Contacts of the helix formed by residues 40 - 51 (chain A) in PDB entry 4ZCU
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 40 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 5.1 5.4 + - - -
36A ASP* 5.3 2.4 - - - +
38A VAL* 4.1 5.3 - - + +
39A VAL* 1.3 78.8 - - - +
41A ILE* 1.3 65.3 + - - +
42A GLY 3.4 0.5 + - - -
43A GLU* 2.9 52.5 + - - +
44A LEU* 3.0 18.5 + - - +
64A PHE* 3.7 7.2 - - - -
73A GLY 4.8 2.0 - - - -
74A LYS* 5.3 2.0 - - + +
57B GLN* 3.0 28.0 + - - +
58B ASP* 3.2 27.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP* 1.3 73.0 - - - +
42A GLY* 1.3 60.5 + - - +
44A LEU* 3.2 12.1 + - + -
45A GLN* 2.9 55.9 + - + +
57A GLN 6.0 0.2 - - - +
60A GLU* 4.9 5.8 - - + +
61A GLU* 3.9 20.0 - - - +
64A PHE* 3.6 24.8 - - + -
73A GLY 5.3 0.4 + - - -
41B ILE* 4.5 7.0 - - + -
45B GLN* 4.1 18.6 - - - +
57B GLN* 3.7 26.0 - - + +
61B GLU* 3.6 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP* 3.2 1.9 - - - -
41A ILE* 1.3 84.7 - - - +
43A GLU* 1.3 55.2 - - - +
45A GLN* 3.3 10.9 + - - +
46A GLU* 2.9 48.0 + - - +
57B GLN* 3.3 15.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.5 19.7 - - - +
32A ASP* 3.8 0.4 - - - +
33A ARG* 3.3 27.0 + - + +
34A ASN* 2.7 19.9 + - - +
38A VAL 3.1 3.6 - - - +
39A VAL* 3.2 7.9 - - + -
40A ASP* 2.9 44.2 + - - +
42A GLY* 1.3 75.7 - - - +
44A LEU* 1.3 56.7 + - - +
46A GLU* 5.0 3.1 - - - -
47A GLY* 2.9 27.9 + - - +
1001A CA 2.3 31.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.9 25.7 - - + +
39A VAL* 3.7 10.9 - - + +
40A ASP 3.0 12.6 + - - +
41A ILE* 3.6 15.0 - - + +
42A GLY 3.2 0.2 - - - -
43A GLU* 1.3 75.0 - - - +
45A GLN* 1.3 59.5 + - - +
47A GLY* 4.9 0.2 - - - -
48A LEU* 2.9 57.0 + - + +
60A GLU* 3.7 30.5 - - + +
63A ILE* 4.6 16.4 - - + -
64A PHE* 3.9 21.8 - - + -
75A LEU* 4.8 4.9 - - + -
80A PHE* 5.2 5.8 - - + -
153A PHE* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 2.9 44.5 + - + +
42A GLY* 3.7 9.4 - - - +
44A LEU* 1.3 74.6 - - - +
46A GLU* 1.3 69.6 + - + +
48A LEU* 3.2 2.4 + - - +
49A ARG* 3.0 23.6 + - - +
57A GLN* 4.9 7.1 + - - +
60A GLU* 3.3 32.5 + - + +
41B ILE* 4.2 18.2 - - - +
45B GLN* 5.5 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 3.5 24.0 + - - +
42A GLY* 2.9 25.2 + - - +
43A GLU* 4.7 2.2 - - - +
45A GLN* 1.3 76.9 - - + +
47A GLY* 1.3 56.7 + - - +
49A ARG* 3.3 9.3 + - - +
50A ASN* 2.9 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 5.6 1.3 - - - -
31A LEU* 3.7 20.6 - - - -
43A GLU* 2.9 23.1 + - - +
46A GLU* 1.3 74.6 - - - +
48A LEU* 1.3 63.1 + - - +
50A ASN* 3.1 7.3 + - - +
51A LEU* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 4.1 7.8 - - + +
44A LEU* 2.9 40.5 + - + +
45A GLN 3.7 3.6 - - - +
47A GLY* 1.3 75.3 - - - +
49A ARG* 1.3 59.7 + - - +
51A LEU* 3.6 4.3 + - + +
52A GLY 3.2 3.1 + - - -
53A ILE* 2.7 56.6 + - + +
55A LEU* 3.7 31.0 - - + -
60A GLU* 3.7 22.7 - - + +
63A ILE* 5.1 4.5 - - + -
153A PHE* 3.9 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLN 3.0 16.7 + - - +
46A GLU* 3.7 7.9 - - - +
48A LEU* 1.3 78.1 - - - +
50A ASN* 1.3 75.1 + - - +
52A GLY* 3.2 12.7 + - - -
53A ILE 4.7 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 4.9 13.1 - - - +
46A GLU* 2.9 33.0 + - - +
47A GLY* 3.1 6.8 + - - +
49A ARG* 1.3 88.2 - - - +
51A LEU* 1.3 64.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 4.1 22.2 - - + -
30A ALA* 4.2 21.8 - - + -
31A LEU* 3.8 22.7 - - + -
47A GLY 3.0 18.8 + - - +
48A LEU* 4.2 2.9 - - + +
50A ASN* 1.3 82.1 - - + +
52A GLY* 1.3 60.5 + - - +
53A ILE* 3.4 25.3 + - + +
----------------------------------------------------------
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