Contacts of the strand formed by residues 533 - 539 (chain A) in PDB entry 5J5J
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 533 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A PRO 3.8 21.1 - - - +
447A THR* 3.4 16.1 + - - -
448A LEU* 3.2 30.9 - - + +
518A GLN* 3.7 1.1 - - - -
519A PHE* 2.8 48.5 + - + +
520A LEU* 6.0 0.2 - - - -
521A ILE* 4.3 21.5 - - + +
529A CYS* 3.2 24.3 - - + +
531A GLU* 3.2 35.3 + - - +
532A LYS* 1.3 68.4 - - - +
534A VAL* 1.3 57.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 534 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A LEU* 4.2 6.3 - - - +
451A PRO* 3.8 20.8 - - - +
516A GLU* 4.0 39.7 - - + +
517A ILE 3.5 13.2 - - - +
518A GLN* 4.3 7.9 - - + +
532A LYS* 3.1 16.9 + - + +
533A GLN* 1.3 73.4 + - - +
535A LEU* 1.3 63.9 + - - +
536A THR* 3.9 7.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 535 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A LEU* 4.2 6.5 - - + -
450A GLU 3.3 26.7 - - - +
451A PRO* 3.4 11.9 - - + +
453A GLN* 4.4 11.7 - - + -
462A VAL* 4.4 11.4 - - + -
464A VAL* 3.5 31.9 - - + -
505A LEU* 5.5 2.2 - - + -
515A SER 3.1 6.4 - - - +
516A GLU* 3.5 0.2 - - - -
517A ILE* 2.9 56.2 + - + +
519A PHE* 3.9 13.7 - - + -
534A VAL* 1.3 71.4 - - - +
536A THR* 1.3 60.0 + - - +
537A LEU* 3.4 22.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 536 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A PRO 2.7 14.0 + - - +
452A VAL* 3.6 14.6 - - + +
453A GLN 3.5 22.7 + - - +
514A ARG* 3.1 39.9 - - + +
515A SER 3.8 3.8 - - - +
516A GLU* 3.7 24.8 + - + +
534A VAL* 3.9 9.1 + - - +
535A LEU* 1.3 69.5 - - - +
537A LEU* 1.3 59.5 + - - +
538A THR* 4.0 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 537 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A GLN* 3.5 26.2 - - + +
455A ILE* 3.8 36.1 - - + +
462A VAL* 3.7 27.1 - - + -
493A TRP* 3.4 38.7 - - + -
505A LEU* 5.5 0.2 - - + -
513A GLY 3.8 2.8 - - - +
514A ARG* 3.3 2.0 - - - -
515A SER* 3.0 37.6 + - - +
517A ILE* 4.4 7.4 - - + -
535A LEU* 4.0 15.0 - - + +
536A THR* 1.3 72.2 - - - +
538A THR* 1.3 62.4 + - - +
539A VAL* 4.0 2.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A VAL* 6.1 0.7 - - - +
453A GLN 3.4 6.7 + - - -
454A THR* 3.3 25.2 - - + +
455A ILE 3.1 25.8 + - - +
513A GLY* 4.7 1.1 - - - -
514A ARG* 3.9 33.6 + - + +
536A THR* 4.7 4.7 + - - +
537A LEU* 1.3 73.2 + - - +
539A VAL* 1.3 69.2 + - - +
540A CYS* 3.8 5.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ILE* 3.8 25.1 - - + -
456A CYS 3.7 20.2 - - - +
457A HIS* 4.0 8.7 - - + -
493A TRP* 4.8 9.2 - - + -
507A GLN* 4.0 20.0 - - - +
511A LYS 4.2 4.0 - - - +
512A LEU* 3.0 34.0 - - + +
513A GLY* 3.3 28.3 + - - +
537A LEU* 4.8 3.8 - - + +
538A THR* 1.3 77.7 - - - +
540A CYS* 1.3 66.0 + - - +
----------------------------------------------------------
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