Contacts of the helix formed by residues 36 - 47 (chain B) in PDB entry 1ZTD
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 PRO 36 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ARG 3.1 10.7 - - - +
35B VAL* 1.3 88.7 - - + +
37B ASN* 1.3 66.8 + - - +
38B ALA* 4.3 8.3 - - + +
39B SER* 3.0 41.6 + - - +
40B LEU* 3.4 7.4 + - - +
101B LYS* 5.3 7.4 - - - -
102B LYS* 4.8 11.4 - - + +
105B ILE* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL 3.6 1.6 + - - -
36B PRO* 1.3 71.3 - - - +
38B ALA* 1.3 64.8 + - - +
40B LEU* 3.2 13.7 + - - +
41B ALA* 3.1 21.3 + - - +
59B HIS 4.9 9.8 + - - +
62B GLY* 3.5 24.7 - - - +
63B ASP* 3.6 18.2 + - - +
66B GLU* 5.3 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PRO* 3.1 4.9 - - + +
37B ASN* 1.3 83.4 - - - +
39B SER* 1.3 62.0 + - - +
41B ALA* 3.4 7.7 + - - +
42B ILE* 3.0 31.5 + - + +
102B LYS* 3.8 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 4.2 2.7 - - - -
36B PRO* 3.0 32.2 + - - +
38B ALA* 1.3 78.3 - - - +
40B LEU* 1.3 58.1 - - - +
42B ILE* 3.4 2.0 + - - +
43B ALA* 3.0 24.0 + - - +
102B LYS* 2.8 30.5 + - - -
105B ILE* 3.6 18.6 - - - +
106B GLY* 3.3 22.9 - - - -
109B LEU* 5.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 4.8 4.3 - - + -
35B VAL* 3.8 24.0 - - + +
36B PRO 3.4 6.2 + - - +
37B ASN* 3.2 12.2 + - - +
39B SER* 1.3 77.3 - - - +
41B ALA* 1.3 62.3 + - - +
43B ALA* 3.4 6.0 + - - +
44B LEU* 3.0 23.6 + - - +
62B GLY* 3.8 16.6 - - - +
65B ALA* 3.9 17.4 - - + +
66B GLU* 3.2 48.2 - - + +
69B ILE* 4.6 13.0 - - + -
109B LEU* 3.8 22.9 - - + -
113B LEU* 5.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN* 3.1 15.9 + - - +
38B ALA* 3.7 11.2 - - - +
39B SER 3.3 0.2 - - - -
40B LEU* 1.3 75.4 - - - +
42B ILE* 1.3 64.4 + - + +
44B LEU* 3.2 4.4 + - - +
45B GLU* 3.0 30.3 + - - +
58B LYS 5.7 0.4 - - - +
61B LYS* 3.9 33.1 - - + +
62B GLY* 3.9 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ALA* 3.0 22.0 + - + +
39B SER* 3.6 4.9 - - - +
41B ALA* 1.3 73.8 - - + +
43B ALA* 1.3 67.1 + - - +
45B GLU* 3.0 23.3 - - + +
46B LEU* 2.9 38.1 + - + +
102B LYS* 4.0 31.9 - - + +
103B GLU* 3.0 41.7 - - + +
106B GLY* 4.4 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B SER 3.0 15.6 + - - +
40B LEU* 3.5 8.1 - - + +
42B ILE* 1.3 76.3 - - - +
44B LEU* 1.3 63.1 + - - +
46B LEU* 3.1 15.5 + - - +
47B THR* 3.1 19.1 + - - +
106B GLY* 3.4 24.7 - - - +
109B LEU* 4.2 8.3 - - + -
110B ALA* 3.9 9.6 - - - +
113B LEU* 3.6 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU 3.0 14.2 + - - +
41B ALA 3.2 9.2 + - - +
43B ALA* 1.3 75.9 - - - +
45B GLU* 1.3 59.9 + - - +
47B THR* 2.7 20.5 + - - -
49B LEU* 3.2 39.7 + - + -
50B SER* 3.5 19.9 + - - +
53B LEU* 4.4 3.6 - - + -
61B LYS* 3.5 42.6 - - + +
64B TYR* 3.9 30.1 - - + -
65B ALA* 4.3 13.9 - - + -
68B LEU* 4.7 2.7 - - + -
113B LEU* 3.7 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ALA* 3.0 18.5 + - - +
42B ILE* 3.0 37.3 + - + +
44B LEU* 1.3 75.2 - - - +
46B LEU* 1.3 66.8 + - + +
48B GLY* 3.0 12.6 + - - -
50B SER* 3.3 21.4 + - - +
51B LYS* 5.3 3.9 + - - +
61B LYS* 3.3 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 2.9 38.2 + - + +
43B ALA* 3.1 7.2 + - - +
45B GLU* 1.3 80.3 - - + +
47B THR* 1.3 59.9 + - - +
48B GLY* 3.3 0.7 + - - -
103B GLU* 5.4 1.3 - - - +
106B GLY 4.0 17.5 - - - +
107B ARG* 4.0 49.1 - - - +
110B ALA* 4.3 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ALA 3.3 12.3 - - - +
44B LEU* 2.7 21.7 + - - -
46B LEU* 1.3 76.5 - - - +
48B GLY* 1.3 57.3 + - - +
49B LEU* 3.1 30.8 + - - +
110B ALA* 3.4 33.7 - - + +
113B LEU* 4.2 9.6 - - + -
114B VAL* 3.6 18.8 - - + +
----------------------------------------------------------
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