - + +
477A GLU* 2.8 47.5 + - + +
561A GLU* 3.8 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ARG 4.4 5.3 - - - +
473A LYS* 1.3 77.3 - - - +
475A LEU* 1.3 56.7 + - - +
477A GLU* 3.6 5.5 - - - +
478A ARG* 3.0 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ARG* 3.2 45.4 + - - +
473A LYS 3.1 0.4 - - - -
474A GLN* 1.3 76.4 - - - +
476A ARG* 1.3 61.3 + - - +
478A ARG* 3.3 7.3 + - + +
479A LEU* 2.9 49.3 + - + +
497A CYS 4.2 2.9 - - - +
498A GLY 3.5 21.5 - - - +
499A SER* 4.7 1.3 - - - -
500A LEU* 5.9 3.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
472A ARG* 3.0 18.3 + - - +
473A LYS* 3.7 7.2 - - + +
475A LEU* 1.3 76.5 - - - +
477A GLU* 1.3 58.1 + - - +
479A LEU* 3.3 6.0 + - - +
480A VAL* 2.8 35.4 + - + +
493A ILE* 5.7 0.4 - - - +
494A CYS 5.3 0.2 + - - -
495A ILE 2.7 27.7 + - - -
496A SER 3.3 22.5 + - - -
497A CYS* 3.4 25.8 - - - +
498A GLY* 3.9 5.1 - - - +
539A ILE* 4.0 3.2 - - - +
540A CYS* 4.4 4.6 - - - +
561A GLU* 3.2 27.5 + - - +
562A CYS* 3.2 36.4 - - - +
565A LEU* 3.6 28.5 - - + +
566A LEU* 4.3 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A LYS* 2.8 39.3 + - + +
474A GLN* 3.6 7.2 - - - +
476A ARG* 1.3 78.9 - - - +
478A ARG* 1.3 61.5 + - - +
480A VAL* 4.0 2.1 - - - +
481A TYR* 3.1 23.4 + - - +
561A GLU* 5.4 2.1 - - - +
565A LEU* 3.3 31.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A GLN* 3.0 19.0 + - + +
475A LEU* 3.3 8.7 + - + +
477A GLU* 1.3 75.0 - - - +
479A LEU* 1.3 65.6 + - + +
481A TYR* 3.3 32.9 + - - +
482A GLU* 2.6 58.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
475A LEU* 2.9 36.6 + - + +
476A ARG* 3.8 4.3 - - - +
478A ARG* 1.3 75.9 - - + +
480A VAL* 1.3 60.7 + - - +
482A GLU* 3.1 13.2 + - - +
483A VAL* 2.9 33.2 + - - +
488A ARG* 3.4 37.0 - - - +
493A ILE* 4.2 18.6 - - + -
498A GLY* 2.9 37.5 - - - +
500A LEU* 4.0 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A ARG* 2.8 20.2 + - + +
477A GLU 4.0 1.6 - - - +
479A LEU* 1.3 74.3 - - - +
481A TYR* 1.3 66.2 + - - +
482A GLU 3.2 0.2 + - - -
483A VAL* 3.2 7.5 + - + +
484A ARG* 2.9 32.2 + - - +
490A ILE* 6.4 0.2 - - + -
493A ILE* 4.9 11.0 - - + -
565A LEU* 3.4 49.6 - - + +
566A LEU* 4.0 18.8 - - + -
594A LEU* 3.8 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A GLU 3.1 14.0 + - - +
478A ARG* 3.4 41.3 - - - +
480A VAL* 1.3 78.6 - - - +
482A GLU* 1.3 60.6 + - + +
484A ARG* 3.4 13.2 + - - +
485A GLN* 2.9 68.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A ARG* 2.6 61.4 + - - +
479A LEU* 3.1 14.5 + - - +
481A TYR* 1.3 75.5 - - + +
483A VAL* 1.3 59.5 + - - +
485A GLN* 3.4 5.8 + - - -
486A LYS 3.0 7.3 + - - -
487A CYS* 2.8 41.4 + - + +
488A ARG* 2.6 55.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A LEU 2.9 17.3 + - - +
480A VAL* 3.6 9.2 - - - +
482A GLU* 1.3 74.5 - - - +
484A ARG* 1.3 58.4 + - - +
486A LYS* 2.9 24.8 + - - +
488A ARG* 3.4 25.3 - - + +
489A ASN 4.3 2.5 - - - +
490A ILE* 3.9 36.1 - - + +
493A ILE* 4.2 16.2 - - + -
594A LEU* 3.9 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A VAL* 2.9 30.5 + - - +
481A TYR* 3.6 16.5 - - + +
483A VAL* 1.3 76.4 - - - +
485A GLN* 1.3 76.9 + - - +
486A LYS* 3.4 9.2 + - - +
565A LEU 5.5 2.0 - - - -
567A VAL 5.8 0.8 + - - -
568A GLY* 5.6 3.4 - - - -
569A PRO* 5.2 13.0 - - - +
594A LEU* 4.0 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A TYR* 2.9 58.3 + - + +
482A GLU* 3.9 7.0 - - - +
483A VAL 3.2 0.4 - - - -
484A ARG* 1.3 91.4 + - - +
486A LYS* 1.3 69.6 + - - +
487A CYS* 3.3 15.1 + - + +
----------------------------------------------------------
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