Contacts of the helix formed by residues 41 - 48 (chain A) in PDB entry 3N3B
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 ASP 41 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.2 11.8 + - - +
39A SER 3.1 1.4 - - - -
40A ASN* 1.3 78.6 - - - +
42A ILE* 1.3 57.5 + - - +
43A PRO* 3.4 1.8 - - - -
44A ALA* 3.1 9.7 + - - +
45A TRP* 2.8 28.1 + - - +
112A LEU* 3.7 11.7 - - + -
178A LEU* 3.4 21.9 - - + +
179A THR* 3.6 5.9 + - - -
180A ASN* 2.8 36.1 + - - -
181A THR* 2.8 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER* 3.4 29.2 - - - +
41A ASP* 1.3 77.5 - - - +
43A PRO* 1.4 69.6 - - + +
45A TRP* 3.3 15.9 + - + +
46A GLN* 3.3 13.2 + - - +
111A THR* 4.0 19.5 - - + +
112A LEU* 3.8 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER 4.1 2.7 - - - +
40A ASN* 3.7 17.3 - - - +
41A ASP 3.6 2.9 - - - -
42A ILE* 1.4 96.3 - - + +
44A ALA* 1.3 58.0 + - - +
46A GLN* 3.6 21.8 - - + +
47A THR* 3.7 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASN 5.0 2.0 + - - +
41A ASP* 3.1 14.4 + - - +
43A PRO* 1.3 75.8 - - - +
45A TRP* 1.3 63.6 + - - +
46A GLN 3.2 2.0 - - - -
47A THR* 2.7 27.1 + - - +
48A LEU* 3.7 10.7 + - - +
176A GLY 5.5 0.9 - - - +
177A LYS* 4.6 9.5 - - + +
178A LEU* 3.8 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASP 2.8 15.7 + - - +
42A ILE* 3.3 13.7 + - + +
44A ALA* 1.3 75.8 - - - +
46A GLN* 1.3 63.7 + - - +
48A LEU* 3.6 29.4 + - + +
53A GLN* 3.0 71.6 + - + +
56A THR* 3.7 30.7 - - + -
57A MET* 4.3 9.2 - - + -
108A ILE* 6.2 0.2 - - + -
112A LEU* 3.2 40.5 + - + -
113A CYS* 3.6 30.4 - - + +
178A LEU* 4.0 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE 3.3 10.7 + - - +
43A PRO* 3.6 16.8 - - - +
44A ALA 3.2 0.2 - - - -
45A TRP* 1.3 81.9 - - - +
47A THR* 1.3 66.6 + - - +
48A LEU 3.3 8.1 + - - +
53A GLN* 4.8 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO 3.7 15.0 - - - +
44A ALA* 2.7 24.0 + - - +
46A GLN* 1.3 81.4 - - + +
48A LEU* 1.3 62.6 + - - +
49A THR* 3.8 3.5 + - - +
52A GLU* 4.9 0.7 - - - +
177A LYS* 3.1 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA 3.7 9.0 - - - +
45A TRP* 3.7 43.5 - - + +
46A GLN 3.2 9.7 - - - +
47A THR* 1.3 80.7 + - - +
49A THR* 1.3 63.6 + - - +
52A GLU* 3.6 20.2 - - + +
53A GLN* 4.0 18.5 + - + -
56A THR* 4.7 2.7 - - - +
172A PHE* 3.7 31.0 - - + -
177A LYS* 3.9 22.7 - - + +
178A LEU* 3.8 19.3 - - + -
----------------------------------------------------------
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