Contacts of the strand formed by residues 445 - 451 (chain A) in PDB entry 4ICU
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 445 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLN* 1.3 76.3 + - - +
446A LEU* 1.3 63.6 + - - +
447A THR* 3.8 3.1 + - - -
464A GLN* 3.1 40.1 + - + +
465A LEU 3.7 29.2 - - - +
466A PRO* 3.7 14.8 - - + -
519A ASN* 4.2 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLN* 3.9 20.9 - - - +
445A LEU* 1.3 75.7 - - - +
447A THR* 1.3 61.1 + - - +
448A LEU* 3.5 18.0 + - + +
464A GLN* 3.3 2.8 - - - -
465A LEU* 2.8 42.8 + - - +
467A GLY* 4.1 16.4 - - - -
512A LEU* 4.3 11.2 - - + -
513A GLN* 5.1 4.3 - - + +
517A VAL* 3.5 41.1 - - + +
518A GLU* 4.1 3.1 - - - -
519A ASN* 3.5 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A LEU 3.8 1.3 + - - -
446A LEU* 1.3 68.6 - - - +
448A LEU* 1.3 64.4 + - - +
449A LYS* 5.5 3.8 - - + +
462A GLU* 3.6 28.0 - - + +
463A LYS 3.7 7.0 - - - +
464A GLN* 2.8 32.5 + - + -
519A ASN* 2.9 22.3 + - - -
520A GLY* 2.7 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A LEU* 3.9 16.4 - - + +
447A THR* 1.3 82.9 - - - +
449A LYS* 1.3 67.3 + - - +
450A ILE* 4.0 4.3 + - + +
462A GLU* 3.3 4.9 - - - +
463A LYS* 2.8 38.4 + - + +
465A LEU* 3.9 27.4 - - + -
512A LEU* 4.1 20.9 - - + -
517A VAL* 3.7 21.3 - - + -
518A GLU 3.4 25.6 - - - +
521A ASP* 3.5 12.1 - - + +
523A LEU* 4.8 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A THR* 5.5 3.8 - - + +
448A LEU* 1.3 74.0 - - - +
450A ILE* 1.3 59.1 + - - +
459A LYS* 3.6 44.7 - - + +
461A LEU 3.5 6.5 - - - +
462A GLU* 3.7 32.9 + - + +
520A GLY* 4.4 8.3 - - - +
521A ASP 3.1 10.8 + - - +
522A CYS* 3.4 5.8 - - + -
523A LEU* 2.7 33.4 + - - +
490D LEU* 5.1 10.7 - - - +
504D GLU* 4.5 1.0 + - - -
506D GLU* 2.0 53.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A LEU* 4.5 10.1 - - + +
449A LYS* 1.3 75.9 - - - +
451A LYS* 1.3 59.0 + - - +
452A TYR* 3.6 33.0 - - + +
459A LYS* 3.4 5.4 - - - -
460A VAL* 2.7 33.3 + - + -
461A LEU* 2.8 43.1 + - + +
463A LYS* 4.7 9.6 - - + -
465A LEU* 5.6 3.1 - - + -
478A LEU* 4.7 13.5 - - + -
523A LEU* 3.5 36.8 - - + -
525A VAL* 3.9 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A ILE* 1.3 75.5 - - - +
452A TYR* 1.3 69.4 + - - +
453A PRO* 3.4 20.3 - - + +
456A LEU 4.2 3.6 - - - +
457A ASP* 3.2 40.8 + - - +
458A GLN 4.1 15.7 - - - +
459A LYS* 4.8 4.9 - - + +
460A VAL* 4.6 1.3 - - - +
494A GLU* 4.2 11.9 + - - +
522A CYS* 3.8 27.1 - - - -
523A LEU 2.9 7.1 + - - +
524A LEU* 4.2 15.0 - - + +
525A VAL* 2.8 27.7 + - - +
----------------------------------------------------------
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