Contacts of the strand formed by residues 446 - 454 (chain C) in PDB entry 2YWB
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 TYR 446 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C GLU* 3.4 15.6 + - - -
398C ARG* 3.2 30.2 + - + +
401C ILE* 3.6 26.9 - - + -
429C LEU* 3.6 36.6 - - + -
430C THR 3.2 7.9 - - - +
431C PRO* 3.4 37.7 - - + -
432C VAL* 3.1 6.6 - - - +
445C GLY* 1.3 92.0 - - - -
447C VAL* 1.3 65.0 + - - +
484C GLU* 3.3 21.9 + - + +
485C ILE* 3.6 5.9 - - + -
486C GLY* 3.0 26.5 + - - +
487C ARG 3.6 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 447 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C VAL 3.7 0.5 - - - +
429C LEU* 3.8 1.3 - - - +
430C THR* 2.8 47.3 + - + +
432C VAL* 4.1 21.3 - - + -
446C TYR* 1.3 78.1 - - - +
448C LEU* 1.3 66.0 + - - +
449C ALA* 4.1 1.5 + - + +
485C ILE* 4.7 0.2 - - - -
487C ARG* 3.3 22.9 - - + +
489C VAL* 4.2 17.7 - - + -
391D LEU* 5.6 1.3 - - + -
502D TRP* 4.0 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 448 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C LEU* 3.9 21.1 - - + -
405C ALA* 3.5 28.0 - - + -
427C ALA* 4.0 9.9 - - + -
428C VAL 3.3 20.9 - - - +
429C LEU* 4.0 13.0 - - + -
447C VAL* 1.3 75.9 - - - +
449C ALA* 1.3 61.3 + - - +
450C LEU* 4.0 13.9 - - + -
478C ILE* 3.7 26.9 - - + -
485C ILE* 3.8 19.2 - - + +
487C ARG 2.9 7.9 + - - +
488C VAL* 3.3 8.7 - - + +
489C VAL* 3.0 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 449 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C ALA* 3.3 4.4 - - - -
428C VAL* 2.8 44.4 + - + +
430C THR* 5.7 1.8 - - - +
447C VAL* 4.1 1.7 + - + -
448C LEU* 1.3 72.7 - - - +
450C LEU* 1.3 65.7 + - - +
451C ARG* 3.8 1.2 + - - +
489C VAL* 3.5 22.0 - - + -
491C ASP 5.5 0.7 - - - +
502C TRP* 3.6 37.7 - - + -
489D VAL* 5.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 450 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C PHE* 3.8 39.7 - - + -
426C LEU 3.8 1.8 - - - -
427C ALA* 4.3 3.4 - - + -
448C LEU* 4.0 24.0 - - + -
449C ALA* 1.3 72.6 - - - +
451C ARG* 1.3 58.8 + - - +
471C LEU* 5.0 4.7 - - + -
474C ALA* 4.0 26.5 - - + -
478C ILE* 4.1 6.7 - - + -
488C VAL* 3.7 25.8 - - + -
489C VAL 2.8 10.7 + - - +
490C TYR* 3.3 14.8 - - + -
491C ASP* 2.9 27.9 + - - +
492D LEU* 4.3 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 451 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C PHE* 4.4 2.3 - - - -
424C GLN* 3.9 1.3 - - - +
425C ALA* 3.4 1.9 + - - -
426C LEU* 2.8 58.1 + - + +
428C VAL* 5.5 0.2 - - + -
449C ALA 4.7 2.0 - - - +
450C LEU* 1.3 73.0 - - - +
452C ALA* 1.3 62.9 + - - +
453C VAL* 3.7 27.5 - - - +
463C TRP* 4.3 4.4 - - - +
490C TYR* 4.6 0.2 - - - -
491C ASP* 3.2 41.5 + - + +
493C THR 2.6 32.7 + - - -
494C SER 4.6 4.8 - - - -
495C LYS* 5.0 0.8 - - - +
498C ALA* 4.4 2.8 - - - +
499C THR 3.1 11.7 + - - -
500C ILE* 2.8 29.9 + - - +
502C TRP* 3.7 11.2 - - + +
487D ARG* 2.8 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 452 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C PHE* 4.8 4.3 - - + -
413C LEU* 6.0 0.9 - - + -
422C VAL* 4.3 7.4 - - + -
424C GLN 3.1 13.0 - - - +
425C ALA* 4.3 8.7 - - + -
451C ARG* 1.3 76.9 + - - +
453C VAL* 1.3 68.9 + - - +
463C TRP* 3.4 5.5 - - - +
464C ALA* 2.8 27.3 + - + -
466C LEU* 4.1 13.2 - - + -
490C TYR* 3.6 23.0 + - + +
491C ASP 5.2 0.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 453 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C VAL* 3.5 5.2 - - - +
423C ALA* 2.8 29.3 + - + -
424C GLN* 3.1 27.4 + - + +
451C ARG* 3.7 35.4 - - - +
452C ALA* 1.3 81.2 - - - +
454C THR* 1.3 65.2 + - - +
461C ALA* 4.0 25.6 - - + +
462C ASP 3.0 15.5 - - - +
463C TRP* 4.2 2.0 - - - -
464C ALA* 3.7 1.3 - - - +
493C THR 5.1 0.2 - - - +
494C SER* 5.8 0.2 - - - -
495C LYS 6.1 0.2 - - - +
500C ILE* 4.2 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 454 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LYS* 3.3 29.6 - - - +
421C LYS 3.7 10.1 - - - +
422C VAL* 4.0 4.3 - - + -
423C ALA* 4.1 7.6 - - - +
453C VAL* 1.3 79.7 - - - +
455C THR* 1.3 62.8 + - - +
456C GLU* 4.4 8.8 + - - -
461C ALA* 3.3 6.0 - - - -
462C ASP* 2.9 42.8 + - - +
463C TRP 4.8 0.2 + - - -
464C ALA* 4.0 18.6 - - + -
465C ARG 5.5 0.8 + - - +
----------------------------------------------------------
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