Contacts of the helix formed by residues 37 - 47 (chain E) in PDB entry 3I6A
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 SER 37 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E ILE* 3.4 9.5 - - - +
36E LYS* 1.3 82.1 - - - +
38E ALA* 1.3 65.3 + - - +
39E GLU* 3.3 20.6 + - - +
40E ASP* 3.1 33.7 + - - -
41E LEU 3.2 8.7 + - - -
219E ILE* 3.9 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E SER* 1.3 74.2 - - - +
39E GLU* 1.3 61.2 + - - +
41E LEU* 3.2 3.0 + - - +
42E ASP* 2.7 49.5 + - - +
218E ASN 4.7 3.6 - - - +
219E ILE* 3.1 38.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 39 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E SER* 3.3 21.4 + - - +
38E ALA* 1.3 85.5 + - - +
40E ASP* 1.3 67.0 + - - +
42E ASP* 3.7 12.2 - - - +
43E LYS* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 40 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E LYS* 6.6 0.2 - - - -
34E PHE 4.1 4.8 - - - +
35E ILE* 3.6 17.6 - - + -
36E LYS* 2.8 31.4 + - - +
37E SER* 3.1 19.3 + - - +
39E GLU* 1.3 78.6 - - - +
41E LEU* 1.3 61.7 + - - +
43E LYS* 3.5 6.3 + - - +
44E LEU* 3.3 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E PHE* 5.2 2.9 - - + -
35E ILE* 3.8 22.8 - - + +
37E SER 3.2 9.5 + - - +
38E ALA* 3.5 7.9 - - - +
40E ASP* 1.3 77.9 - - - +
42E ASP* 1.3 65.2 + - - +
43E LYS 3.2 0.2 + - - -
44E LEU* 3.2 4.5 + - + +
45E ARG* 3.0 46.8 + - - +
50E LEU* 3.9 24.7 - - + -
53E GLN 4.6 1.8 - - - +
54E GLN* 5.6 0.2 - - - -
55E VAL* 4.7 7.4 - - + +
219E ILE* 4.0 13.0 - - + +
220E PHE* 3.2 40.4 - - + -
5105E GSH 5.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 42 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E ALA* 2.7 38.1 + - - +
39E GLU* 3.7 12.9 - - - +
41E LEU* 1.3 71.5 - - - +
43E LYS* 1.3 51.3 + - - +
45E ARG* 3.1 24.0 + - - +
46E ASN* 2.7 53.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 43 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E GLU 3.0 18.1 + - - +
40E ASP* 3.6 7.4 - - - +
41E LEU 3.1 0.2 - - - -
42E ASP* 1.3 74.8 - - - +
44E LEU* 1.3 67.4 + - + +
46E ASN* 4.5 6.3 - - + +
47E ASP* 2.9 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E HIS* 3.7 31.9 - - + +
33E LYS* 6.3 1.1 - - + -
35E ILE* 3.8 34.1 - - + -
40E ASP 3.3 10.4 + - - +
41E LEU* 3.2 9.5 + - + +
43E LYS* 1.3 80.1 - - + +
45E ARG* 1.3 61.1 + - - +
47E ASP* 3.6 4.9 + - - +
48E GLY 3.6 1.6 + - - -
49E TYR* 3.1 53.9 + - + +
50E LEU* 4.0 15.6 + - + -
55E VAL* 4.1 14.6 - - + -
57E MET* 4.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E LEU* 3.0 45.3 + - - +
42E ASP* 3.1 21.4 + - - +
44E LEU* 1.3 77.3 - - - +
46E ASN* 1.3 61.5 + - - +
48E GLY* 3.0 19.8 + - - -
49E TYR 5.0 0.2 - - - +
50E LEU* 3.8 17.7 - - + -
53E GLN* 2.8 55.8 + - - +
220E PHE* 4.1 5.3 - - - -
5105E GSH 3.2 32.3 + - - -
131F ARG* 4.3 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 46 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E ASP* 2.7 38.9 + - - +
43E LYS* 4.0 6.8 - - + +
45E ARG* 1.3 76.4 - - - +
47E ASP* 1.3 63.0 + - - +
48E GLY 3.1 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E LYS* 2.9 58.8 + - - +
44E LEU* 3.9 3.3 - - - +
45E ARG 3.2 0.2 - - - -
46E ASN* 1.3 77.3 - - - +
48E GLY* 1.3 61.1 + - - +
49E TYR* 3.3 34.5 + - + -
----------------------------------------------------------
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