Contacts of the helix formed by residues 448 - 456 (chain D) in PDB entry 3KHU
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 448 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421D LYS* 3.8 27.6 - - + +
425D TYR* 5.2 6.3 - - + -
444D VAL 5.4 0.4 - - - +
445D LEU* 3.1 35.1 + - + +
446D ASP 4.3 4.9 - - - +
447D GLY* 1.3 80.0 - - - +
449D HIS* 1.3 63.1 + - - +
450D ASN 3.5 1.8 - - - -
451D GLU* 3.4 23.4 + - + +
452D LEU* 3.0 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 449 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440D ASP* 5.1 0.8 + - - -
445D LEU* 3.3 26.9 + - + +
446D ASP* 4.5 7.4 + - - -
447D GLY 3.4 3.4 - - - -
448D LEU* 1.3 78.7 - - - +
450D ASN* 1.3 60.3 + - - +
452D LEU* 3.3 3.1 + - + +
453D GLN* 2.9 41.5 + - - +
459D ILE* 3.6 46.6 + - + +
461D THR* 3.9 21.3 - - + +
464D LYS* 3.5 39.5 - - + +
618D EPE 3.3 22.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 450 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447D GLY 5.8 0.2 - - - +
448D LEU 3.5 0.2 - - - -
449D HIS* 1.3 71.8 - - - +
451D GLU* 1.3 66.4 + - - +
453D GLN* 3.3 16.8 + - - +
454D THR* 2.9 28.5 + - - +
618D EPE 2.9 47.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 451 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426D GLU* 5.5 2.6 - - - +
447D GLY 5.7 0.2 + - - -
448D LEU* 3.4 23.7 + - + +
449D HIS 3.3 0.6 - - - -
450D ASN* 1.3 77.7 - - - +
452D LEU* 1.3 59.8 + - + +
454D THR* 3.2 9.2 + - + -
455D ILE* 3.0 43.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 452 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425D TYR* 3.6 39.9 - - + -
438D ILE* 4.1 7.9 - - + -
445D LEU* 4.0 29.2 - - + -
448D LEU* 3.0 37.7 + - + +
449D HIS* 3.8 4.0 - - - +
451D GLU* 1.3 79.0 - - + +
453D GLN* 1.3 58.6 + - - +
455D ILE* 3.4 7.9 + - + -
456D GLY 3.1 6.1 + - - -
457D PHE* 3.0 45.6 + - + +
459D ILE* 4.3 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 453 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449D HIS* 2.9 28.5 + - - +
450D ASN* 3.7 15.7 - - - +
452D LEU* 1.3 75.1 - - - +
454D THR* 1.3 60.9 + - - +
456D GLY* 3.0 21.1 + - - -
457D PHE 3.7 13.8 - - - +
459D ILE* 3.8 26.1 + - + +
464D LYS* 5.5 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 454 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450D ASN* 2.9 18.7 + - - +
451D GLU* 3.5 9.0 - - + -
453D GLN* 1.3 74.1 - - - +
455D ILE* 1.3 69.1 + - + +
456D GLY* 3.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 455 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425D TYR* 4.3 4.9 - - + -
426D GLU* 4.1 47.3 - - + +
429D HIS* 2.9 50.8 + - + -
451D GLU* 3.0 33.0 + - + +
452D LEU* 3.6 23.3 - - + +
454D THR* 1.3 77.8 - - + +
456D GLY* 1.3 56.5 + - - +
457D PHE* 4.0 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 456 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429D HIS* 3.3 16.7 + - - -
436D ALA* 4.5 6.4 + - - +
452D LEU 3.1 0.8 + - - -
453D GLN 3.0 13.6 + - - -
454D THR 4.1 0.7 - - - -
455D ILE* 1.3 79.0 - - - +
457D PHE* 1.3 67.0 + - - +
458D GLN* 3.9 0.7 + - - +
----------------------------------------------------------
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