Contacts of the helix formed by residues 481 - 492 (chain A) in PDB entry 3MY0
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 THR 481 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A TRP* 5.5 8.5 - - - +
398A ILE* 3.9 4.9 - - - -
479A ARG 4.8 4.3 - - - +
480A LEU* 1.3 77.3 - - - +
482A ALA* 1.3 64.2 + - - +
483A LEU* 3.6 8.6 + - - +
484A ARG* 3.1 25.7 + - + +
485A ILE* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ALA* 4.4 4.2 - - - +
310A LEU* 4.1 11.4 - - + -
311A ALA* 3.7 30.7 - - - +
314A HIS* 4.1 21.9 + - + +
398A ILE* 3.5 16.7 - - + +
481A THR* 1.3 73.9 - - - +
483A LEU* 1.3 56.0 + - - +
485A ILE* 3.3 7.9 + - - +
486A LYS* 2.8 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ALA* 4.3 9.5 - - + +
315A VAL* 5.4 13.9 - - + -
481A THR* 3.2 8.0 + - - +
482A ALA* 1.3 80.1 - - - +
484A ARG* 1.3 56.1 + - - +
486A LYS* 3.4 28.9 - - + +
487A LYS* 2.9 64.8 + - + +
----------------------------------------------------------
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 LEU* 3.5 26.7 - - + +
481A THR* 3.1 24.4 + - + +
483A LEU* 1.3 79.4 - - - +
485A ILE* 1.3 57.3 + - - +
487A LYS* 3.8 13.8 - - - +
488A THR* 3.0 41.3 + - - +
491A LYS* 4.0 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ALA* 4.2 9.9 - - + -
310A LEU* 6.2 0.4 - - + -
398A ILE* 4.4 13.0 - - + -
401A PHE* 3.7 33.0 - - + -
467A MET* 3.8 21.0 - - + +
471A CYS* 3.9 26.9 - - - -
480A LEU* 3.9 25.1 - - + -
481A THR 3.1 18.8 + - - +
482A ALA* 3.6 8.3 - - - +
484A ARG* 1.3 73.2 - - - +
486A LYS* 1.3 66.1 + - - +
488A THR* 3.3 6.8 + - - -
489A LEU* 3.0 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A VAL* 5.4 1.3 - - + -
307A ALA* 4.0 21.0 - - + +
308A CYS* 4.1 27.4 + - - +
311A ALA* 4.1 19.2 - - + +
482A ALA 2.8 17.2 + - - +
483A LEU* 3.4 24.2 - - + +
485A ILE* 1.3 74.7 - - - +
487A LYS* 1.3 67.2 + - + +
489A LEU* 3.1 11.4 + - - +
490A GLN* 3.2 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A LEU* 2.9 51.5 + - + +
484A ARG* 3.8 15.9 - - - +
485A ILE 3.2 0.2 - - - -
486A LYS* 1.3 80.4 - - + +
488A THR* 1.3 53.4 + - - +
489A LEU 3.2 0.2 + - - -
490A GLN* 3.4 10.0 + - - +
491A LYS* 2.7 55.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A GLY* 6.4 2.0 - - - -
467A MET* 3.7 28.5 - - + +
480A LEU* 5.3 2.6 - - - +
484A ARG* 3.0 30.2 + - - +
485A ILE* 3.3 4.4 + - - -
487A LYS* 1.3 75.8 - - - +
489A LEU* 1.3 56.8 + - - +
491A LYS* 3.2 23.0 + - - +
492A ILE* 3.0 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LEU* 5.4 8.9 - - + +
303A ALA* 3.3 37.7 - - + +
304A VAL* 3.4 23.3 - - + +
307A ALA* 3.8 14.1 - - + -
401A PHE* 5.0 2.0 - - + -
405A LEU* 5.3 0.2 - - + -
464A LEU* 3.9 18.4 - - + -
467A MET* 3.9 25.1 - - + -
485A ILE* 3.0 18.2 + - + +
486A LYS 3.1 9.4 + - - +
488A THR* 1.3 77.7 - - - +
490A GLN* 1.3 60.6 + - - +
492A ILE* 3.3 17.0 - - + +
493A SER 3.2 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A VAL* 3.6 23.3 - - + +
308A CYS* 4.7 6.7 - - - -
486A LYS* 3.2 35.5 + - - +
487A LYS* 4.2 10.6 - - - +
489A LEU* 1.3 70.9 - - - +
491A LYS* 1.3 60.8 + - - +
492A ILE 3.0 2.0 - - - -
493A SER* 2.4 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ARG* 4.0 24.7 - - - +
487A LYS* 2.7 41.7 + - + +
488A THR* 3.4 30.4 + - + +
490A GLN* 1.3 73.0 - - - +
492A ILE* 1.3 57.2 + - + +
493A SER* 3.5 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LEU* 6.0 1.4 - - - +
459A PRO 3.8 22.9 - - - +
460A VAL* 4.3 33.7 - - + +
462A SER* 5.6 0.4 - - - +
463A GLY* 5.5 9.6 - - - -
464A LEU* 6.4 0.7 - - + -
467A MET* 6.5 0.2 - - - -
488A THR* 3.0 20.6 + - + +
489A LEU* 3.3 23.1 - - + +
491A LYS* 1.3 74.8 - - - +
493A SER* 1.3 65.0 + - - +
----------------------------------------------------------
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