Contacts of the helix formed by residues 26 - 36 (chain E) in PDB entry 3JCA
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 26 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ARG* 4.0 3.6 - - - +
25E ILE* 1.3 78.4 - - - +
27E ARG* 1.3 65.3 + - - +
28E GLU* 3.5 8.3 + - - +
29E GLN* 2.8 43.9 + - - +
30E ALA* 3.0 21.8 + - - +
10J C 3.3 33.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 27 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ALA* 6.3 1.3 - - + -
20E ARG* 3.5 33.1 - - - +
26E THR* 1.3 74.9 - - - +
28E GLU* 1.3 81.4 + - + +
30E ALA* 3.2 3.3 + - + +
31E ARG* 2.8 57.3 + - + +
11I T 3.8 9.3 + - - +
12I C 4.9 0.4 - - - +
10J C 4.1 19.5 - - + +
11J G 2.7 58.1 + - - +
12J A 3.4 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E THR* 3.2 7.0 + - - +
27E ARG* 1.3 94.2 + - + +
29E GLN* 1.3 65.0 + - - +
31E ARG* 2.8 41.0 + - - +
32E GLU* 2.9 31.9 + - + +
224G LEU* 4.2 13.6 - - + +
260G PHE* 4.5 23.1 - - + -
11I T 5.4 1.7 - - - +
10J C 6.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 29 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E LEU* 3.8 28.5 - - + +
25E ILE* 3.4 11.3 - - + +
26E THR* 2.8 50.9 + - - +
28E GLU* 1.3 76.3 - - - +
30E ALA* 1.3 61.8 + - - +
32E GLU* 3.2 5.9 + - - +
33E ILE* 3.1 28.6 + - - +
224G LEU 4.2 7.2 - - - +
225G LEU* 2.8 36.3 + - - +
226G THR* 4.1 11.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ALA* 3.2 35.7 - - + +
19E LEU* 4.2 2.9 - - + +
20E ARG* 3.8 9.0 - - + -
25E ILE* 3.8 16.7 - - + +
26E THR 3.0 13.2 + - - +
27E ARG 3.5 7.4 - - - +
29E GLN* 1.3 76.7 - - - +
31E ARG* 1.3 63.2 + - - +
33E ILE* 3.1 8.5 + - - +
34E VAL* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 31 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ALA* 4.6 8.3 - - + -
27E ARG* 2.8 49.2 + - + +
28E GLU* 2.8 45.4 + - - +
29E GLN 3.2 0.2 - - - -
30E ALA* 1.3 73.6 - - - +
32E GLU* 1.3 58.4 + - - +
34E VAL* 3.1 10.5 - - + +
35E LYS* 2.8 43.3 + - + +
9I A 3.7 27.4 + - + +
10I G 2.9 46.7 + - - -
11I T 3.8 16.4 + - - +
12J A 4.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E GLU* 2.9 21.4 + - + +
29E GLN 3.2 4.0 + - - +
31E ARG* 1.3 74.6 - - - +
33E ILE* 1.3 66.6 + - - +
35E LYS* 2.9 38.9 + - - +
36E LEU* 2.9 40.8 + - + +
224G LEU* 3.6 51.1 - - + +
225G LEU* 3.6 21.7 - - + +
254G ILE* 5.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E LEU* 4.1 12.8 - - + -
5E ALA* 3.5 29.2 - - + -
6E GLN* 3.8 35.7 - - + +
9E HIS* 3.5 39.6 - - + -
19E LEU* 3.8 8.5 - - + -
25E ILE* 3.8 17.0 - - + -
29E GLN 3.1 16.0 + - - +
30E ALA* 3.1 8.0 + - - +
32E GLU* 1.3 80.0 - - + +
34E VAL* 1.3 62.6 + - - +
36E LEU* 3.6 10.8 + - - +
37E CYS 3.8 3.3 + - - -
225G LEU* 5.4 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E HIS* 3.1 34.8 - - + +
14E GLN 3.9 9.0 - - - +
15E ASN* 5.3 0.2 - - - -
16E ALA* 3.9 22.0 - - + +
19E LEU* 4.0 3.6 - - + -
30E ALA 3.1 13.1 + - - +
31E ARG* 3.1 21.5 - - + +
33E ILE* 1.3 74.4 - - - +
35E LYS* 1.3 67.9 + - + +
37E CYS* 3.1 20.8 + - - +
40E CYS* 4.4 6.4 - - + +
9I A 5.3 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 35 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E ARG* 2.8 32.7 + - + +
32E GLU* 2.9 37.7 + - - +
34E VAL* 1.3 80.9 - - + +
36E LEU* 1.3 62.3 + - + +
37E CYS 3.1 5.4 + - - +
224G LEU* 5.0 0.4 - - - +
242G TYR* 5.0 4.3 - - - -
255G TRP 4.9 5.3 + - - -
257G PRO* 4.3 21.8 - - - +
263H PRO* 5.8 7.0 - - - -
9I A 5.2 20.2 - - + +
10I G 4.5 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E GLN* 4.5 19.3 - - - +
32E GLU* 2.9 29.5 + - + +
33E ILE* 4.0 5.8 - - - +
34E VAL 3.2 0.6 - - - -
35E LYS* 1.3 76.8 - - + +
37E CYS* 1.3 61.7 + - - +
38E PRO* 3.2 10.6 - - - +
225G LEU* 5.1 14.1 - - + -
252G SER* 5.2 7.4 - - - +
265H THR* 5.0 20.4 - - + +
----------------------------------------------------------
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