Contacts of the strand formed by residues 469 - 473 (chain A) in PDB entry 4RPP
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 ILE 469 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ALA* 3.5 34.3 - - + +
439A HIS* 4.0 9.9 - - + +
442A ALA* 3.9 16.8 - - + -
450A ILE* 3.3 14.1 - - + +
452A ALA* 3.7 27.4 - - + -
463A ALA* 3.8 29.5 - - + +
464A HIS* 4.8 4.0 + - - -
466A TYR* 3.5 28.6 + - + +
467A ARG 3.2 1.0 - - - -
468A GLY* 1.3 78.9 + - - +
470A PHE* 1.3 63.6 + - - +
471A PRO* 3.2 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA* 3.7 20.0 - - + -
43A ARG 3.2 26.9 - - - -
44A ASN* 3.4 21.1 - - - -
106A ARG* 3.7 29.2 - - - +
449A PRO* 3.5 24.7 - - + -
450A ILE 2.5 14.7 + - - +
451A ILE* 3.5 8.9 - - + -
452A ALA 3.2 17.3 + - - -
468A GLY 3.3 14.8 - - - -
469A ILE* 1.3 72.5 - - - +
471A PRO* 1.3 69.4 - - - +
472A VAL* 3.7 7.9 + - + +
500A ARG* 6.2 0.2 - - - -
502A PHE* 3.6 29.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A TYR 5.1 0.7 - - - +
106A ARG* 5.1 8.0 + - - +
107A PRO* 3.9 18.5 - - + +
452A ALA* 3.7 11.9 - - + +
454A THR* 5.8 0.4 - - + -
460A ALA* 3.0 36.3 - - + +
463A ALA* 3.7 18.2 - - + -
464A HIS* 3.5 34.1 - - + +
469A ILE 3.2 13.2 - - - +
470A PHE* 1.3 85.1 - - - +
472A VAL* 1.3 64.2 + - - +
500A ARG* 5.6 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO 5.3 1.6 - - - +
105A TYR 5.6 2.0 - - - -
107A PRO* 4.9 1.3 - - - +
451A ILE* 3.9 9.6 - - + -
452A ALA 2.9 12.2 + - - +
453A VAL* 3.6 6.6 - - + +
454A THR* 3.2 28.0 + - - +
460A ALA* 5.0 1.9 - - - +
470A PHE* 3.7 12.1 - - + +
471A PRO* 1.3 81.1 - - - +
473A LEU* 1.3 59.7 + - - +
474A CYS 3.6 0.7 + - - -
492A PHE* 3.4 32.3 - - + -
493A ALA* 5.2 0.7 - - - -
496A VAL* 3.6 39.9 - - + -
500A ARG* 4.5 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO* 4.4 9.4 + - - +
105A TYR* 4.1 37.9 + - + +
107A PRO* 4.8 3.2 - - + +
454A THR* 3.3 15.0 - - - +
455A ARG* 3.5 26.0 - - - +
456A ASN 4.0 3.1 - - - +
457A PRO* 3.8 33.4 - - + -
460A ALA* 4.4 11.0 - - + -
472A VAL* 1.3 71.5 - - - +
474A CYS* 1.3 63.9 + - - +
475A LYS* 3.6 27.0 + - + +
492A PHE* 3.5 14.7 - - - -
----------------------------------------------------------
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