Contacts of the helix formed by residues 42 - 57 (chain E) in PDB entry 3CQ6
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 42 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E PRO 3.5 2.7 + - - -
41E PRO* 1.3 73.5 - - - +
43E GLU* 1.3 65.4 + - - +
44E ALA* 3.8 7.8 + - - +
45E LEU* 3.1 27.5 + - - +
46E VAL* 3.0 25.4 + - - +
273E HIS* 4.8 2.9 - - - +
276E ASP* 3.7 23.4 + - - -
277E THR* 5.1 5.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E PRO 3.9 0.8 + - - -
42E SER* 1.3 73.6 - - - +
44E ALA* 1.3 56.9 + - - +
46E VAL* 3.6 7.6 + - - +
47E ALA* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E SER* 3.2 7.7 + - - +
43E GLU* 1.3 76.5 - - - +
45E LEU* 1.3 64.0 + - - +
47E ALA* 3.5 4.3 + - - +
48E ASP* 3.1 25.1 + - - +
273E HIS* 3.6 18.9 + - + +
276E ASP* 5.7 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E PRO* 4.8 16.6 - - + -
42E SER* 3.1 25.2 + - - +
44E ALA* 1.3 75.1 - - - +
46E VAL* 1.3 54.6 + - + +
48E ASP* 3.3 3.3 + - - +
49E LEU* 2.7 46.8 + - + -
232E PHE* 4.8 14.8 - - + -
269E VAL* 3.8 19.4 - - + +
270E ALA* 3.8 26.5 - - + +
273E HIS* 3.9 27.7 - - + -
277E THR* 4.1 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E PRO* 4.2 23.3 - - + +
42E SER 3.0 21.1 + - - +
43E GLU* 3.8 7.4 - - - +
45E LEU* 1.3 77.0 - - + +
47E ALA* 1.3 52.9 + - - +
49E LEU* 3.2 13.8 + - + +
50E VAL* 2.7 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E GLU 3.0 18.7 + - - +
44E ALA* 4.0 5.8 - - - +
46E VAL* 1.3 76.6 - - - +
48E ASP* 1.3 58.6 + - - +
50E VAL* 3.4 7.4 + - - +
51E ALA* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E ALA 3.1 18.9 + - - +
45E LEU 3.5 3.1 - - - +
47E ALA* 1.3 74.4 - - - +
49E LEU* 1.3 59.2 + - - +
51E ALA* 3.2 6.2 + - - +
52E THR* 2.8 37.9 + - - -
269E VAL* 3.8 6.0 - - + +
272E ARG* 3.0 38.6 + - - -
273E HIS* 2.9 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E LEU* 2.7 31.7 + - + +
46E VAL* 3.3 17.7 - - + +
48E ASP* 1.3 72.8 - - - +
50E VAL* 1.3 58.1 + - + +
52E THR* 3.3 3.2 + - + -
53E VAL* 3.0 46.2 + - + +
232E PHE* 5.5 7.0 - - + -
265E ALA 5.3 0.4 - - - -
266E ALA* 3.7 37.2 - - + +
269E VAL* 3.8 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E VAL* 2.7 37.8 + - + +
47E ALA* 3.7 7.2 - - - +
49E LEU* 1.3 75.8 - - + +
51E ALA* 1.3 65.7 + - - +
53E VAL* 3.5 6.1 + - - +
54E ASP* 3.1 23.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E ALA 3.0 17.6 + - - +
48E ASP* 3.7 8.1 - - - +
50E VAL* 1.3 77.3 - - - +
52E THR* 1.3 61.9 + - - +
54E ASP* 3.4 9.7 + - - +
55E LYS* 3.2 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 52 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E ASP* 2.8 34.8 + - - -
49E LEU* 3.5 5.6 - - + -
51E ALA* 1.3 73.8 - - - +
53E VAL* 1.3 59.7 + - + +
55E LYS* 2.7 39.1 + - - +
56E ILE* 2.9 20.6 + - + +
265E ALA* 4.1 23.6 - - + +
269E VAL* 3.4 23.2 - - + +
272E ARG* 3.6 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E LEU* 3.0 35.6 + - + +
50E VAL* 3.8 6.5 - - - +
52E THR* 1.3 75.4 - - + +
54E ASP* 1.3 58.7 + - - +
56E ILE* 4.2 7.9 - - + -
57E ALA* 2.9 43.9 + - + +
60E LEU* 6.4 0.7 - - + -
262E LEU* 3.9 27.8 - - + -
265E ALA* 6.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E VAL* 3.1 15.4 + - + +
51E ALA* 3.6 12.4 - - - +
52E THR 3.2 0.2 - - - -
53E VAL* 1.3 77.5 - - - +
55E LYS* 1.3 61.7 + - - +
57E ALA* 4.3 7.1 + - - +
58E THR* 5.0 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 55 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E ALA 3.2 11.8 + - - +
52E THR* 2.7 30.8 + - - +
54E ASP* 1.3 75.1 + - - +
56E ILE* 1.3 85.3 + - + +
57E ALA 3.6 0.2 + - - -
58E THR* 3.7 13.9 + - - +
59E GLU* 5.3 1.2 - - - +
272E ARG* 5.7 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E THR* 2.9 22.3 + - + +
53E VAL* 4.0 8.1 - - - +
55E LYS* 1.3 101.1 - - - +
57E ALA* 1.3 66.3 + - - +
58E THR 3.2 2.9 - - - -
59E GLU* 3.0 27.1 + - + +
60E LEU* 3.8 7.4 + - + +
261E ALA* 3.8 20.2 - - + +
262E LEU* 4.0 17.9 - - + -
265E ALA* 3.3 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E VAL* 2.9 28.4 + - + +
54E ASP* 4.6 7.0 - - - +
55E LYS 3.4 1.0 - - - -
56E ILE* 1.3 78.7 - - - +
58E THR* 1.3 59.5 + - + +
59E GLU 3.1 4.9 + - - -
60E LEU* 3.1 34.6 + - + +
262E LEU* 6.1 0.4 - - - -
----------------------------------------------------------
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