Contacts of the strand formed by residues 543 - 549 (chain D) in PDB entry 3U1K
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 MET 543 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511D ILE* 3.7 23.6 - - + +
512D GLY* 3.7 18.3 - - - +
513D LEU* 3.7 18.7 + - + -
529D LEU* 3.6 31.0 - - + -
533D ILE* 3.9 6.1 - - - +
537D GLU 5.0 0.5 - - - +
538D ASP* 4.1 2.9 - - - +
542D ASP* 1.3 83.5 + - - +
544D ASP* 1.3 61.1 + - - +
545D PHE* 3.7 26.5 - - + -
560D ASP 3.1 14.1 - - - +
561D ILE* 4.0 11.4 - - + -
562D LYS* 3.1 15.3 + - - +
566D ILE* 4.1 24.7 - - - -
570D ILE* 4.9 1.6 - - + -
571D VAL* 6.4 0.4 - - - -
574D ALA* 4.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 544 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D CIT 2.6 37.6 - - - +
510D ALA* 3.4 24.6 - - - +
511D ILE 4.1 1.1 - - - -
533D ILE* 3.5 8.0 - - - +
538D ASP* 3.3 20.3 - - - +
543D MET* 1.3 72.1 - - - +
545D PHE* 1.3 57.6 + - - +
546D LYS* 3.4 9.5 + - - +
558D GLN 3.3 7.6 - - - +
560D ASP* 2.8 32.1 + - + +
562D LYS* 4.0 0.8 - - - +
670D CIT 3.5 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 545 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D LEU* 4.3 3.8 - - + -
509D VAL 3.5 2.1 - - - +
510D ALA* 3.3 2.3 - - - -
511D ILE* 2.9 49.2 + - + +
543D MET* 3.7 28.5 - - + -
544D ASP* 1.3 70.5 + - - +
546D LYS* 1.3 60.3 + - - +
547D ILE* 3.6 14.7 + - + +
557D LEU* 3.4 26.0 - - + -
558D GLN 3.8 2.0 - - - -
559D ALA* 3.6 26.2 - - + +
561D ILE* 5.6 0.7 - - + -
571D VAL* 4.1 22.7 - - + -
574D ALA* 4.0 19.1 - - + -
575D ILE* 3.7 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 546 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D CIT 3.0 28.8 + - - -
453D LEU* 4.2 5.9 - - + +
482D SER* 5.9 0.9 - - - -
484D SER* 3.7 6.1 - - - +
485D MET* 4.0 24.4 - - + +
509D VAL 3.6 4.0 - - - -
510D ALA* 4.0 9.6 - - + -
544D ASP* 3.6 24.0 - - - +
545D PHE* 1.3 72.6 - - - +
547D ILE* 1.3 59.7 + - - +
556D ALA 4.1 0.3 - - - +
557D LEU* 3.3 3.4 - - - +
558D GLN* 2.4 86.6 + - - +
560D ASP* 5.1 0.9 - - - -
670D CIT 3.0 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 547 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D PHE* 4.7 2.7 - - + -
485D MET* 3.8 2.2 - - - -
508D GLY* 3.3 1.4 - - - -
509D VAL* 3.0 34.0 + - + +
545D PHE* 4.2 9.0 - - + +
546D LYS* 1.3 74.8 - - - +
548D ALA* 1.3 66.8 + - - +
554D ILE* 4.0 25.6 - - + -
556D ALA 3.3 12.3 - - - +
557D LEU* 3.9 20.9 - - + -
575D ILE* 4.0 34.1 - - + +
578D ALA* 3.3 32.3 - - + -
582D LYS* 5.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 548 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457D ALA* 3.8 28.3 - - + -
485D MET* 4.1 9.6 - - + -
488D ALA* 4.9 2.2 - - + -
506D VAL* 4.8 2.0 - - + -
507D ALA 3.3 14.4 - - - +
508D GLY* 3.8 7.4 - - - -
547D ILE* 1.3 78.2 - - - +
549D GLY* 1.3 59.9 + - - +
554D ILE* 3.6 7.2 - - - +
555D THR* 2.9 21.4 + - - +
556D ALA* 2.8 15.2 + - + +
582D LYS* 4.6 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 549 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506D VAL* 3.2 9.7 - - - +
507D ALA 3.0 32.2 + - - +
548D ALA* 1.3 76.5 - - - +
550D THR* 1.3 63.9 + - - -
553D GLY 3.3 13.0 - - - -
555D THR* 3.4 16.4 - - - -
582D LYS* 3.7 7.8 - - - +
586D LEU* 4.7 0.3 - - - +
----------------------------------------------------------
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