Contacts of the strand formed by residues 517 - 524 (chain A) in PDB entry 4R8A
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 ARG 517 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A CYS* 4.3 8.5 + - - -
483A PRO* 3.3 32.5 - - - +
486A HIS* 4.5 5.1 - - - -
511A PHE* 3.7 0.9 - - - -
512A TRP* 2.8 35.4 + - + -
515A GLN* 3.3 12.3 + - + +
516A ARG* 1.3 82.6 + - - +
518A TYR* 1.3 90.0 + - - +
519A ARG* 3.6 35.7 - - - +
545A GLU 6.0 0.4 + - - -
547A PRO* 4.4 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A CYS* 4.3 4.6 - - + +
482A LEU* 3.8 18.6 - - + -
483A PRO* 3.5 17.7 - - + -
486A HIS* 2.8 24.8 + - - -
490A TRP* 3.4 18.3 - + - -
509A ILE* 4.5 4.5 - - + -
510A GLN 3.4 5.4 - - - +
511A PHE* 3.8 26.7 - - + -
512A TRP* 4.5 0.2 - - - -
517A ARG* 1.3 107.8 + - - +
519A ARG* 1.3 78.9 + - - +
520A MET* 3.5 27.8 - - + -
546A MET* 3.7 4.8 - - + +
547A PRO* 3.2 42.1 - - + +
548A VAL* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A GLN* 2.9 51.3 + - - +
512A TRP* 3.2 46.9 - - - +
515A GLN* 3.6 23.0 - - - +
517A ARG* 3.6 24.9 - - - +
518A TYR* 1.3 78.5 - - - +
520A MET* 1.3 61.5 + - - +
521A VAL* 4.3 1.5 + - + -
547A PRO* 3.5 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ILE* 4.4 7.9 - - + -
482A LEU* 4.9 1.8 - - + -
490A TRP* 3.7 26.2 - - + -
505A LEU* 4.8 7.6 - - - -
506A PRO* 3.5 28.6 - - + +
508A LEU 3.4 3.6 - - - +
509A ILE* 3.4 37.5 - - + -
518A TYR* 3.5 26.0 - - + -
519A ARG* 1.3 74.3 - - - +
521A VAL* 1.3 64.3 + - - +
538A LEU* 5.7 0.2 - - - +
541A CYS* 5.2 3.6 - - - -
546A MET* 6.4 0.2 - - + -
547A PRO 2.9 12.5 + - - +
548A VAL* 3.2 25.7 - - + +
549A ALA 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LEU* 5.4 5.6 - - + -
371A VAL* 5.6 0.2 - - + -
375A LEU* 4.7 11.9 - - + -
506A PRO* 3.6 4.7 - - - +
507A ASP* 3.4 1.0 + - - +
508A LEU* 2.7 54.4 + - + +
510A GLN* 4.3 21.3 - - + +
519A ARG* 4.3 2.0 + - + +
520A MET* 1.3 81.4 - - - +
522A GLU* 1.3 62.4 + - - +
523A VAL* 4.2 5.8 - - + -
549A ALA* 3.2 23.6 - - + +
550A VAL 4.5 0.2 - - - -
551A CYS* 3.5 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A LEU 4.0 1.0 - - - +
506A PRO* 3.3 21.1 - - + +
507A ASP* 2.8 52.3 + - - +
521A VAL* 1.3 74.6 - - - +
523A VAL* 1.3 63.5 + - - +
524A LYS* 3.1 28.9 + - - -
530A LEU* 4.0 15.0 - - + -
534A GLN* 3.8 18.4 + - + +
538A LEU* 5.3 7.4 - - + -
549A ALA 3.2 6.5 + - - +
550A VAL* 3.4 10.3 - - + +
551A CYS 2.9 19.4 + - - -
5B A 2.9 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A VAL* 4.0 8.1 - - + -
368A GLU* 3.5 44.0 - - + +
371A VAL* 3.7 38.6 - - + -
507A ASP* 3.0 17.5 + - - +
508A LEU* 3.8 21.8 - - + -
521A VAL* 4.2 4.0 - - + -
522A GLU* 1.3 85.8 - - - +
524A LYS* 1.3 66.6 + - - +
551A CYS* 3.2 18.2 - - + +
553A VAL* 5.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A VAL* 4.4 3.6 - - - -
368A GLU* 5.2 1.1 - - - -
522A GLU* 3.1 15.2 + - - -
523A VAL* 1.3 79.9 - - - +
525A GLY* 1.3 64.0 + - - +
528A ASP* 2.9 45.1 + - - +
529A ARG 3.2 25.4 + - - +
530A LEU* 3.6 18.2 - - - +
531A GLN* 4.4 0.6 - - - +
534A GLN* 2.9 21.0 + - - -
550A VAL* 4.4 9.2 - - + -
551A CYS 2.8 11.3 + - - +
552A TYR* 3.8 25.8 - - + +
553A VAL* 3.0 26.0 + - - +
5B A 3.0 12.5 + - - +
----------------------------------------------------------
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