Contacts of the helix formed by residues 541 - 551 (chain F) in PDB entry 6K4Y
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 541 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540F LEU* 1.3 84.7 - - + +
542F ALA* 1.3 57.2 + - - +
544F THR* 2.7 22.1 + - - -
545F HIS* 2.9 14.8 + - - +
573F LEU* 4.5 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 542 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1303C LYS* 5.8 8.3 - - - -
540F LEU 3.4 1.8 - - - +
541F ARG* 1.3 76.1 - - - +
543F ALA* 1.3 59.8 + - - +
545F HIS* 3.5 11.2 - - + -
546F ASP* 2.8 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 543 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540F LEU* 3.2 24.9 + - + +
542F ALA* 1.3 80.6 - - - +
544F THR* 1.3 61.9 + - + +
546F ASP* 3.7 6.2 + - - +
547F VAL* 3.3 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 544 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540F LEU* 2.9 32.7 + - + +
541F ARG* 2.7 23.6 + - - -
543F ALA* 1.3 76.3 - - + +
545F HIS* 1.3 63.7 + - - +
547F VAL* 3.2 9.2 + - - +
548F LEU* 3.2 20.6 + - - +
573F LEU* 4.8 12.9 + - - +
576F VAL* 4.2 18.9 - - - +
577F GLY* 4.4 19.5 - - - +
580F PHE* 3.8 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 545 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541F ARG 2.9 18.4 + - - +
542F ALA* 3.3 12.1 + - + +
544F THR* 1.3 78.0 + - - +
546F ASP* 1.3 66.4 + - - +
548F LEU* 3.5 17.3 + - + +
549F ALA* 3.0 29.7 + - + +
573F LEU* 5.1 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 546 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1303C LYS* 5.7 4.5 - - - -
1306C LYS* 5.8 2.1 + - - -
542F ALA* 2.8 27.8 + - - +
543F ALA* 4.1 7.1 - - - +
545F HIS* 1.3 83.0 - - - +
547F VAL* 1.3 55.6 + - + +
549F ALA* 3.1 10.4 + - - +
550F GLY* 2.5 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 547 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543F ALA 3.3 16.1 + - - +
544F THR* 3.2 10.0 + - - +
546F ASP* 1.3 76.7 - - + +
548F LEU* 1.3 59.7 + - - +
550F GLY* 2.9 16.2 + - - +
551F LEU* 3.2 20.3 + - + +
580F PHE* 3.6 26.0 - - + -
20I LYS* 5.1 8.0 + - + -
21I PHE* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 548 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544F THR 3.2 11.5 + - - +
545F HIS* 3.7 18.8 - - + +
547F VAL* 1.3 75.8 - - - +
549F ALA* 1.3 60.5 + - - +
550F GLY 3.5 0.3 + - - -
551F LEU* 3.6 21.4 + - + +
567F MET* 3.7 27.6 - - + -
573F LEU* 4.9 6.7 - - + -
576F VAL* 3.8 29.4 - - + -
580F PHE* 3.6 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 549 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545F HIS* 3.0 21.6 + - + +
546F ASP* 3.2 17.9 - - - +
548F LEU* 1.3 75.9 - - - +
550F GLY* 1.3 62.8 + - - +
551F LEU 3.5 5.0 + - - +
552F THR* 5.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 550 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546F ASP 2.5 18.8 + - - -
547F VAL* 2.9 6.9 + - - -
549F ALA* 1.3 74.4 - - - +
551F LEU* 1.3 62.4 + - - +
552F THR* 3.5 2.3 + - - +
555F GLU* 4.2 0.2 - - - +
20I LYS* 3.0 26.6 + - - -
75I GLU 4.7 0.3 - - - +
76I GLY* 3.3 28.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 551 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547F VAL* 3.2 29.9 + - + +
548F LEU* 3.6 17.9 + - + +
549F ALA 3.3 7.5 - - - +
550F GLY* 1.3 79.6 - - - +
552F THR* 1.3 57.2 + - - +
553F ALA* 3.2 8.9 + - - +
555F GLU* 3.3 22.7 - - + +
556F ALA* 3.8 27.6 - - + +
559F LEU* 4.5 10.1 - - + -
567F MET* 4.4 18.8 - - + -
580F PHE* 5.6 2.9 - - + -
17I ILE* 6.0 1.1 - - + -
20I LYS* 4.2 11.4 - - + +
21I PHE* 4.7 13.5 - - + -
----------------------------------------------------------
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