Contacts of the helix formed by residues 5 - 17 (chain D) in PDB entry 1A0Z
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 5 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LEU 3.8 1.7 - - - +
4D THR* 1.3 86.0 - - + +
6D GLU* 1.3 69.9 + - - +
8D LYS* 3.5 10.7 + - + +
9D SER* 2.7 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 6 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D THR* 3.0 17.2 + - - +
5D PRO* 1.3 101.5 - - - +
7D GLU* 1.3 64.5 - - + +
9D SER* 3.4 5.4 + - - -
10D ALA* 3.2 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 7 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LEU* 3.5 7.3 - - + -
4D THR* 2.9 34.4 + - - +
6D GLU* 1.3 79.8 - - + +
8D LYS* 1.3 66.4 + - - +
10D ALA* 3.4 4.5 + - - +
11D VAL* 3.1 29.8 + - - +
125D PRO 4.9 2.9 - - - +
128D ALA* 4.5 6.9 - - - +
129D ALA* 3.8 27.7 + - + -
132D LYS* 2.9 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 8 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET 4.1 10.2 + - - -
3D LEU* 3.7 31.7 + - + +
4D THR 2.7 15.5 + - - +
5D PRO* 3.8 9.4 - - + +
6D GLU 3.3 0.2 - - - -
7D GLU* 1.3 76.2 - - - +
9D SER* 1.3 57.8 + - - +
11D VAL* 3.5 4.7 + - - +
12D THR* 3.1 30.4 + - - -
78D LEU* 3.7 34.7 - - + +
79D ASP* 3.4 34.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 9 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D PRO 2.7 18.7 + - - -
6D GLU* 3.4 4.1 + - - -
7D GLU 3.2 0.2 - - - -
8D LYS* 1.3 77.3 - - - +
10D ALA* 1.3 56.3 + - - +
11D VAL 3.1 0.4 - - - -
12D THR* 3.6 6.8 - - - -
13D ALA* 2.7 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 10 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D GLU 3.2 16.6 + - - +
7D GLU* 3.4 8.3 + - - +
9D SER* 1.3 75.6 - - - +
11D VAL* 1.3 63.0 + - + +
13D ALA* 3.8 5.4 - - - +
14D LEU* 3.1 24.8 + - - +
125D PRO 6.1 0.2 - - - -
126D VAL* 4.3 29.4 - - + +
129D ALA* 5.2 2.2 - - + -
130D TYR* 4.7 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LEU* 4.9 1.6 - - + -
7D GLU 3.1 18.7 + - - +
8D LYS* 3.5 7.4 - - - +
10D ALA* 1.3 74.5 - - - +
12D THR* 1.3 68.2 + - - +
14D LEU 3.3 0.3 + - - -
15D TRP* 3.0 11.4 + - - +
75D LEU* 4.3 20.0 - - + -
78D LEU* 4.5 7.6 - - + -
129D ALA* 3.7 23.6 - - + -
130D TYR* 2.8 48.2 + - + +
133D VAL* 4.1 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LYS 3.1 16.2 + - - -
9D SER* 3.2 7.4 + - - +
11D VAL* 1.3 81.2 - - - +
13D ALA* 1.3 68.8 + - - +
15D TRP* 3.2 7.1 + - - +
16D GLY* 3.2 19.4 + - - -
75D LEU* 5.0 9.1 + - - +
78D LEU* 5.3 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D SER 2.7 21.7 + - - +
10D ALA* 3.8 6.5 - - - +
12D THR* 1.3 78.5 - - - +
14D LEU* 1.3 63.1 + - - +
16D GLY* 3.5 9.5 + - - -
17D LYS* 4.1 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ALA 3.1 18.0 + - - +
12D THR 3.2 0.2 - - - -
13D ALA* 1.3 74.5 - - - +
15D TRP* 1.3 66.4 - - - +
17D LYS* 2.9 25.5 + - + +
18D VAL* 3.6 6.4 - - + +
114D LEU* 4.9 4.5 - - + -
118D PHE* 3.9 38.8 - - + -
121D GLU* 3.7 35.2 - - + +
122D PHE* 3.8 28.0 - - + -
126D VAL* 4.2 7.0 - - + -
130D TYR* 3.8 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D VAL 3.0 18.4 + - - +
12D THR* 3.7 5.8 - - - +
14D LEU* 1.3 78.4 - - - +
16D GLY* 1.3 53.4 + - - +
18D VAL* 2.8 49.4 + - + +
20D VAL* 3.9 18.9 - - + +
23D VAL* 5.4 0.2 - - + -
68D LEU* 4.0 21.8 - - + -
71D PHE* 3.6 33.0 - + - -
72D SER* 2.9 36.4 + - - -
75D LEU* 3.5 27.3 - - + +
110D LEU* 4.7 4.5 - - + -
114D LEU* 4.4 15.9 - - + -
130D TYR* 3.5 23.9 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D THR 3.2 11.8 + - - -
13D ALA 3.9 5.6 - - - -
14D LEU 3.1 1.4 - - - -
15D TRP* 1.3 77.0 - - - +
17D LYS* 1.3 58.9 + - - +
18D VAL 3.3 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ALA 4.1 11.9 - - - +
14D LEU* 2.9 15.7 + - - +
16D GLY* 1.3 77.5 - - - +
18D VAL* 1.3 62.9 + - - +
19D ASN 3.8 1.7 + - - -
117D HIS* 4.4 6.2 + - - -
118D PHE* 3.8 23.9 - - + -
121D GLU* 3.0 35.4 + - - +
----------------------------------------------------------
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