Contacts of the helix formed by residues 56 - 64 (chain D) in PDB entry 1I43
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 SER 56 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ASP* 2.9 39.4 + - - +
432A ASP* 6.4 0.4 - - - -
433A ASP* 3.2 19.0 + - - -
55D ASN* 1.3 80.0 - - - +
57D ASP* 1.3 67.5 + - - +
58D GLY 3.4 5.9 + - - -
59D SER* 3.3 4.6 + - - -
60D VAL* 3.1 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ASN 4.9 3.3 - - - +
56D SER* 1.3 74.9 + - - +
58D GLY* 1.3 54.8 + - - +
60D VAL* 2.9 10.8 + - - +
61D ALA* 2.7 37.5 + - - +
126D LEU* 3.6 7.5 - - + +
243D LEU* 3.3 36.5 - - + +
246D LYS* 3.0 36.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ASP* 4.7 2.2 - - - -
56D SER* 3.2 8.2 + - - -
57D ASP* 1.3 81.5 - - - +
59D SER* 1.3 61.7 + - - +
60D VAL 3.2 0.2 + - - -
61D ALA* 3.3 4.1 + - - +
62D ILE* 3.2 25.6 + - - +
311D HIS* 3.4 44.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A GLU* 3.7 17.2 - - - +
430A ASP* 3.1 21.9 + - - +
433A ASP* 2.6 32.3 + - - +
54D LEU* 3.6 27.6 - - - +
56D SER* 3.3 5.1 + - - -
57D ASP 3.3 0.2 - - - -
58D GLY* 1.3 75.4 - - - +
60D VAL* 1.3 57.5 + - - +
62D ILE* 3.3 3.2 + - - +
63D HIS* 3.0 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D TYR* 5.6 8.3 - - + -
51D ALA 6.3 0.2 - - - +
54D LEU* 4.6 20.9 - - + +
55D ASN 5.3 0.7 - - - -
56D SER 3.1 17.8 + - - +
57D ASP* 2.9 14.3 + - - +
59D SER* 1.3 73.1 - - - +
61D ALA* 1.3 60.8 + - - +
62D ILE 2.8 7.1 + - - -
64D ALA* 2.7 53.3 + - + +
125D ALA* 3.7 19.5 - - + +
126D LEU* 3.6 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D ASP 2.7 19.2 + - - +
58D GLY* 3.3 8.3 + - - +
60D VAL* 1.3 71.8 - - - +
62D ILE* 1.3 56.2 + - - +
122D LYS* 3.0 27.7 + - - +
126D LEU* 4.0 26.7 - - + -
243D LEU* 5.5 1.6 - - + -
307D MET* 3.3 30.1 - - + +
310D LEU* 4.3 12.6 - - + -
311D HIS* 5.0 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A CYS* 4.1 8.3 - - + +
393A GLU* 4.1 15.9 - - + -
428A VAL* 3.4 32.5 - - + -
429A GLU* 3.7 21.3 - - + +
58D GLY 3.2 15.9 - - - +
59D SER 3.5 6.5 - - - +
60D VAL 2.8 2.2 + - - -
61D ALA* 1.3 80.0 - - - +
63D HIS* 1.3 81.6 + - + +
66D GLU* 3.5 0.9 - - - +
122D LYS* 2.6 22.9 + - - +
308D LYS* 3.1 44.9 + - + +
311D HIS* 3.9 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ILE* 3.9 15.8 + - + -
384A TYR* 4.2 10.4 - + - -
393A GLU* 4.0 17.8 - - + +
394A SER 4.7 0.2 + - - -
429A GLU* 2.9 40.8 + - + +
50D TYR* 3.4 6.1 + - + -
54D LEU* 4.0 17.3 - - + +
59D SER 3.0 15.5 + - - +
62D ILE* 1.3 89.0 - - + +
64D ALA* 1.3 68.6 + - - +
65D GLY 3.0 0.7 + - - -
66D GLU* 2.8 19.8 + - + -
67D ARG* 3.1 46.1 + - + +
308D LYS* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D TYR* 3.9 13.2 - - + -
54D LEU* 5.5 0.2 - - - +
60D VAL* 2.7 47.7 + - + +
62D ILE 3.6 0.2 - - - -
63D HIS* 1.3 69.5 - - - +
65D GLY* 1.3 58.6 + - - +
122D LYS* 2.9 48.6 - - + +
125D ALA* 3.7 18.2 - - + -
----------------------------------------------------------
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