Contacts of the helix formed by residues 24 - 34 (chain D) in PDB entry 2NPP
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 24 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ASN* 3.0 29.2 + - - +
23D GLU* 1.3 78.5 - - - +
25D VAL* 1.3 69.6 + - - +
26D GLN* 2.5 17.8 + - - +
27D LEU* 2.5 28.5 + - - +
28D ARG* 3.5 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLU 3.9 0.2 - - - -
24D ASP* 1.3 74.0 - - - +
26D GLN* 1.3 67.3 + - - +
27D LEU 2.7 1.0 + - - -
28D ARG* 3.0 17.5 + - - +
29D LEU* 2.6 31.1 + - + +
62D GLU* 3.3 43.5 - - + +
64D GLU* 4.8 6.7 - - + +
65D VAL* 4.4 12.1 - - + -
309F LEU* 4.3 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ASP* 2.5 20.8 + - - +
25D VAL* 1.3 79.0 - - - +
27D LEU* 1.3 67.3 + - + +
29D LEU* 3.8 7.5 - - - +
30D ASN* 3.7 13.0 + - - +
309F LEU* 4.6 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D GLU* 3.3 38.5 - - + +
22D ASN* 2.9 36.1 - - + +
24D ASP* 2.5 19.3 + - - +
26D GLN* 1.3 78.8 - - + +
28D ARG* 1.3 57.5 + - - +
29D LEU 2.9 1.6 - - - -
30D ASN* 2.7 37.1 + - + +
31D SER* 3.2 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D GLU 3.4 16.7 + - - +
20D LEU* 3.8 15.9 - - - +
21D ARG* 4.5 2.1 - - - +
22D ASN* 4.8 2.4 - - - +
23D GLU* 3.1 44.3 - - - +
24D ASP 3.5 6.5 + - - +
25D VAL* 3.0 18.1 + - - +
27D LEU* 1.3 78.7 - - - +
29D LEU* 1.3 64.6 + - - +
31D SER* 3.6 2.9 + - - -
32D ILE* 3.2 21.1 + - + +
60D TYR* 3.1 46.5 - - + +
61D ASP 4.9 0.4 - - - +
62D GLU* 2.5 38.4 + - - -
65D VAL* 4.9 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D VAL* 2.6 28.5 + - + +
26D GLN* 3.8 8.3 - - - +
28D ARG* 1.3 72.0 - - - +
30D ASN* 1.3 67.8 + - - +
32D ILE* 2.8 15.4 + - + +
33D LYS* 2.8 41.6 + - + +
64D GLU* 3.7 28.9 - - + +
65D VAL* 3.2 48.8 - - + +
68D ALA* 4.6 8.1 - - + -
309F LEU* 5.9 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LEU* 3.9 13.6 - - + +
19D GLU* 5.5 1.9 - - - +
26D GLN 3.7 7.5 + - - +
27D LEU* 2.7 23.9 + - + +
29D LEU* 1.3 74.3 - - - +
31D SER* 1.3 63.8 + - - +
33D LYS* 3.1 8.8 + - - +
34D LYS* 3.0 64.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LEU* 3.2 40.9 + - - +
19D GLU* 3.6 21.5 + - - +
20D LEU* 3.0 30.5 - - - -
27D LEU 3.2 3.1 + - - -
28D ARG 3.8 4.7 - - - -
29D LEU 3.2 0.6 - - - -
30D ASN* 1.3 77.1 - - - +
32D ILE* 1.3 56.7 + - - +
34D LYS* 2.8 20.5 + - - +
35D LEU* 2.9 12.5 + - - +
38D ILE* 3.8 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 3.7 19.1 - - + -
28D ARG 3.2 13.7 + - - +
29D LEU* 2.8 15.0 + - - +
31D SER* 1.3 73.2 - - - +
33D LYS* 1.3 57.0 + - - +
35D LEU* 3.0 30.7 + - + +
55D LEU* 4.0 25.1 - - + -
60D TYR* 4.1 15.0 - - + +
65D VAL* 4.2 17.9 - - + +
68D ALA* 3.9 9.0 - - + -
69D LEU* 3.6 41.5 - - + +
72D GLN* 3.8 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LEU* 2.8 47.5 + - + +
30D ASN* 3.1 11.6 + - - +
32D ILE* 1.3 71.6 - - - +
34D LYS* 1.3 62.3 + - + +
35D LEU 3.4 0.7 - - - -
36D SER* 4.4 1.4 + - - -
64D GLU* 5.4 5.5 + - - -
68D ALA* 4.1 20.0 - - + -
72D GLN* 3.7 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LEU* 4.0 26.6 - - + +
30D ASN* 3.0 48.3 + - - +
31D SER 2.8 6.7 + - - +
33D LYS* 1.3 80.6 - - + +
35D LEU* 1.3 55.2 + - - +
36D SER* 3.0 4.5 - - - -
37D THR* 2.7 41.8 + - + +
38D ILE* 3.2 8.9 + - - +
----------------------------------------------------------
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