Contacts of the strand formed by residues 455 - 462 (chain A) in PDB entry 4MSL
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 VAL 455 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A THR* 6.6 0.2 - - + -
374A VAL* 3.6 37.5 - - + -
376A SER* 3.8 2.7 - - - +
382A ILE* 6.3 2.5 - - + -
445A PRO* 5.1 9.6 - - + -
446A LEU 3.6 11.7 - - - +
447A SER* 4.3 4.5 - - - +
453A GLY 3.9 7.6 - - - +
454A ILE* 1.3 79.6 - - - +
456A ILE* 1.3 68.3 + - - +
457A ALA* 4.3 0.9 - - + -
474A ILE* 3.2 6.6 - - - +
475A SER* 2.7 40.2 + - - +
478A GLY* 4.0 14.8 - - - -
479A GLY* 4.3 3.1 - - - +
482A TRP* 3.7 23.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A PRO* 3.4 1.2 - - - +
446A LEU* 2.8 45.8 + - + +
454A ILE* 4.3 4.9 - - + -
455A VAL* 1.3 79.8 - - - +
457A ALA* 1.3 66.1 + - - +
472A VAL* 3.7 20.0 - - + -
473A TYR 3.5 3.6 - - - +
474A ILE* 3.7 13.9 - - + -
485A MET* 4.0 11.2 - - + -
492A TYR* 3.6 35.1 + - + -
493A THR 5.4 0.2 - - - +
494A ILE* 4.3 18.6 - - + -
501A ILE* 4.0 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ILE* 3.7 31.1 - - + +
445A PRO* 4.1 12.3 - - + -
455A VAL* 4.3 1.1 - - + -
456A ILE* 1.3 78.1 - - - +
458A HIS* 1.3 72.1 + - - +
472A VAL* 4.5 4.0 - - - -
473A TYR* 2.8 40.1 + - - +
482A TRP* 4.8 7.6 - - + -
492A TYR* 3.7 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ILE* 3.7 1.6 - - - +
430A HIS* 3.0 42.3 + - + +
441A VAL* 4.2 4.9 - - + +
442A PRO* 3.2 24.1 - - + +
443A MET 3.1 25.1 + - - +
457A ALA* 1.3 82.8 - - - +
459A GLY* 1.3 59.2 + - - +
470A PRO* 3.9 17.5 - - + -
471A ASP 3.5 6.3 - - - -
472A VAL* 3.6 9.8 - - + +
489A PRO* 3.6 15.9 - - + -
490A HIS 3.1 40.1 + - - -
492A TYR* 3.4 16.3 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LEU* 4.4 2.5 - - - -
428A HIS 3.0 13.9 - - - -
429A ILE* 4.3 1.3 - - - -
430A HIS* 3.5 11.4 - - - -
457A ALA 3.7 1.4 + - - -
458A HIS* 1.3 77.8 - - - +
460A SER* 1.3 62.3 + - - -
470A PRO* 3.5 20.1 - - - +
471A ASP 3.4 6.5 + - - -
473A TYR* 3.8 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ASP* 4.2 6.5 - - - -
426A SER 3.7 0.7 - - - +
427A LEU* 3.6 2.7 - - - +
428A HIS* 2.8 33.5 + - - +
430A HIS* 4.3 6.8 + - - -
459A GLY* 1.3 74.6 - - - -
461A VAL* 1.3 65.1 + - - +
462A GLY 3.9 0.3 + - - -
464A ALA 3.7 7.4 + - - -
465A ILE* 3.8 5.0 - - - -
466A SER* 3.2 42.2 + - - -
470A PRO* 5.9 0.9 - - - -
473A TYR* 4.7 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A LYS* 4.0 18.8 - - + -
410A PRO* 4.2 4.3 - - + -
413A SER* 3.9 18.4 - - - +
414A GLU 3.7 17.2 - - - +
416A ASP* 2.5 39.3 + - - +
425A CYS* 3.6 23.6 - - - -
426A SER 3.3 7.4 - - - +
427A LEU* 4.1 9.9 - - + -
460A SER* 1.3 74.7 - - - +
462A GLY* 1.3 50.1 + - - +
473A TYR* 3.4 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ASP* 3.0 14.8 - - - -
418A THR* 3.5 3.1 - - - -
419A ALA* 3.7 3.4 - - - -
425A CYS* 3.6 13.7 - - - -
426A SER 2.9 19.1 + - - +
428A HIS* 2.8 17.8 + - - -
460A SER 3.9 1.8 + - - -
461A VAL* 1.3 74.0 - - - +
463A ASP* 1.3 66.3 + - - -
464A ALA 3.4 2.7 + - - -
----------------------------------------------------------
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