Contacts of the strand formed by residues 544 - 552 (chain A) in PDB entry 3RFU
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 544 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ASP* 5.3 6.9 + - - -
446A PHE* 6.1 1.8 - - - -
516A GLY* 3.8 0.6 - - - -
517A GLY* 3.8 7.6 - - - +
518A ASP 6.0 0.7 - - - +
540A ALA* 3.1 16.4 - - - +
541A VAL* 3.2 15.9 + - - +
542A ASP* 3.1 13.0 - - - +
543A GLY* 1.3 79.7 - - - +
545A THR* 1.3 68.2 + - - +
546A VAL* 3.1 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A MET* 3.8 29.4 - - - +
517A GLY 2.9 29.9 + - - +
518A ASP 5.3 0.4 + - - +
519A ASN* 3.1 29.3 + - + +
522A LEU* 3.8 24.2 - - + -
523A PHE* 4.2 9.8 - - + -
538A PHE* 4.8 11.7 - - + -
539A MET 4.2 6.3 - - - +
540A ALA* 3.4 9.7 - - - +
544A LYS* 1.3 72.5 - - - +
546A VAL* 1.3 61.7 + - - +
547A ALA 4.7 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A THR* 3.6 12.5 + - - -
444A ASP* 3.7 8.8 - - - +
446A PHE* 3.9 32.2 - - + +
519A ASN* 4.8 0.2 - - - +
522A LEU* 3.7 11.2 - - - +
539A MET* 2.9 26.4 + - + +
540A ALA* 3.8 0.2 - - - -
541A VAL* 3.5 49.8 - - + +
544A LYS* 3.1 28.3 - - + +
545A THR* 1.3 75.7 - - - +
547A ALA* 1.3 66.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ILE* 4.4 6.5 - - + -
442A VAL 3.5 12.3 - - - +
443A THR* 4.2 5.2 - - - +
446A PHE* 4.6 0.4 - - + -
451A ALA* 3.7 15.3 - - + -
522A LEU* 3.8 9.6 - - - +
538A PHE* 3.9 2.6 - - - +
539A MET* 3.0 57.8 + - + +
545A THR* 4.8 0.7 - - - +
546A VAL* 1.3 80.8 - - + +
548A LEU* 1.3 62.3 + - - +
549A LEU* 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ARG 3.9 0.4 - - - +
441A ILE* 3.1 10.4 - - - +
442A VAL* 3.0 59.3 + - + -
522A LEU* 3.2 33.4 - - + +
525A LYS* 4.3 5.6 - - + +
526A ALA* 3.9 17.9 - - + +
529A LEU* 5.4 0.7 - - + -
536A VAL* 3.8 17.9 - - + -
537A MET 3.6 11.9 - - - +
538A PHE* 3.3 35.7 - - + -
547A ALA* 1.3 76.4 - - - +
549A LEU* 1.3 65.1 + - - +
550A VAL* 4.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A LEU* 4.4 7.4 - - + -
440A ARG 4.0 1.3 - - - -
441A ILE* 3.5 35.7 - - + -
451A ALA* 5.6 0.2 - - + -
452A LEU* 5.3 2.5 - - + -
455A ALA* 3.6 29.8 - - + -
459A GLU* 6.1 0.4 - - - +
470A ILE* 4.3 23.3 - - + -
506A ILE* 3.8 23.1 - - + -
535A SER 3.8 1.4 - - - +
536A VAL* 3.7 1.4 - - - -
537A MET* 3.0 41.5 + - + +
539A MET* 4.8 14.6 - - + -
548A LEU* 1.3 85.1 - - - +
550A VAL* 1.3 64.6 + - - +
551A VAL* 4.1 3.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A LEU* 3.1 18.2 - - - +
439A THR* 3.2 14.9 + - - +
440A ARG* 3.0 45.4 + - + +
442A VAL* 4.8 7.2 - - + -
529A LEU* 3.6 31.4 - - + -
534A ALA* 4.7 11.0 - - + -
535A SER 3.7 4.9 - - - +
536A VAL* 3.8 17.5 - - + -
549A LEU* 1.3 79.0 - - - +
551A VAL* 1.3 64.3 + - - +
552A GLU* 5.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ILE* 6.2 2.7 - - + -
436A PRO* 5.0 4.7 - - + -
437A LYS 3.3 14.6 - - - +
438A LEU* 4.0 18.2 - - + +
466A LEU* 3.5 43.3 - - + -
469A ALA* 4.8 2.7 - - + -
470A ILE* 4.4 5.8 - - + -
534A ALA* 3.4 4.3 - - - +
535A SER* 3.0 55.1 + - - +
537A MET* 6.1 2.5 - - + -
549A LEU* 5.0 3.4 - - + +
550A VAL* 1.3 78.8 - - - +
552A GLU* 1.3 71.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A PRO* 3.4 5.5 - - - +
437A LYS 2.8 32.6 + - - +
439A THR* 3.1 30.6 + - + +
532A LYS* 4.6 15.1 + - - +
534A ALA* 3.3 27.8 - - + +
535A SER* 5.0 0.9 - - - +
550A VAL* 5.6 1.8 - - - -
551A VAL* 1.3 80.6 - - - +
553A ASP* 1.3 60.4 + - - +
554A PRO* 3.0 17.6 - - + +
----------------------------------------------------------
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