Contacts of the helix formed by residues 31 - 39 (chain J) in PDB entry 2NVX
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 31 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038B SER 4.4 3.8 - - - +
1039B GLY 5.0 0.5 - - - +
1040B ASN* 5.4 2.6 + - - -
30J LEU* 1.3 74.8 - - - +
32J GLU* 1.3 74.0 + - - +
33J GLY* 3.4 18.5 + - - -
34J THR* 2.7 30.5 + - - -
35J ALA* 2.9 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039B GLY* 2.9 23.4 - - - +
1040B ASN* 4.4 8.8 - - - +
21J TYR* 4.3 12.1 - - + +
25J LEU* 3.9 25.0 - - + +
31J ASP* 1.3 80.0 - - - +
33J GLY* 1.3 56.2 + - - +
35J ALA* 3.4 2.3 - - - +
36J LEU* 2.8 38.5 + - - +
51J LEU* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 33 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037B LEU 5.1 0.2 - - - -
1038B SER 3.0 33.0 + - - -
1039B GLY* 3.6 3.0 + - - -
31J ASP* 3.0 9.0 + - - -
32J GLU* 1.3 81.5 - - - +
34J THR* 1.3 59.9 + - - +
36J LEU 3.2 6.6 + - - -
37J SER* 3.4 3.3 + - - -
47J ARG* 3.3 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 34 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J LEU* 4.0 25.9 - - + +
31J ASP* 2.7 29.8 + - - -
33J GLY* 1.3 72.5 - - - +
35J ALA* 1.3 64.8 + - - +
37J SER* 3.5 7.2 + - - +
38J ARG* 3.3 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J TYR* 4.5 10.5 - - + -
24J LEU* 4.4 22.5 - - + +
25J LEU* 4.2 14.8 - - + -
30J LEU* 4.7 8.9 - - + +
31J ASP 2.9 13.1 + - - +
32J GLU* 3.4 13.0 - - - +
33J GLY 3.2 0.2 - - - -
34J THR* 1.3 78.4 - - - +
36J LEU* 1.3 60.6 + - - +
38J ARG* 3.5 4.5 + - - +
39J LEU* 3.2 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039B GLY* 4.3 3.6 - - - -
21J TYR* 3.9 23.1 - - + -
32J GLU 2.8 20.1 + - - +
33J GLY 3.2 6.0 + - - +
35J ALA* 1.3 77.1 - - - +
37J SER* 1.3 57.4 + - - +
39J LEU* 3.7 5.6 + - + +
41J LEU* 3.2 60.0 + - + +
47J ARG* 3.7 37.5 - - + +
50J ILE* 4.0 13.5 - - + -
51J LEU* 3.8 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 37 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J GLY 3.4 4.7 + - - -
34J THR* 4.0 10.5 - - - -
35J ALA 3.3 0.4 - - - -
36J LEU* 1.3 77.0 - - - +
38J ARG* 1.3 63.4 + - - +
39J LEU 3.2 1.8 - - - -
40J GLY* 3.3 13.2 + - - -
41J LEU 4.2 6.3 + - - -
42J LYS* 6.0 0.2 - - - -
47J ARG* 2.8 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C LYS* 5.5 6.9 + - - +
24J LEU* 4.0 24.3 - - + +
28J ASP* 4.3 9.3 + - - -
30J LEU* 3.5 40.4 - - - +
34J THR* 3.3 22.6 + - - +
35J ALA* 3.5 4.9 + - - +
37J SER* 1.3 78.3 - - - +
39J LEU* 1.3 61.1 + - - +
40J GLY* 3.2 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C LYS* 5.4 5.4 - - - +
12J LYS* 6.1 0.3 - - - -
17J LYS* 4.0 40.4 - - + +
20J SER* 3.8 28.7 - - - -
21J TYR* 3.6 40.2 - - + +
24J LEU* 3.9 17.0 - - + -
35J ALA 3.2 20.7 + - - +
36J LEU* 4.0 13.0 - - + +
37J SER 3.2 1.2 - - - -
38J ARG* 1.3 76.5 - - - +
40J GLY* 1.3 59.6 + - - +
41J LEU* 3.4 13.5 + - + +
50J ILE* 5.1 1.1 - - + -
----------------------------------------------------------
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