Contacts of the strand formed by residues 450 - 455 (chain C) in PDB entry 4KPF
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 GLN 450 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C ALA* 3.9 8.8 - - - +
428C GLU* 3.3 25.9 + - + +
430C TYR* 3.5 22.4 + - + -
445C ARG* 3.2 36.7 + - + +
446C ASP 2.9 37.7 + - - +
447C ARG 4.3 0.5 - - - +
449C PHE* 1.3 103.8 - - + +
451C ALA* 1.3 60.3 + - - +
592C TRP* 3.4 12.4 - - - -
596C MET* 3.2 26.6 + - - +
598C PRO* 4.4 0.4 - - - +
601C ARG* 3.8 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 451 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C LEU* 4.4 4.0 - - + -
417C THR 3.3 13.0 - - - +
418C PRO* 3.8 3.6 - - + -
419C ALA* 3.5 18.7 - - + +
428C GLU 3.1 13.2 + - - +
429C LEU* 4.8 4.9 - - + -
430C TYR* 3.2 25.5 + - - +
449C PHE 4.1 1.0 + - - -
450C GLN* 1.3 73.8 - - - +
452C ILE* 1.3 69.3 + - - +
498C TYR* 4.0 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 452 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C LEU* 3.6 4.5 - - - +
417C THR* 2.7 51.0 + - - +
429C LEU* 4.9 0.7 - - - -
430C TYR* 3.9 14.6 - - + -
432C VAL* 4.3 11.0 - - + -
438C GLY* 3.6 22.7 - - - +
441C ALA* 3.4 31.0 - - + +
442C LYS* 3.9 8.5 - - + +
445C ARG* 3.8 26.0 - - + +
450C GLN 5.0 0.7 - - - +
451C ALA* 1.3 84.1 - - - +
453C LEU* 1.3 62.5 + - - +
454C PRO* 3.9 13.2 - - + +
596C MET* 4.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 453 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C LYS* 4.9 12.8 - - + -
416C LEU* 4.7 17.0 - - + +
429C LEU* 4.0 14.8 - - + +
430C TYR 3.0 12.6 + - - +
431C LEU* 3.6 24.5 - - + +
432C VAL 3.2 20.2 + - - -
452C ILE* 1.3 76.5 - - - +
454C PRO* 1.3 98.1 - - + +
455C LEU* 3.7 7.9 + - + +
475C GLU* 5.5 0.7 - - - +
478C THR* 4.3 20.4 - - - +
479C MET* 4.1 29.8 - - + -
482C THR* 4.8 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 454 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C LYS* 3.6 23.1 - - - +
417C THR* 5.6 1.1 - - - +
432C VAL* 3.6 9.2 - - + +
434C GLY 4.0 14.8 - - - +
435C ASP* 4.0 25.6 - - - +
438C GLY* 4.2 16.6 - - - -
452C ILE* 3.9 7.2 - - + +
453C LEU* 1.3 107.4 - - + +
455C LEU* 1.3 62.8 + - - +
456C ARG* 3.7 5.0 + - + +
475C GLU* 5.0 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 455 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C LEU* 4.1 15.0 - - + +
432C VAL 2.7 20.3 + - - +
433C GLU* 4.2 5.6 - - - +
434C GLY* 3.4 17.7 + - - +
453C LEU* 4.5 15.0 - - + +
454C PRO* 1.3 78.3 - - - +
456C ARG* 1.3 60.4 + - - +
457C GLY 3.1 18.3 + - - +
459C VAL* 3.8 12.8 - - + -
475C GLU* 4.2 25.8 - - + +
479C MET* 4.6 14.6 - - + -
514C ILE* 4.9 6.1 - - + -
518C LEU* 3.4 42.8 - - + -
----------------------------------------------------------
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