Contacts of the strand formed by residues 440 - 445 (chain C) in PDB entry 3K0J
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 ILE 440 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C HIS* 4.1 27.2 - - + +
434C PHE* 3.8 37.9 - - + +
435C SER* 3.8 8.7 - - - +
438C GLY 3.6 5.1 + - - +
439C GLN* 1.3 85.8 - - - +
441C LEU* 1.3 66.1 + - - +
442C ASP* 3.6 14.4 - - - +
443C ILE* 3.8 26.2 - - + -
457C VAL* 4.3 8.3 - - + -
458C ILE 3.7 6.7 - - - +
459C PHE* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 441 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C HIS* 5.6 4.9 - - + -
439C GLN* 4.3 10.1 - - + +
440C ILE* 1.3 77.0 - - - +
442C ASP* 1.3 67.1 + - + +
458C ILE* 2.7 27.3 + - + +
459C PHE 4.3 0.9 - - - +
460C LYS* 3.8 40.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 442 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C LYS* 5.8 1.2 + - - +
440C ILE* 3.3 6.8 - - - +
441C LEU* 1.3 85.9 - - + +
443C ILE* 1.3 79.2 + - - +
444C LEU* 3.3 31.6 - - - +
457C VAL* 3.8 0.2 - - - -
458C ILE* 2.8 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 443 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C LYS* 3.8 42.5 + - + +
430C LEU* 3.9 17.5 - - + +
431C HIS* 3.5 48.5 - - + +
440C ILE* 3.8 19.5 - - + -
442C ASP* 1.3 91.2 + - - +
444C LEU* 1.3 65.4 + - - +
445C VAL* 3.9 10.8 + - + -
455C ALA* 5.1 0.4 - - + -
456C PHE 3.2 9.9 - - - +
457C VAL* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 444 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C ASP* 3.3 21.8 - - - +
443C ILE* 1.3 70.5 - - - +
445C VAL* 1.3 64.7 + - - +
446C SER 3.8 0.3 + - - -
455C ALA* 3.1 4.3 - - - -
456C PHE* 2.8 62.1 + - + +
458C ILE* 4.1 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 445 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C LYS* 3.9 34.1 - - + +
426C LEU* 4.1 19.7 - - + -
427C LYS* 3.6 49.3 - - + +
430C LEU* 4.7 3.4 - - + -
443C ILE* 3.9 7.7 + - + -
444C LEU* 1.3 75.0 - - - +
446C SER* 1.3 68.2 + - - +
447C ARG* 3.9 3.1 + - - +
454C GLN 4.1 7.6 - - - +
455C ALA* 3.7 10.1 - - + -
----------------------------------------------------------
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