Contacts of the strand formed by residues 456 - 460 (chain A) in PDB entry 3K72
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 LEU 456 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A SER* 3.5 1.0 - - - -
446A VAL* 3.1 54.5 + - + +
448A VAL* 4.3 12.3 - - + -
454A THR* 3.5 3.6 - - - +
455A ASP* 1.3 79.5 - - - +
457A VAL* 1.3 77.1 + - - +
458A LEU* 4.3 9.0 - - + -
475A VAL* 3.9 20.0 - - + -
476A CYS 4.2 0.2 - - - -
477A PRO* 3.5 24.2 - - + -
478A LEU* 4.2 1.8 - - - +
542A GLY 3.8 11.4 - - - +
543A PRO* 3.9 3.1 - - + -
544A SER 3.7 33.0 - - - +
545A ILE* 4.9 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A GLU* 6.4 1.1 - - + -
393A ALA* 5.3 2.5 - - + -
402A VAL* 5.3 11.4 - - + -
416A ILE* 5.8 1.6 - - + -
443A LEU* 4.3 17.7 - - + -
444A CYS 3.6 9.2 - - - +
445A SER* 3.9 17.7 - - - +
456A LEU* 1.3 84.0 - - - +
458A LEU* 1.3 79.2 + - - +
459A ILE* 4.7 4.7 - - + -
474A SER 3.6 0.2 - - - +
476A CYS* 2.8 45.1 + - + +
478A LEU* 3.5 26.9 - - + -
485A TRP* 5.1 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LEU* 3.2 19.5 - - - -
444A CYS* 2.9 38.1 + - + +
446A VAL* 4.9 2.9 - - + -
456A LEU* 4.3 9.6 - - + -
457A VAL* 1.3 77.7 - - - +
459A ILE* 1.3 68.7 + - - +
473A VAL* 4.2 16.4 - - + -
474A SER 3.3 2.9 - - - +
475A VAL* 4.0 31.9 - - + +
506A LEU* 4.4 15.9 - - + -
520A VAL* 4.4 33.2 - - + -
522A ILE* 5.0 4.3 - - + -
545A ILE* 4.9 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ALA* 3.9 14.4 - - + -
439A PHE* 3.2 53.8 - - + -
440A GLY* 3.8 13.7 - - - +
442A SER* 3.1 11.0 - - - +
443A LEU* 4.0 12.8 - - + -
457A VAL* 4.6 3.4 - - + +
458A LEU* 1.3 81.4 - - - +
460A GLY* 1.3 68.0 + - - +
473A VAL* 3.0 13.8 - - - +
474A SER* 2.9 32.4 + - - +
476A CYS* 3.8 3.4 - - + -
485A TRP* 4.7 4.5 - - + -
487A CYS* 3.3 22.9 - - - -
506A LEU* 5.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A TYR 3.1 1.7 - - - +
439A PHE* 3.6 0.9 - - - -
440A GLY 3.0 25.8 + - - -
441A ALA* 3.4 3.7 + - - -
442A SER* 2.8 23.9 + - - -
459A ILE* 1.3 77.0 - - - +
461A ALA* 1.3 63.7 + - - +
462A PRO* 3.7 4.5 - - - -
472A GLN 3.6 3.1 - - - -
473A VAL* 4.7 0.9 - - - -
503A GLY* 3.9 15.7 - - - -
506A LEU* 5.4 0.2 - - - -
----------------------------------------------------------
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