Contacts of the helix formed by residues 30 - 37 (chain A) in PDB entry 1ZJA
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 30 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PRO* 3.8 7.8 + - - +
21A LYS 3.0 4.9 + - - +
22A ASP* 3.1 0.5 - - - +
23A THR* 2.6 42.0 + - - -
24A ASN* 3.8 3.3 - - - +
29A GLY* 1.3 74.8 - - - +
31A PHE* 1.3 68.5 + - - +
32A LYS* 3.5 3.9 + - + +
33A GLY* 2.8 31.7 + - - -
34A LEU* 3.1 12.9 + - - +
75A GLU 3.7 11.4 - - - +
76A TYR* 3.3 19.3 - - - +
7001A CA 2.4 25.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PRO* 5.5 6.1 - - + -
30A ASP* 1.3 70.0 - - - +
32A LYS* 1.3 62.5 + - - +
34A LEU* 3.2 9.4 + - + +
35A THR* 2.8 35.3 + - - +
51A ILE* 4.4 6.5 - - + -
54A HIS* 3.5 32.5 - + + -
72A VAL* 3.1 34.8 - - + -
76A TYR* 2.9 41.8 + + + +
77A GLY 4.0 0.4 - - - -
81A ASP* 4.0 29.6 - - + +
82A PHE* 3.9 27.4 - + + -
84A ARG* 6.0 0.2 - - - -
85A LEU* 3.9 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A THR* 3.4 23.8 - - + +
30A ASP* 3.3 3.1 + - - +
31A PHE* 1.3 78.9 - - - +
33A GLY* 1.3 61.7 + - - +
35A THR* 3.3 6.4 + - - -
36A GLU* 2.8 35.7 + - + +
76A TYR 4.4 1.3 + - - +
81A ASP* 3.3 28.3 - - - +
84A ARG* 3.8 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 3.4 28.4 - - - +
23A THR* 3.4 19.7 - - - +
30A ASP* 2.8 12.5 + - - -
32A LYS* 1.3 78.9 - - - +
34A LEU* 1.3 62.2 + - - +
36A GLU* 3.3 7.0 + - - +
37A LYS* 3.3 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 4.1 19.5 - - + -
17A PRO* 5.4 5.2 - - + -
20A PHE* 3.8 32.9 - - + -
21A LYS* 4.5 0.8 - - - +
30A ASP 3.1 11.4 + - - +
31A PHE* 3.2 11.9 + - + +
33A GLY* 1.3 75.1 - - - +
35A THR* 1.3 64.7 + - - +
37A LYS 3.0 11.3 + - - -
38A LEU* 3.4 22.1 + - + +
41A LEU* 4.2 6.1 - - + -
49A ILE* 4.4 5.2 - - + -
51A ILE* 3.8 29.2 - - + -
85A LEU* 3.8 30.7 - - + -
96A LEU* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE 2.8 18.2 + - - -
32A LYS* 3.3 7.8 + - - -
34A LEU* 1.3 76.6 - - - +
36A GLU* 1.3 63.0 + - + +
37A LYS 3.2 0.9 + - - -
38A LEU* 3.3 25.2 + - + +
39A ASP 5.1 0.2 + - - -
81A ASP 4.7 1.4 + - - -
84A ARG* 4.7 15.9 + - - +
85A LEU* 3.6 26.7 + - - +
88A GLU* 3.8 33.0 - - + -
92A ARG* 5.1 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 4.8 5.8 + - + +
23A THR* 3.4 22.4 - - - +
32A LYS* 2.8 26.6 + - + +
33A GLY* 3.7 5.2 - - - +
34A LEU 3.2 0.2 - - - -
35A THR* 1.3 78.0 - - + +
37A LYS* 1.3 68.6 + - + +
38A LEU 3.5 1.0 + - - -
39A ASP* 4.8 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 3.7 17.5 - - + -
21A LYS* 4.0 24.2 - - + +
33A GLY 3.3 16.6 - - - +
34A LEU 3.0 7.6 + - - +
36A GLU* 1.3 87.5 + - - +
38A LEU* 1.3 62.9 + - - +
39A ASP 3.2 2.9 - - - +
40A TYR* 3.2 18.2 + - + +
41A LEU* 3.2 15.7 + - - +
423A TRP* 3.6 56.4 - - + +
----------------------------------------------------------
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