Contacts of the strand formed by residues 444 - 451 (chain B) in PDB entry 2YA6
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 LYS 444 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B LYS 3.5 2.3 - - - +
440B LYS* 3.2 2.2 - - - +
441B ILE* 2.7 38.6 + - - +
442B ASP 3.2 5.1 - - - +
443B GLY* 1.3 83.2 - - - +
445B THR* 1.3 61.1 + - - +
446B TYR* 3.5 27.6 + - + +
462B GLU* 2.9 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B TYR* 3.8 28.9 - - + -
439B LYS 3.4 8.5 - - - +
440B LYS* 4.0 18.0 - - + +
443B GLY 4.3 1.1 + - - -
444B LYS* 1.3 72.3 - - - +
446B TYR* 1.3 67.6 + - - +
447B GLN 4.4 0.2 + - - -
541B PRO* 4.2 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B TYR* 3.3 6.4 - - - -
439B LYS* 2.7 41.9 + - - +
441B ILE* 3.8 39.1 + - + +
444B LYS* 3.5 35.2 - - + +
445B THR* 1.3 78.8 - - - +
447B GLN* 1.3 62.5 + - - +
459B THR* 3.8 15.5 - - + -
460B ILE 3.2 22.7 - - - +
461B ARG* 3.6 35.1 + - + -
462B GLU* 3.1 33.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B ALA 3.5 12.6 - - - +
438B TYR* 3.8 18.8 - - + -
446B TYR* 1.3 71.2 - - - +
448B ILE* 1.3 71.9 + - - +
459B THR* 3.4 2.3 - - - -
460B ILE* 2.9 55.3 + - + +
503B ILE* 4.6 4.2 - - - +
504B TYR* 5.0 7.6 + - - -
515B ILE* 3.5 29.0 - - + +
516B ALA 5.9 0.2 - - - +
520B TYR* 3.6 27.4 + - - +
538B ASP* 4.3 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B GLU* 3.8 26.5 - - + +
437B ALA 2.9 16.0 + - - +
438B TYR 3.5 30.7 - - - +
439B LYS* 4.0 15.9 - - + -
447B GLN* 1.3 84.9 - - - +
449B LEU* 1.3 80.1 + - - +
450B TYR* 3.7 23.6 - - + +
457B ALA* 3.6 25.8 - - + -
458B TYR 3.1 12.8 - - - +
459B THR* 4.5 2.0 - - + +
515B ILE* 3.8 10.9 - - - -
516B ALA 4.3 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B ILE* 1.3 82.2 - - - +
450B TYR* 1.3 63.6 + - - +
457B ALA* 3.8 2.1 - - - -
458B TYR* 2.7 48.7 + - + +
459B THR 5.2 0.4 - - - +
460B ILE* 3.7 22.0 - - + -
466B VAL* 3.7 32.3 - - + -
478B VAL* 4.0 8.3 - - + -
493B LEU* 4.7 0.4 - - + -
503B ILE* 3.8 20.0 - - + -
513B PHE* 3.9 21.8 - - + -
514B ARG 3.4 26.7 - - - +
515B ILE* 3.7 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A ASN* 4.1 28.4 - - + +
435B GLU* 4.3 12.2 - - + -
436B GLU* 2.7 46.5 + - - +
448B ILE* 3.7 19.4 - - + +
449B LEU* 1.3 73.5 - - - +
451B ARG* 1.3 63.5 + - - +
452B GLU 4.1 0.5 + - - -
454B GLU 5.1 3.4 - - - +
455B LYS 4.3 4.9 - - - -
456B GLY 4.1 11.7 - - - -
457B ALA* 4.5 7.7 - - + +
512B PRO 3.5 0.9 - - - +
513B PHE* 3.4 7.1 - - - -
514B ARG* 2.8 73.5 + - - +
516B ALA* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LEU 4.1 1.2 + - - -
450B TYR* 1.3 74.9 - - - +
452B GLU* 1.3 75.8 + - + +
453B GLY 3.3 0.5 + - - -
454B GLU* 3.0 49.3 + - + +
456B GLY 4.8 1.2 + - - -
458B TYR* 3.6 38.5 + - + -
474B THR* 5.9 1.4 - - - +
476B TYR* 3.3 30.4 + - - -
512B PRO* 3.2 34.6 - - + +
513B PHE* 3.8 17.5 - - + -
----------------------------------------------------------
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