Contacts of the helix formed by residues 42 - 50 (chain A) in PDB entry 4ITY
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 42 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU 3.2 5.0 + - - -
40A LYS 2.9 7.8 + - - -
41A GLN* 1.3 80.8 - - - +
43A LEU* 1.3 66.6 + - - +
44A GLN 3.2 2.7 - - - -
45A GLN* 3.0 25.7 + - - +
46A ASP* 3.0 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 3.9 24.5 - - + -
38A LEU* 3.2 31.4 + - + +
39A LEU* 4.0 13.6 + - + -
41A GLN 3.7 0.8 - - - -
42A GLY* 1.3 75.3 - - - +
44A GLN* 1.3 63.6 + - - +
46A ASP* 3.3 10.6 + - - +
47A MET* 3.1 33.4 + - + +
108A LEU* 5.0 3.8 - - + -
110A ILE* 3.7 33.4 - - + -
308A CYS* 4.6 16.3 - - - +
311A ALA* 3.6 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 3.9 16.1 - - + +
39A LEU* 4.4 7.7 - - + +
42A GLY 3.2 1.0 - - - -
43A LEU* 1.3 75.7 - - - +
45A GLN* 1.3 75.6 + - - +
47A MET* 3.2 2.4 + - - +
48A GLU* 2.8 34.8 + - + +
54A THR* 2.7 44.6 + - - +
55A ARG* 4.2 1.6 - - - +
56A LEU* 3.5 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU 4.5 3.6 - - - +
42A GLY* 3.0 27.9 + - - +
44A GLN* 1.3 90.4 + - - +
46A ASP* 1.3 56.2 + - - +
48A GLU* 3.3 6.7 + - - +
49A LYS* 2.7 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLN 4.4 5.5 - - - +
42A GLY* 3.0 25.6 + - - +
43A LEU* 3.4 11.1 + - - +
45A GLN* 1.3 78.6 - - - +
47A MET* 1.3 61.2 + - + +
49A LYS* 3.2 16.0 + - - +
50A LEU* 2.9 33.1 + - - +
308A CYS* 4.3 12.5 - - - +
312A ARG* 3.7 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A MET* 3.8 20.4 - - + -
17A ILE* 4.3 8.3 - - + -
43A LEU* 3.1 18.3 + - + +
44A GLN 3.2 4.5 + - - +
46A ASP* 1.3 87.3 - - + +
48A GLU* 1.3 64.7 + - - +
50A LEU* 3.0 32.2 + - + +
51A GLY 3.4 0.3 + - - -
52A TRP* 3.0 20.7 + - - +
54A THR* 3.5 20.6 - - + -
108A LEU* 3.9 10.3 - - + -
311A ALA* 3.8 25.6 - - + +
312A ARG* 3.9 4.5 - - + +
315A MET* 3.6 27.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLN* 2.8 25.8 + - + +
45A GLN* 3.8 6.1 - - - +
47A MET* 1.3 71.9 - - - +
49A LYS* 1.3 55.0 + - - +
51A GLY* 2.7 26.0 + - - -
52A TRP 2.5 29.2 + - - +
53A ASP* 3.8 6.2 - - - +
54A THR* 2.6 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLN 2.7 22.9 + - - +
46A ASP* 3.3 17.3 + - - +
48A GLU* 1.3 72.7 - - - +
50A LEU* 1.3 60.3 + - + +
51A GLY 3.2 1.2 + - - -
312A ARG* 6.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LYS* 3.2 21.3 + - - -
46A ASP 2.9 13.0 + - - +
47A MET* 3.5 32.5 - - + +
48A GLU 3.0 0.6 - - - -
49A LYS* 1.3 80.0 - - + +
51A GLY* 1.3 58.1 + - - +
52A TRP* 3.5 10.1 + - + -
312A ARG* 3.6 31.2 - - + +
315A MET* 3.9 15.4 - - + +
316A GLY* 4.1 5.2 - - - +
317A GLU* 3.7 27.4 - - + +
----------------------------------------------------------
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