Contacts of the helix formed by residues 40 - 49 (chain B) in PDB entry 3NX4
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 ASN 40 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B SER* 3.4 6.4 + - - -
39B LEU* 1.3 77.1 - - - +
41B TYR* 1.3 68.6 + - - +
42B LYS* 3.1 4.0 - - + +
43B ASP* 2.7 29.9 + - - +
44B ALA* 2.9 21.1 + - - +
63B ILE* 3.5 15.7 - - + +
64B ASP* 2.7 30.5 + - - -
126B THR* 3.4 10.9 + - + +
127B ALA* 3.2 29.6 + - - +
310B ILE* 5.0 2.7 - - - -
318B ARG* 3.5 12.0 + - - +
330B NAP 4.5 6.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ASN* 1.3 73.3 - - - +
42B LYS* 1.3 60.8 + - - +
44B ALA* 3.2 4.3 + - - +
45B LEU* 3.1 54.8 + - + +
50B LYS* 4.7 8.8 + - - -
242B LEU* 4.6 10.4 - - + +
243B ALA* 4.9 17.5 + - + -
310B ILE* 4.1 22.1 - - + +
311B ILE* 4.4 17.4 + - + +
330B NAP 3.3 90.3 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 6.1 2.6 - - - +
40B ASN* 3.1 2.0 - - + +
41B TYR* 1.3 79.2 - - - +
43B ASP* 1.3 64.0 + - - +
45B LEU* 3.4 11.2 + - + +
46B ALA* 3.0 21.5 + - - +
53B ILE* 3.7 26.6 - - + +
63B ILE* 3.9 27.8 - - + +
92B GLU* 3.1 48.4 + - + +
268B VAL* 3.5 24.0 - - - +
330B NAP 4.7 16.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B SER 3.5 9.4 - - - +
39B LEU* 4.2 14.8 - - + -
40B ASN* 2.7 44.9 + - - +
42B LYS* 1.3 77.1 - - - +
44B ALA* 1.3 57.8 + - - +
46B ALA* 3.2 6.6 + - - +
47B ILE* 2.8 38.8 + - + +
62B GLY* 3.3 15.1 + - - +
63B ILE* 2.9 39.0 + - - +
64B ASP 5.0 0.2 + - - -
91B GLY 5.2 0.5 - - - +
98B LEU* 5.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 5.5 1.1 - - - +
40B ASN 2.9 7.9 + - - +
41B TYR 3.4 9.4 - - - +
42B LYS 3.2 0.2 - - - -
43B ASP* 1.3 77.4 - - - +
45B LEU* 1.3 50.8 + - - +
47B ILE* 3.7 0.7 - - - +
48B THR* 2.7 42.7 + - - +
307B ALA* 3.6 27.8 - - - +
310B ILE* 3.6 22.7 - - + -
311B ILE* 3.5 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TYR* 3.1 48.1 + - + +
42B LYS* 3.7 11.9 - - + +
44B ALA* 1.3 76.1 - - - +
46B ALA* 1.3 63.7 + - - +
48B THR* 3.1 3.8 + - - -
49B GLY 3.0 3.8 + - - -
50B LYS* 2.9 71.4 + - + +
51B GLY* 4.5 6.5 - - - +
53B ILE* 3.9 17.7 - - + -
242B LEU* 5.9 2.7 - - + -
311B ILE* 3.6 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.2 19.6 - - + +
13B THR* 4.1 2.8 + - - +
42B LYS 3.0 14.5 + - - +
43B ASP* 3.2 12.3 + - - +
45B LEU* 1.3 76.8 - - - +
47B ILE* 1.3 62.7 + - - +
49B GLY* 3.3 12.1 + - - -
50B LYS 4.6 0.7 - - - -
53B ILE* 4.2 12.1 - - + +
54B ILE* 3.8 33.1 - - + +
57B PHE* 5.6 0.7 - - - -
61B PRO* 4.6 7.9 - - + -
91B GLY 4.7 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.0 18.4 - - + -
6B LEU* 4.1 6.9 - - + +
13B THR* 3.7 14.9 - - - +
15B ALA* 4.1 18.8 - - + +
39B LEU* 4.0 26.9 - - + -
43B ASP* 2.8 21.7 + - + +
45B LEU 3.2 0.2 - - - -
46B ALA* 1.3 72.6 - - - +
48B THR* 1.3 60.0 + - + +
49B GLY 3.1 5.5 + - - -
61B PRO* 4.1 19.3 - - + -
98B LEU* 4.2 6.3 - - + -
303B ALA* 4.5 4.0 - - + -
304B PRO* 3.9 18.6 - - + +
307B ALA* 3.6 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B THR* 4.6 4.8 + - - +
44B ALA 2.7 26.0 + - - +
45B LEU* 3.1 12.6 + - - -
47B ILE* 1.3 76.6 - - + +
49B GLY* 1.3 59.3 + - - +
50B LYS* 3.0 15.9 + - - +
304B PRO 5.4 0.4 - - - +
307B ALA* 4.0 18.2 - - + +
308B ASP* 4.1 11.2 - - + +
311B ILE* 3.6 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B THR* 3.4 29.9 + - - -
45B LEU 3.0 5.1 + - - -
46B ALA* 3.3 5.5 + - - -
47B ILE 3.1 5.5 + - - -
48B THR* 1.3 78.1 - - - +
50B LYS* 1.3 60.6 + - - +
52B LYS 4.9 2.4 + - - -
57B PHE* 6.0 0.7 - - - -
----------------------------------------------------------
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