Contacts of the strand formed by residues 534 - 541 (chain C) in PDB entry 3A8P
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 534 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A LYS* 4.8 25.5 - - + +
512C PHE* 4.0 2.7 - - - -
513C PHE* 2.6 40.0 + - + +
532C LYS 3.5 3.5 + - - +
533C TRP* 1.3 76.5 - - - +
535C GLN* 1.3 69.6 + - - +
536C TYR* 2.9 40.4 - - + +
549C GLU* 3.2 31.1 + - - +
563C ARG* 5.2 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 535 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510C TRP* 3.5 44.2 - - + +
511C LEU 3.5 11.0 - - - +
512C PHE* 3.7 44.4 - - + -
534C LYS* 1.3 88.4 + - - +
536C TYR* 1.3 70.5 + - - +
548C TYR 5.0 0.2 - - - +
549C GLU* 5.1 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 536 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510C TRP* 3.4 10.5 - - - -
511C LEU 2.9 31.9 + - - +
513C PHE* 4.0 23.6 - + + -
534C LYS* 2.9 51.4 - - + +
535C GLN* 1.3 79.1 - - - +
537C TRP* 1.3 61.6 + - - +
538C VAL* 3.5 8.7 + - + +
547C PHE* 3.6 43.3 - + + -
548C TYR 3.5 14.8 - - - +
549C GLU* 3.6 20.4 - - - -
563C ARG* 4.6 14.4 + - + +
564C CYS* 4.9 7.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 537 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508C ALA* 3.7 20.4 - - + +
509C GLY* 3.3 39.0 - - - -
510C TRP* 3.6 36.6 - + + -
536C TYR* 1.3 71.4 - - - +
538C VAL* 1.3 57.4 + - - +
539C THR* 3.7 22.2 - - + +
546C LEU 3.5 1.4 - - - +
548C TYR* 2.8 47.4 + + + +
550C THR 3.7 26.0 - - - +
551C TYR* 3.4 47.2 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 538 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508C ALA* 3.1 4.0 - - - +
509C GLY 2.9 34.4 + - - +
511C LEU* 3.9 31.9 - - + +
513C PHE* 6.1 0.2 - - + -
536C TYR* 3.9 23.1 - - + +
537C TRP* 1.3 75.0 + - - +
539C THR* 1.3 73.4 + - - +
545C LEU* 4.0 28.3 - - + -
546C LEU 3.2 10.1 - - - +
547C PHE* 4.0 21.3 - - + -
609C TRP* 3.6 8.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 539 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C VAL* 4.4 17.9 - - + +
507C LYS 3.3 7.9 - - - -
508C ALA* 4.0 8.3 - - + -
537C TRP* 3.7 23.3 - - + +
538C VAL* 1.3 81.5 - - - +
540C LEU* 1.3 59.9 + - - +
541C LYS* 4.7 2.4 + - - +
544C THR 3.6 1.0 - - - +
545C LEU* 3.4 4.2 - - - -
546C LEU* 2.9 50.0 + - - +
548C TYR* 3.8 19.3 - - + -
609C TRP* 4.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 540 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C VAL* 3.5 3.4 - - - -
506C ARG* 2.9 42.1 + - + +
507C LYS* 2.7 22.4 + - + +
539C THR* 1.3 72.4 - - - +
541C LYS* 1.3 58.7 + - - +
542C GLY 3.6 20.2 - - - +
543C CYS* 4.2 5.2 - - - -
544C THR 3.5 15.0 - - - +
545C LEU* 3.6 25.1 - - + -
568C ALA* 5.6 2.9 - - + -
609C TRP* 4.3 2.7 - - + -
612C ALA* 3.5 44.6 - - + +
613C ILE* 3.8 14.6 - - + +
616C ALA* 4.2 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 541 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504C VAL* 4.3 27.6 - - - +
505C VAL* 4.7 9.0 - - + +
539C THR* 3.9 3.7 + - - +
540C LEU* 1.3 72.5 - - - +
542C GLY* 1.3 68.1 + - - +
543C CYS 3.1 0.3 + - - -
544C THR* 2.9 29.2 + - - +
546C LEU* 4.5 23.1 - - + -
----------------------------------------------------------
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