Contacts of the helix formed by residues 26 - 39 (chain B) in PDB entry 2ZNZ
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 26 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 1.3 79.8 - - - +
27B GLU* 1.3 58.1 + - - +
28B ILE* 3.0 10.8 + - + +
29B ASP* 3.4 27.6 + - - +
30B LYS* 3.1 24.9 + - - +
61B ARG* 2.9 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU 3.6 0.8 + - - -
26B ASP* 1.3 73.6 + - - +
28B ILE* 1.3 59.3 + - + +
30B LYS* 3.3 36.2 + - + +
31B LYS* 3.1 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP* 3.0 8.7 - - - +
27B GLU* 1.3 78.7 - - + +
29B ASP* 1.3 65.9 + - - +
31B LYS* 3.3 25.7 + - + +
32B ILE* 3.2 28.9 + - + +
51B THR* 4.6 2.5 - - - +
53B LEU* 3.6 47.3 - - + +
57B THR* 5.7 0.4 - - + -
61B ARG* 3.6 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.6 18.7 - - + +
26B ASP* 3.4 21.5 + - - +
28B ILE* 1.3 74.6 - - - +
30B LYS* 1.3 57.6 + - - +
32B ILE* 3.4 6.3 + - - +
33B ILE* 2.9 36.0 + - - +
61B ARG* 3.1 47.7 + - - +
64B LYS* 3.7 19.0 + - - -
65B LEU* 4.0 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 4.8 10.1 - - + -
25B LEU* 3.5 37.1 + - + -
26B ASP 3.1 12.1 + - - +
27B GLU* 3.3 35.2 + - + +
28B ILE 3.3 0.2 - - - -
29B ASP* 1.3 73.0 - - - +
31B LYS* 1.3 61.1 + - + +
33B ILE* 3.8 5.9 - - - +
34B LYS* 3.0 30.5 + - - +
170B ILE* 3.8 31.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLU* 3.1 28.3 + - + +
28B ILE* 3.3 23.5 + - + +
30B LYS* 1.3 77.7 - - - +
32B ILE* 1.3 62.5 + - + +
34B LYS* 3.7 12.6 + - - +
35B ILE* 3.4 29.1 + - + +
51B THR* 3.6 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 3.2 24.7 + - + +
29B ASP* 3.8 7.0 - - - +
31B LYS* 1.3 76.7 - - + +
33B ILE* 1.3 65.9 + - - +
35B ILE* 3.0 19.8 + - - +
36B LEU* 3.0 25.3 + - + +
47B ILE* 4.2 18.8 - - + -
51B THR* 5.4 1.6 - - - +
53B LEU* 4.3 7.6 - - + -
58B ILE* 4.3 15.7 - - + -
61B ARG* 3.7 34.5 - - + -
62B ILE* 3.9 28.3 - - + -
65B LEU* 4.6 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 3.8 39.9 - - + -
83A LEU* 4.8 5.6 - - + -
25B LEU* 4.2 13.7 - - + -
29B ASP 2.9 26.9 + - - +
30B LYS* 3.8 4.0 - - - +
32B ILE* 1.3 76.1 - - + +
34B LYS* 1.3 64.7 + - - +
36B LEU* 3.9 6.1 - - - +
37B GLN* 3.0 27.2 + - - +
65B LEU* 4.2 20.2 - - + -
70B VAL* 3.9 26.2 - - + -
71B ILE* 5.1 2.0 - - + -
170B ILE* 3.6 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LYS 3.0 18.5 + - - +
31B LYS* 3.7 13.5 - - - +
33B ILE* 1.3 76.1 - - - +
35B ILE* 1.3 72.0 + - - +
37B GLN* 3.7 6.3 + - - +
38B ASN* 3.4 20.8 + - - +
50B ILE* 5.9 3.6 - - - +
167B GLU* 4.7 1.9 - - - +
170B ILE* 3.7 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LYS* 3.4 20.4 - - + +
32B ILE* 3.0 7.9 + - - +
34B LYS* 1.3 88.8 - - - +
36B LEU* 1.3 60.2 + - - +
38B ASN* 3.3 7.7 + - - +
39B ASP* 2.9 26.4 + - + +
42B ALA* 3.6 25.4 - - + -
47B ILE* 3.9 33.4 - - + +
50B ILE* 4.1 42.0 - - + -
51B THR* 5.2 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ALA* 2.9 32.7 + - + -
32B ILE* 3.0 36.5 + - + +
33B ILE* 4.2 4.5 - - - +
35B ILE* 1.3 72.0 - - - +
37B GLN* 1.3 63.8 + - - +
39B ASP 3.5 13.2 - - - +
40B GLY 3.2 27.1 + - - +
42B ALA* 4.2 7.6 - - + +
47B ILE* 3.9 23.8 - - + -
62B ILE* 3.9 20.9 - - + -
71B ILE* 4.1 11.7 - - + -
74B PHE* 4.1 21.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
73A LYS* 3.2 13.3 + - - -
75A THR* 2.7 24.2 + - - +
76A ALA* 3.8 8.6 + - - +
78A ILE* 3.4 33.0 - - + +
83A LEU* 4.9 0.4 - - - +
33B ILE* 3.0 24.6 + - - +
34B LYS* 3.8 5.2 - - - +
36B LEU* 1.3 76.8 - - - +
38B ASN* 1.3 60.7 + - - +
166B THR 4.4 2.0 + - - -
167B GLU* 3.6 22.3 - - + +
168B LEU* 2.9 56.2 + - - +
170B ILE* 3.8 12.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LYS* 3.7 19.6 - - - +
74A PHE 4.1 1.5 - - - +
34B LYS 3.4 10.4 + - - +
35B ILE* 3.3 10.4 + - - +
37B GLN* 1.3 78.6 - - - +
39B ASP* 1.3 67.8 + - - +
167B GLU* 3.7 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 4.1 12.3 + - - -
74A PHE* 3.6 8.0 + - - +
35B ILE* 2.9 16.0 + - + +
36B LEU* 3.4 5.8 - - - -
38B ASN* 1.3 89.1 - - - +
40B GLY* 1.3 63.1 + - - +
41B LYS* 3.1 19.9 + - - +
42B ALA* 3.1 34.3 + - + +
43B PRO* 5.3 1.4 - - - +
----------------------------------------------------------
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