Contacts of the helix formed by residues 39 - 54 (chain A) in PDB entry 1ZYX
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 39 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 2.7 32.1 + - - -
37A PRO 3.4 1.0 - - - -
38A LYS* 1.3 80.0 - - - +
40A ALA* 1.3 59.1 + - - +
41A THR* 3.8 6.6 - - - -
42A ASP* 2.9 22.2 + - - +
43A ARG* 2.8 43.9 + - - +
112A THR* 3.8 16.0 - - - +
117A TYR* 3.6 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASP* 1.3 77.6 - - - +
41A THR* 1.3 60.7 + - - +
43A ARG* 3.0 31.3 + - - +
44A CYS* 3.0 26.8 + - - -
105A CYS* 4.6 0.3 - - - -
109A ASN* 3.1 32.8 + - + +
112A THR* 4.1 11.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 3.6 33.6 + - + -
25A TYR* 3.7 28.0 - - + -
29A CYS* 3.7 2.5 - - - -
39A ASP* 3.3 8.9 + - - -
40A ALA* 1.3 77.4 - - - +
42A ASP* 1.3 62.9 + - - +
44A CYS* 3.1 24.8 + - - +
45A CYS 3.4 4.5 + - - -
106A PHE* 3.7 11.3 + - + -
109A ASN* 3.7 23.2 + - - +
110A LEU* 5.5 0.2 - - - -
112A THR* 4.8 1.3 + - - -
113A TYR* 4.3 12.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.6 6.5 - - + +
26A GLY* 3.6 6.5 - - - -
27A CYS* 2.8 26.1 + - - +
28A TYR* 2.8 26.9 + - - +
29A CYS* 3.6 11.5 + - - -
37A PRO* 3.3 10.7 - - - +
38A LYS* 2.9 27.9 + - + +
39A ASP* 2.9 21.8 + - - +
41A THR* 1.3 75.0 - - - +
43A ARG* 1.3 59.7 + - - +
45A CYS* 3.3 1.6 + - - +
46A PHE* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PRO* 3.6 27.0 + - + -
38A LYS 4.9 0.2 - - - -
39A ASP* 2.8 26.5 + - - +
40A ALA* 3.0 35.6 + - - +
42A ASP* 1.3 76.9 - - - +
44A CYS* 1.3 64.9 + - - +
46A PHE* 3.1 7.2 + - + +
47A VAL* 3.0 30.5 + - + +
105A CYS* 5.2 0.7 - - - -
262A SO4 2.9 37.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA 3.0 19.3 + - - -
41A THR* 3.2 13.7 - - - +
43A ARG* 1.3 78.6 - - - +
45A CYS* 1.3 57.6 + - - +
47A VAL* 3.5 5.7 + - - +
48A HIS* 2.9 27.6 + - - +
102A ALA* 4.8 6.7 - - - +
105A CYS* 2.0 68.4 - - + -
106A PHE* 3.6 16.4 - - + -
109A ASN* 3.6 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR 4.8 0.7 - - - -
28A TYR* 3.7 4.5 - - - +
29A CYS* 1.9 67.1 - - - +
41A THR 3.4 0.4 + - - -
42A ASP 3.3 4.4 + - - +
43A ARG 3.2 0.4 - - - -
44A CYS* 1.3 76.6 - - - +
46A PHE* 1.3 55.1 + - - +
48A HIS* 3.5 8.0 - - - +
49A ASP* 2.7 39.7 + - - +
106A PHE* 3.5 27.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 3.4 43.0 - + + +
37A PRO* 3.9 14.1 - - + -
42A ASP 3.0 14.0 + - - +
43A ARG* 3.4 9.2 - - + +
45A CYS* 1.3 77.0 - - - +
47A VAL* 1.3 72.7 + - + +
49A ASP* 3.2 5.8 + - + +
50A CYS* 3.0 50.6 + - - -
130A LEU* 3.7 59.5 - - + -
131A LYS 3.8 9.2 - - - -
133A CYS* 4.1 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 3.0 22.4 + - + +
44A CYS* 3.8 5.6 - - - +
46A PHE* 1.3 87.1 - - + +
48A HIS* 1.3 52.3 + - - +
50A CYS* 3.2 9.1 + - + +
51A CYS* 2.8 35.0 + - + +
101A ALA* 6.2 3.6 - - + -
105A CYS* 6.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 3.6 24.6 - + - -
44A CYS 2.9 18.4 + - - +
45A CYS* 3.5 9.5 - - - +
47A VAL* 1.3 76.2 - - - +
49A ASP* 1.3 70.0 + - - +
51A CYS* 3.1 6.7 + - - +
52A TYR* 3.0 59.7 + + - +
98A CYS* 3.4 27.4 - - + -
99A ASP* 2.8 22.2 + - - -
102A ALA* 3.5 19.1 - - + -
106A PHE* 6.2 0.7 - + + -
2001A LCF 5.6 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 3.5 28.5 - - + +
30A GLY 4.9 2.6 - - - +
32A GLY* 3.2 28.0 - - - +
45A CYS* 2.7 23.5 + - - +
46A PHE* 3.3 7.4 - - + +
48A HIS* 1.3 79.5 + - - +
50A CYS* 1.4 56.7 + - - +
52A TYR* 3.4 9.5 + - - +
53A GLY* 3.0 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.0 36.8 + - - -
47A VAL* 3.4 11.4 - - + +
49A ASP* 1.4 72.8 - - - +
51A CYS* 1.3 66.2 + - - +
53A GLY* 3.1 11.9 + - - +
54A ASN* 3.2 22.7 + - - +
133A CYS* 2.0 60.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 2.8 17.6 + - + +
48A HIS* 3.1 12.5 + - - +
50A CYS* 1.3 77.6 - - - +
52A TYR* 1.3 60.8 + - - +
54A ASN* 3.2 24.6 + - - +
55A LEU* 3.6 6.2 - - - +
97A GLU* 5.0 0.9 - - - -
98A CYS* 2.0 60.9 - - + -
101A ALA* 6.0 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SER 5.8 0.5 - - - -
2A LEU* 5.2 8.5 - - + +
5A PHE* 4.5 5.9 - - - +
48A HIS* 3.0 38.8 + + - +
49A ASP* 3.6 11.7 - - - +
51A CYS* 1.3 75.7 - - - +
53A GLY* 1.3 58.2 + - - +
55A LEU* 2.9 35.8 + - + +
68A PRO* 3.4 47.9 + - + +
69A LYS* 5.1 0.7 - - + -
95A ILE* 4.4 7.3 - - + +
98A CYS* 3.9 18.6 - - + -
99A ASP* 2.6 33.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASP 3.0 14.4 + - - -
50A CYS* 3.1 8.8 + - - -
52A TYR* 1.3 78.2 - - - +
54A ASN* 1.3 57.9 + - - +
55A LEU 3.1 2.0 + - - -
56A PRO* 3.4 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A CYS* 3.2 17.8 + - - +
51A CYS* 3.6 15.9 + - - +
52A TYR 3.1 1.4 - - - -
53A GLY* 1.3 75.3 - - - +
55A LEU* 1.3 62.1 + - + +
56A PRO* 2.9 12.3 - - - +
94A ARG* 3.6 18.1 + - - +
133A CYS* 6.0 2.3 - - - +
----------------------------------------------------------
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