Contacts of the helix formed by residues 565 - 573 (chain A) in PDB entry 3FBD
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 THR 565 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ALA* 3.3 14.4 + - + +
469A GLY* 3.5 7.4 - - - +
529A THR* 3.4 18.8 - - - +
533A ASP* 3.5 31.1 + - + +
541A PHE* 3.7 16.4 - - + -
542A GLU* 5.1 0.7 - - - -
564A VAL* 1.3 76.3 - - - +
566A PRO* 1.3 71.7 - - - +
567A LYS* 4.3 1.9 - - - +
568A ARG* 3.2 22.7 + - - +
569A HIS* 2.7 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A THR* 4.1 11.7 - - + -
533A ASP 3.6 10.8 - - - +
534A VAL* 4.7 0.2 - - - -
535A SER* 3.7 17.3 - - - +
538A ARG* 3.4 33.2 - - + +
539A THR 4.3 1.6 - - - +
540A SER 3.3 28.5 - - - +
542A GLU* 3.9 20.4 - - + +
564A VAL 4.4 0.7 - - - +
565A THR* 1.3 79.7 - - - +
567A LYS* 1.3 63.8 + - - +
569A HIS* 3.0 17.9 + - + +
570A ILE* 3.0 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A GLN 3.4 26.1 + - - +
533A ASP* 3.2 20.5 + - - +
534A VAL 4.0 10.9 + - - +
535A SER* 3.8 11.3 - - - -
565A THR* 3.2 2.9 - - - +
566A PRO* 1.3 78.7 - - - +
568A ARG* 1.3 64.1 + - - +
570A ILE* 3.4 9.0 + - - +
571A ASP* 3.3 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ALA 4.0 7.0 - - - +
469A GLY* 3.3 34.3 - - - +
470A LYS 4.2 0.2 - - - +
471A ASP* 3.0 38.1 + - - +
472A LEU* 5.4 2.6 - - - +
564A VAL* 4.8 3.8 - - + -
565A THR* 3.0 20.1 + - - +
567A LYS* 1.3 78.5 - - - +
569A HIS* 1.3 68.8 + - - +
571A ASP* 3.0 24.9 + - - +
572A ILE* 3.2 34.1 + - + +
576A LYS* 3.2 36.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ARG* 3.5 11.3 + - - +
542A GLU* 2.6 31.2 + - + +
543A LEU 5.1 0.2 - - - -
544A HIS* 3.7 25.1 + + + +
564A VAL* 3.7 26.4 - - + +
565A THR 2.7 16.8 + - - +
566A PRO* 3.3 13.7 - - + +
568A ARG* 1.3 74.0 - - - +
570A ILE* 1.3 60.8 + - - +
572A ILE* 3.3 21.7 + - + +
573A HIS* 3.5 30.2 + + - -
10B T 4.1 1.6 - - - -
11B C 3.4 31.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A SER* 2.8 36.3 - - - +
538A ARG* 3.6 29.4 - - - +
566A PRO 3.0 6.5 + - - +
567A LYS* 3.6 7.4 - - - +
568A ARG 3.1 0.2 - - - -
569A HIS* 1.3 73.0 - - - +
571A ASP* 1.3 68.2 + - - +
572A ILE 3.0 1.3 - - - -
573A HIS* 3.0 21.1 + - + +
574A ARG* 3.5 27.9 - - - +
28C T 3.7 3.4 - - - +
29C C 3.4 45.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A LYS* 3.3 17.1 - - - +
568A ARG* 3.0 29.6 + - - +
570A ILE* 1.3 78.0 - - - +
572A ILE* 1.3 62.0 + - - +
574A ARG* 3.2 35.0 + - - +
576A LYS* 3.2 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ASP 3.8 15.7 - - - +
472A LEU* 4.7 11.2 - - + -
544A HIS* 3.8 46.2 - - + +
564A VAL* 4.4 12.3 - - + -
568A ARG* 3.2 34.5 + - + +
569A HIS* 3.4 17.5 - - + +
570A ILE 3.0 0.8 - - - -
571A ASP* 1.3 73.1 - - - +
573A HIS* 1.3 62.1 + - + +
574A ARG 2.8 10.2 + - - -
575A GLY* 3.5 10.1 + - - -
576A LYS 4.7 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ARG* 5.9 3.1 - - - -
544A HIS* 4.4 18.4 - + - -
548A PRO* 5.9 5.4 - - + -
569A HIS* 3.5 35.8 + + - -
570A ILE* 3.0 11.5 + - + +
572A ILE* 1.3 75.7 + - + +
574A ARG* 1.3 63.2 + - - +
9B A 5.2 11.0 - + + -
10B T 3.2 52.5 + - - -
30C G 4.9 8.0 - - - +
----------------------------------------------------------
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