Contacts of the helix formed by residues 439 - 448 (chain A) in PDB entry 5EFX
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 GLY 439 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ALA* 1.3 62.3 + - - +
441A ARG* 4.0 10.3 - - - +
442A LEU* 3.8 21.0 + - - +
443A GLN* 4.0 10.4 + - - +
473A LEU* 4.3 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A GLY* 1.3 70.1 - - - -
441A ARG* 1.3 60.9 + - - +
442A LEU 3.2 0.4 - - - -
443A GLN* 3.1 14.5 + - + +
444A GLU* 2.9 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A GLY 4.4 5.4 - - - +
440A ALA* 1.3 79.1 - - - +
442A LEU* 1.3 62.8 + - - +
444A GLU* 3.1 39.2 + - - +
445A ILE* 3.0 37.2 + - + +
448A ARG* 5.0 4.8 - - - +
473A LEU* 3.6 21.8 - - + -
476A ASP* 3.2 28.1 + - - +
492A LEU* 3.8 19.4 - - - +
510A TYR* 3.5 24.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A GLY 3.8 12.6 + - - +
440A ALA 3.2 0.6 - - - -
441A ARG* 1.3 79.9 - - - +
443A GLN* 1.3 60.7 + - + +
445A ILE* 3.1 8.1 + - + +
446A TYR* 2.9 27.0 + - - +
468A LEU* 3.7 30.1 - - + +
469A LEU* 4.2 16.4 - - + -
471A ARG 3.4 26.2 - - - +
472A LYS* 5.0 0.2 - - - -
473A LEU* 3.7 32.2 - - + +
494A LEU* 4.8 5.8 - - + -
496A MET* 3.6 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A GLY 4.0 13.6 + - - +
440A ALA* 3.1 14.4 + - + +
442A LEU* 1.3 75.2 - - + +
444A GLU* 1.3 67.9 + - - +
446A TYR* 3.3 15.7 + - - +
447A ASN* 2.9 37.8 + - - +
469A LEU* 4.6 21.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ALA* 2.9 18.3 + - - +
441A ARG* 3.1 40.5 + - - +
443A GLN* 1.3 74.6 - - - +
445A ILE* 1.3 63.4 + - - +
447A ASN* 3.1 8.7 + - - +
448A ARG* 2.9 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ARG* 3.0 50.1 + - - +
442A LEU* 3.1 8.3 + - + +
444A GLU* 1.3 75.7 - - - +
446A TYR* 1.3 64.3 + - - +
448A ARG* 3.0 14.2 + - - +
449A MET* 3.5 31.3 + - + +
468A LEU* 4.3 8.3 - - + -
473A LEU* 4.1 16.2 - - + -
476A ASP* 4.9 1.1 - - - +
492A LEU* 4.5 0.9 - - + -
494A LEU* 3.8 29.2 - - + -
503A LEU* 3.8 11.7 - - + -
510A TYR* 3.7 24.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LEU 2.9 13.2 + - - +
443A GLN* 3.5 13.9 - - - +
445A ILE* 1.3 76.8 - - - +
447A ASN* 1.3 78.7 + - - +
449A MET* 3.3 5.8 + - - +
465A ARG* 3.1 93.8 + - + -
466A GLU* 2.4 32.5 + - - -
468A LEU* 4.8 4.5 - - + -
469A LEU* 3.5 42.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A GLN* 2.9 30.2 + - - +
444A GLU* 3.7 6.3 - - - +
446A TYR* 1.3 91.2 - - - +
448A ARG* 1.3 59.1 + - + +
449A MET 3.1 12.1 + - - +
465A ARG* 4.8 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ARG* 5.0 6.7 - - - +
444A GLU* 2.9 25.5 + - + +
445A ILE 3.0 7.0 + - - +
447A ASN* 1.3 78.4 - - + +
449A MET* 1.3 53.4 + - - +
505A GLU* 5.8 2.2 - - - +
508A GLN* 3.3 31.7 + - - +
509A LYS* 3.2 10.2 + - - +
510A TYR* 2.6 79.4 + - + -
----------------------------------------------------------
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