Contacts of the helix formed by residues 56 - 64 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430E ASP* 2.6 42.4 + - - -
433E ASP* 3.1 16.3 + - - -
55H ASN* 1.3 81.1 - - - +
57H ASP* 1.3 67.0 + - - +
58H GLY 3.3 4.9 + - - -
59H SER* 3.3 4.6 + - - -
60H VAL* 3.0 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 57 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H ASN 4.3 1.3 + - - +
56H SER* 1.3 72.1 + - - +
58H GLY* 1.3 58.4 + - - +
60H VAL* 2.9 10.3 + - - +
61H ALA* 2.7 36.4 + - - +
126H LEU* 3.7 8.9 - - + +
242H PRO 4.4 0.5 - - - +
243H LEU* 3.4 34.1 - - + +
246H LYS* 3.3 35.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 58 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430E ASP* 4.9 2.0 - - - -
56H SER* 3.3 7.4 + - - -
57H ASP* 1.3 80.2 - - - +
59H SER* 1.3 60.6 + - - +
61H ALA* 3.4 4.6 + - - +
62H ILE* 3.2 26.8 + - - +
311H HIS* 3.3 45.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429E GLU* 4.2 15.7 - - - +
430E ASP* 3.1 25.0 + - - +
433E ASP* 2.6 31.0 + - - +
54H LEU* 3.3 23.2 - - - +
56H SER* 3.3 6.8 + - - -
57H ASP 3.2 0.4 - - - -
58H GLY* 1.3 75.4 - - - +
60H VAL* 1.3 62.3 + - - +
62H ILE* 3.3 4.1 + - - +
63H HIS* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H TYR* 5.2 9.9 - - + +
54H LEU* 4.5 23.8 - - + +
55H ASN 5.7 0.2 - - - -
56H SER 3.0 17.6 + - - +
57H ASP* 2.9 12.7 + - - +
59H SER* 1.3 72.9 - - - +
61H ALA* 1.3 55.4 + - - +
62H ILE 2.5 17.2 + - - -
63H HIS 3.0 0.2 + - - -
64H ALA* 2.6 49.5 + - + +
125H ALA* 4.0 17.7 - - + +
126H LEU* 3.6 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H ASP 2.7 18.8 + - - +
58H GLY* 3.7 8.7 - - - +
60H VAL* 1.3 75.2 - - - +
62H ILE* 1.3 57.5 + - - +
122H LYS* 3.0 29.8 + - - +
126H LEU* 4.0 24.9 - - + -
243H LEU* 5.5 1.8 - - + -
307H MET* 3.5 27.9 - - + +
310H LEU* 4.4 11.2 - - + -
311H HIS* 5.0 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392E CYS* 4.0 9.6 - - + +
393E GLU* 4.1 11.9 - - + -
428E VAL* 3.3 34.1 - - + -
429E GLU* 3.9 19.3 - - + +
58H GLY 3.2 15.7 + - - +
59H SER 3.5 6.1 - - - +
60H VAL 2.5 6.3 + - - -
61H ALA* 1.3 76.5 - - - +
63H HIS* 1.3 79.7 + - + +
66H GLU* 3.2 1.4 - - - +
122H LYS* 2.7 20.6 + - - +
308H LYS* 2.9 52.0 + - + +
311H HIS* 4.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 63 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382E ILE* 3.8 17.2 + - + +
384E TYR* 4.2 11.3 - + - -
393E GLU* 4.1 15.0 - - + +
394E SER 4.7 0.2 + - - -
429E GLU* 2.9 41.9 + - + +
50H TYR* 3.4 6.3 - - - -
53H PHE* 6.0 0.2 - + - -
54H LEU* 3.9 21.3 - - + +
59H SER 3.1 9.7 + - - -
60H VAL 3.0 1.6 + - - -
62H ILE* 1.3 92.1 - - + +
64H ALA* 1.3 65.7 + - - +
65H GLY 3.1 0.7 + - - -
66H GLU* 3.0 18.8 + - + -
67H ARG* 3.1 47.4 + - + +
308H LYS* 5.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H TYR* 4.1 14.3 - - + -
60H VAL* 2.6 46.1 + - + +
62H ILE 3.6 0.4 - - - -
63H HIS* 1.3 68.5 - - - +
65H GLY* 1.3 58.6 + - - +
121H GLU 5.1 0.2 - - - -
122H LYS* 3.0 47.3 - - + +
125H ALA* 3.9 17.7 - - + -
----------------------------------------------------------
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