Contacts of the helix formed by residues 49 - 58 (chain E) in PDB entry 1Y62
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 ARG 49 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E ILE* 4.2 3.6 - - - -
47E PHE* 3.7 6.6 - - - +
48E ARG* 1.3 88.3 - - + +
50E THR* 1.3 66.5 + - - +
51E TYR* 4.3 11.6 - - - +
52E ASP* 3.1 42.2 + - - +
53E CYS 3.4 6.6 + - - -
100E SO4 2.7 41.9 + - - +
109E SO4 3.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E ILE* 3.6 26.0 - - + +
32E CYS* 3.8 30.1 - - + +
49E ARG* 1.3 70.5 - - - +
51E TYR* 1.3 59.0 + - - +
53E CYS* 3.0 7.4 + - - +
54E GLN* 2.9 37.5 + - - +
100E SO4 3.3 7.3 + - - -
109E SO4 2.4 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 51 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E ARG* 3.2 9.8 - - - +
50E THR* 1.3 70.9 - - - +
52E ASP* 1.3 59.9 + - - +
54E GLN* 3.1 31.8 + - + -
55E ARG* 3.0 73.7 + - + +
100E SO4 2.5 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 52 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E PHE* 3.8 15.9 - - + -
48E ARG* 5.4 2.0 + - - +
49E ARG* 3.1 46.8 + - - +
51E TYR* 1.3 77.0 - - - +
53E CYS* 1.3 57.7 + - - +
55E ARG* 3.8 15.8 + - - +
56E THR* 2.5 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 53 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E ILE* 3.8 10.3 - - + -
24E TYR 3.8 4.0 - - - -
25E TYR* 3.7 28.9 - - - -
32E CYS* 2.0 44.9 - - - -
47E PHE* 3.5 33.3 - - + -
49E ARG 3.4 1.8 + - - -
50E THR 3.0 7.3 + - - +
52E ASP* 1.3 80.8 - - - +
54E GLN* 1.3 54.1 + - - +
56E THR* 3.8 0.2 - - - -
57E CYS* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E GLN* 5.3 5.7 + - - -
32E CYS* 4.0 12.0 - - + +
50E THR* 2.9 29.1 + - + +
51E TYR* 3.1 45.7 + - + +
52E ASP 3.2 0.2 - - - -
53E CYS* 1.3 73.1 - - - +
55E ARG* 1.3 60.1 + - - +
56E THR 3.1 4.3 - - - -
58E LEU* 2.9 62.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E TYR* 3.0 57.6 + - + +
52E ASP* 3.8 19.3 + - - +
54E GLN* 1.3 76.7 - - - +
56E THR* 1.3 60.1 + - - +
58E LEU 4.9 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 56 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E ARG* 4.7 2.1 - - - -
4E PRO* 3.4 35.8 - - + +
6E LEU* 4.7 7.9 - - + -
7E CYS* 4.4 0.7 - - - -
47E PHE* 3.6 23.2 - - + -
52E ASP* 2.5 22.9 + - - +
53E CYS 3.8 3.1 - - - -
54E GLN 3.1 1.0 - - - -
55E ARG* 1.3 81.6 - - - +
57E CYS* 1.3 72.1 + - - +
58E LEU 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E ARG* 4.8 16.9 + - - +
6E LEU* 4.2 7.2 - - - -
7E CYS* 2.0 52.5 - - + +
25E TYR* 3.4 47.9 + - + -
47E PHE* 4.5 4.7 - - - -
53E CYS 2.9 15.6 + - - +
56E THR* 1.3 88.8 - - - +
58E LEU* 1.3 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E ARG* 5.9 3.6 - - - -
25E TYR* 4.0 18.6 - - + +
30E LYS* 3.4 33.0 - - + +
31E GLN* 5.1 10.5 - - - +
32E CYS* 5.1 2.7 - - - +
53E CYS 4.0 0.2 + - - -
54E GLN* 2.9 61.6 + - + +
55E ARG* 5.0 4.7 - - - +
56E THR 3.8 0.8 - - - -
57E CYS* 1.3 75.1 - - - +
----------------------------------------------------------
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