Contacts of the helix formed by residues 45 - 57 (chain E) in PDB entry 1S89
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 THR 45 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E LEU 3.6 2.8 + - - -
17E VAL* 3.7 24.1 - - + +
44E ALA* 1.3 77.2 - - - +
46E GLY* 1.3 61.0 + - - +
48E THR* 3.7 7.3 + - - -
49E GLY* 2.8 26.9 + - - -
62E ALA* 4.5 0.3 - - - +
63E MET* 4.3 2.2 - - - +
64E LEU 3.7 6.7 - - - +
66E GLY 4.2 1.1 - - - +
70E GLY 4.0 22.0 - - - +
71E ASP* 3.9 21.3 - - - +
74E VAL* 4.7 3.6 - - + -
205E PGA 2.5 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 46 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TYR* 4.0 6.1 - - - -
147B LEU* 4.4 4.5 - - - -
45E THR* 1.3 74.4 - - - +
47E THR* 1.3 60.3 + - - +
49E GLY* 4.1 0.3 - - - -
50E ASN* 2.7 35.3 + - - -
62E ALA* 4.7 2.0 - - - -
63E MET 3.1 17.0 + - - -
64E LEU 3.0 13.7 + - - -
65E SER* 3.6 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU* 4.4 4.4 - - - +
150B ARG* 3.1 53.7 + - + +
151B LEU* 4.3 15.0 - - + +
20E ASP* 5.2 0.2 - - - +
23E LYS* 3.8 10.1 - - + -
46E GLY* 1.3 69.6 - - - +
48E THR* 1.3 67.4 + - - +
50E ASN* 3.3 3.6 + - - +
51E LEU* 3.0 35.4 + - + +
65E SER* 3.7 4.0 + - - -
205E PGA 2.7 29.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E LEU 3.7 19.7 - - - +
18E ALA* 3.4 24.8 + - + +
23E LYS* 3.5 12.2 - - + +
26E LEU* 3.7 25.4 - - + -
27E MET* 5.2 0.6 - - - +
44E ALA* 4.2 0.4 - - + -
45E THR* 3.7 7.2 - - - -
47E THR* 1.3 75.4 - - - +
49E GLY* 1.3 63.4 + - - +
51E LEU* 3.1 7.5 + - - +
52E ILE* 3.0 39.4 + - + +
205E PGA 2.9 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E ALA* 3.4 22.4 - - - +
45E THR 2.8 17.6 + - - -
46E GLY 4.1 0.4 - - - -
48E THR* 1.3 76.2 - - - +
50E ASN* 1.3 61.6 + - - +
52E ILE* 3.3 4.2 + - - +
53E SER* 3.1 24.7 + - - -
60E VAL* 4.0 14.5 - - - +
62E ALA* 4.5 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU* 4.3 16.6 - - - +
151B LEU* 3.8 34.6 - - + +
46E GLY* 2.7 28.8 + - - +
47E THR 3.3 1.8 + - - +
49E GLY* 1.3 73.2 - - - +
51E LEU* 1.3 66.5 + - - +
53E SER* 3.1 8.9 + - - -
54E ARG* 3.0 28.9 + - - +
62E ALA* 4.2 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ARG 5.8 0.9 - - - +
151B LEU* 4.4 17.0 - - + -
23E LYS* 3.7 34.1 - - + -
27E MET* 3.4 26.6 - - + +
47E THR* 3.0 24.6 + - + +
48E THR* 3.6 7.4 - - - +
50E ASN* 1.3 76.0 - - - +
52E ILE* 1.3 58.1 + - - +
54E ARG* 3.3 20.6 + - - +
55E ALA* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E LEU* 3.6 30.1 - - + -
26E LEU* 4.6 4.3 - - + -
27E MET* 4.0 19.1 - - - -
30E VAL* 4.2 30.5 - - + -
44E ALA* 5.1 1.6 - - + -
48E THR* 3.0 36.7 + - + +
49E GLY* 3.7 8.7 - - - +
51E LEU* 1.3 73.9 - - - +
53E SER* 1.3 61.5 + - - +
55E ALA* 3.2 1.3 + - - -
56E THR* 2.8 48.5 + - + +
58E MET* 4.4 5.2 - - + -
60E VAL* 3.9 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 53 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E GLY 3.1 14.2 + - - -
50E ASN* 3.1 19.8 + - - -
52E ILE* 1.3 76.7 - - - +
54E ARG* 1.3 56.7 + - - +
57E GLY* 2.9 27.1 + - - +
58E MET 3.4 24.7 - - - +
60E VAL* 4.4 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 3.4 56.5 + - - +
50E ASN* 3.0 21.4 + - - +
51E LEU* 3.5 18.2 - - - +
52E ILE 3.1 0.2 - - - -
53E SER* 1.3 80.7 + - - +
55E ALA* 1.3 62.2 + - + +
57E GLY* 4.5 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E MET* 3.9 19.1 - - + -
31E GLU* 4.0 21.0 - - - +
51E LEU 2.9 17.2 + - - +
52E ILE 4.0 2.0 - - - +
54E ARG* 1.3 79.1 - - + +
56E THR* 1.3 63.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
27E MET* 6.2 1.1 - - - -
30E VAL* 4.2 23.3 - - + -
31E GLU* 4.2 17.3 - - + -
34E GLN* 3.1 44.3 + - - +
52E ILE* 2.8 29.3 + - + +
55E ALA* 1.3 79.7 - - + +
57E GLY* 1.3 57.1 + - - +
58E MET* 3.1 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E SER 2.9 19.1 + - - -
54E ARG 4.5 1.2 + - - -
55E ALA 3.7 0.8 - - - -
56E THR* 1.3 77.9 + - - +
58E MET* 1.3 64.8 + - - +
59E ASN 3.9 0.3 + - - -
----------------------------------------------------------
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