Contacts of the helix formed by residues 525 - 536 (chain A) in PDB entry 5FI4
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 GLU 525 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A ARG* 1.4 74.7 - - - +
526A ASN* 1.3 54.7 + - - +
527A ASP 3.3 0.2 - - - -
528A LYS* 3.8 11.2 - - + +
529A GLU* 3.1 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A ARG 3.0 6.7 - - - +
525A GLU* 1.3 76.9 - - - +
527A ASP* 1.4 66.8 + - - +
529A GLU* 4.1 4.2 - - - +
530A GLN* 3.4 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A ARG* 2.7 26.7 + - - +
526A ASN* 1.4 78.9 + - - +
528A LYS* 1.4 56.6 + - - +
529A GLU 3.3 0.2 - - - -
530A GLN* 3.4 2.1 + - - -
531A LEU* 3.1 37.3 + - + +
550A PHE* 3.4 27.3 - - + -
554A HIS* 3.1 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A ARG 2.7 16.1 + - - +
525A GLU* 4.0 11.9 - - + +
527A ASP* 1.4 69.6 - - - +
529A GLU* 1.3 63.3 + - + +
531A LEU* 3.6 9.6 + - - +
532A LYS* 3.2 23.4 + - - +
557A TYR* 3.6 27.4 - - + +
561A ILE* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A GLU* 3.1 23.1 + - + +
526A ASN* 4.1 5.6 - - - +
528A LYS* 1.3 75.2 - - + +
530A GLN* 1.4 62.6 + - - +
532A LYS* 3.6 12.5 + - - +
533A ALA* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A ASN 3.4 17.4 + - - +
527A ASP* 3.4 2.4 + - - -
529A GLU* 1.4 74.3 - - - +
531A LEU* 1.3 65.2 + - - +
533A ALA* 3.4 8.4 + - + +
534A ILE* 3.1 39.7 + - + +
547A GLU* 4.1 13.8 - - - +
550A PHE* 3.3 50.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ASP 3.1 25.2 + - - +
528A LYS 3.7 3.8 - - - +
530A GLN* 1.3 75.2 - - - +
532A LYS* 1.4 62.5 + - - +
534A ILE* 3.0 5.2 + - - -
535A SER* 3.0 19.4 + - - -
550A PHE* 3.6 18.2 - - + -
551A LEU* 3.7 28.9 - - + -
554A HIS* 4.4 18.6 - - + -
557A TYR* 3.4 37.0 - - + -
558A CYS* 4.1 12.6 - - - -
561A ILE* 3.6 14.6 - - + -
564A ILE* 3.3 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A LYS 3.2 14.4 + - - +
529A GLU* 3.6 13.9 + - - +
531A LEU* 1.4 77.1 - - - +
533A ALA* 1.4 59.6 + - - +
535A SER* 2.6 23.7 + - - +
536A THR* 3.3 25.4 + - + +
561A ILE* 4.4 14.9 - - + +
563A GLU* 5.9 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 533 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A GLU 3.2 13.0 + - - +
530A GLN* 3.5 12.8 - - + +
531A LEU 3.2 0.6 - - - -
532A LYS* 1.4 72.1 - - - +
534A ILE* 1.4 63.8 + - + +
536A THR* 3.1 18.6 + - - -
537A ARG* 3.5 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 534 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A GLN* 3.1 43.0 + - + +
531A LEU* 3.0 9.5 + - - +
533A ALA* 1.4 76.6 - - + +
535A SER* 1.4 56.5 - - - +
537A ARG* 3.2 55.5 + - - +
543A ILE* 5.4 2.7 - - + -
547A GLU* 4.0 17.7 - - + +
550A PHE* 4.0 15.9 - - + -
551A LEU* 4.0 27.6 - - + -
564A ILE* 4.2 4.7 - - + -
567A LYS* 3.8 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 535 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LEU 3.0 6.6 + - - -
532A LYS* 2.6 32.7 + - - +
534A ILE* 1.4 76.4 - - - +
536A THR* 1.4 59.3 + - - +
537A ARG 3.4 5.5 + - - +
561A ILE* 4.8 4.7 - - - +
563A GLU* 4.3 26.8 + - - +
564A ILE* 3.7 38.8 - - - +
567A LYS* 4.9 4.0 - - - +
996A ASN* 4.9 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 536 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A LYS* 3.3 22.1 + - + +
533A ALA* 3.1 17.5 + - - -
534A ILE 3.4 0.2 - - - -
535A SER* 1.4 73.6 - - - +
537A ARG* 1.3 65.8 + - - +
538A ASP 3.8 0.5 + - - -
996A ASN* 4.5 9.6 + - - +
----------------------------------------------------------
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