Contacts of the helix formed by residues 23 - 39 (chain B) in PDB entry 2N23
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 THR 23 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 5.1 17.0 - - - +
22B ASP* 1.3 94.6 + - - +
24B GLN* 1.3 71.3 + - - +
25B ASP 3.0 1.6 - - - -
26B ASP* 2.9 24.6 + - - +
27B PHE* 3.0 28.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASP 5.4 1.8 - - - +
23B THR* 1.3 83.9 + - - +
25B ASP* 1.3 65.8 + - - +
27B PHE* 3.1 29.0 + - + +
28B LEU* 3.4 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASP* 2.7 41.6 + - - +
24B GLN* 1.3 81.1 + - - +
26B ASP* 1.3 58.8 + - - +
28B LEU* 3.1 32.7 - - + +
29B LYS* 3.1 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASP 3.2 19.4 - - - +
23B THR* 2.9 10.8 + - - +
25B ASP* 1.3 79.2 - - - +
27B PHE* 1.3 61.4 + - + +
29B LYS* 2.9 14.8 + - + +
30B TRP* 2.9 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 5.2 13.2 - - - -
57A LYS* 5.8 2.7 - - - -
59A MET* 4.8 11.7 - - + -
88A MET* 3.6 36.3 - - + -
90A SER* 5.2 4.7 - - - -
23B THR* 3.0 41.6 + - - -
24B GLN* 3.1 17.8 + - + +
26B ASP* 1.3 79.7 - - + +
28B LEU* 1.3 59.7 + - - +
30B TRP* 3.2 43.4 + + - +
31B TRP* 3.6 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ARG* 3.8 10.5 - - - +
86A ARG* 3.7 26.7 - - - +
88A MET* 5.0 0.4 - - + +
24B GLN 3.4 9.5 + - - +
25B ASP* 3.1 30.1 - - + +
27B PHE* 1.3 77.7 - - - +
29B LYS* 1.3 79.5 + - + +
31B TRP* 4.0 2.7 - - - +
32B ARG* 3.5 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASP 3.1 18.6 - - - +
26B ASP* 2.9 20.8 + - + +
28B LEU* 1.3 91.9 - - + +
30B TRP* 1.3 61.3 + - - +
31B TRP 3.1 1.3 - - - -
32B ARG* 3.1 10.8 + - - +
33B SER* 2.8 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR* 3.4 26.2 - - + -
52A PRO* 5.3 2.0 - - + -
55A SER* 4.4 7.2 - - - -
57A LYS* 3.3 44.7 - - + +
59A MET* 3.9 13.7 - - + -
26B ASP* 2.9 28.6 + - + +
27B PHE* 3.2 40.6 - + - +
29B LYS* 1.3 77.0 - - - +
31B TRP* 1.3 91.4 + + - +
33B SER* 3.6 9.1 - - - -
34B GLU* 2.8 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLN* 4.5 6.5 + - + +
50A ALA* 3.7 37.7 + - - -
51A THR* 4.0 4.5 - - + -
52A PRO* 4.5 10.9 - - + +
59A MET* 3.5 30.7 - - + -
60A LEU 4.7 0.2 - - - -
61A ARG* 3.6 56.3 - - + +
88A MET* 3.4 32.3 - - + -
27B PHE 3.6 8.9 + - - +
28B LEU 4.0 4.5 - - - +
29B LYS 3.1 0.4 - - - -
30B TRP* 1.3 109.4 - + - +
32B ARG* 1.3 66.6 + - + +
34B GLU* 4.0 3.4 - - - +
35B GLU* 3.3 24.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ARG* 6.3 0.4 - - - +
28B LEU* 3.5 16.1 + - + +
29B LYS* 3.1 13.3 + - - +
31B TRP* 1.3 82.1 - - + +
33B SER* 1.3 56.3 + - - +
35B GLU* 3.1 31.3 + - - +
36B ALA* 2.7 38.8 + - - +
39B MET* 5.4 9.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LYS 2.8 18.3 + - - -
30B TRP* 3.7 11.4 - - - -
32B ARG* 1.3 76.1 - - - +
34B GLU* 1.3 60.7 + - - +
36B ALA* 3.3 7.4 + - - +
37B GLN* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PRO* 3.5 29.0 - - + +
54A SER* 2.7 30.6 + - - +
55A SER* 3.8 21.2 + - - -
30B TRP* 2.8 25.8 + - + +
31B TRP* 4.0 4.5 - - - +
33B SER* 1.3 77.8 - - - +
35B GLU* 1.3 60.3 + - - +
37B GLN* 3.0 41.0 + - - +
38B ASP* 3.6 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PRO* 5.2 15.4 - - + +
31B TRP* 3.3 19.0 + - + +
32B ARG* 3.1 41.0 + - - +
34B GLU* 1.3 77.3 - - - +
36B ALA* 1.3 60.5 + - - +
37B GLN 3.1 1.3 - - - -
38B ASP* 3.1 17.7 + - - +
39B MET* 2.9 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ARG* 2.7 21.5 + - - +
33B SER* 3.3 8.3 + - - +
35B GLU* 1.3 71.2 - - - +
37B GLN* 1.3 62.7 + - - +
39B MET* 3.0 30.4 - - - +
40B GLY* 3.9 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A SER* 3.9 16.4 + - - -
33B SER 3.1 12.7 + - - +
34B GLU* 3.0 41.2 + - - +
35B GLU 3.1 0.4 - - - -
36B ALA* 1.3 81.0 - - - +
38B ASP* 1.3 62.4 + - - +
40B GLY* 4.0 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PRO* 6.5 1.1 - - + -
54A SER* 5.4 7.0 - - - +
34B GLU 3.6 5.7 + - - +
35B GLU* 3.1 21.4 + - - +
37B GLN* 1.3 82.9 - - - +
39B MET* 1.3 60.3 + - - +
40B GLY 3.0 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ARG* 5.4 10.1 - - - -
35B GLU* 2.9 21.2 + - + +
36B ALA* 3.0 19.4 - - - +
37B GLN 3.3 0.2 - - - -
38B ASP* 1.3 75.2 - - - +
40B GLY* 1.3 65.0 + - - +
----------------------------------------------------------
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