Contacts of the helix formed by residues 53 - 64 (chain C) in PDB entry 4BSX
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 GLN 53 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C LEU* 4.8 3.6 - - - +
27C LYS* 2.7 32.7 + - - +
48C LEU* 2.8 25.4 + - + +
51C LEU* 3.5 40.1 + - + +
52C GLY* 1.3 77.1 - - - +
54C GLU* 1.3 57.5 + - - +
55C THR 3.5 2.2 - - - -
56C GLU* 3.6 15.9 + - + +
57C ALA* 3.1 28.2 + - - +
129D ASP* 4.7 4.4 + - - -
130D ASP 5.3 2.0 + - - -
131D HIS* 5.1 6.9 + - - +
134D GLY* 6.2 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 2.9 31.0 + - - -
29B LYS* 3.8 16.4 + - - +
34B ARG* 5.6 1.2 + - - -
49C LEU* 4.3 19.9 - - + +
52C GLY* 3.1 17.6 + - - +
53C GLN* 1.3 71.9 - - - +
55C THR* 1.3 58.6 + - - +
56C GLU 3.2 0.2 - - - -
57C ALA* 4.0 6.7 - - - -
58C ARG* 2.4 85.2 + - - +
77C TRP 4.9 1.2 - - - +
78C ALA 3.8 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLN 3.5 1.0 - - - -
54C GLU* 1.3 78.3 - - - +
56C GLU* 1.3 64.5 + - + +
58C ARG* 3.5 9.4 + - - +
59C ILE* 3.2 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LYS* 4.1 12.6 + - - -
31C LYS* 4.3 18.2 + - - +
44C HIS* 4.4 6.1 + - - +
48C LEU* 3.8 28.3 - - + +
53C GLN* 3.6 26.1 + - + +
54C GLU 3.2 0.2 - - - -
55C THR* 1.3 78.5 - - + +
57C ALA* 1.3 66.3 + - - +
59C ILE* 3.0 13.8 + - + +
60C SER* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ALA* 3.6 17.2 - - - +
48C LEU* 3.8 14.4 - - + +
49C LEU* 3.4 32.5 - - + -
53C GLN 3.1 19.5 + - - +
54C GLU 3.5 2.0 - - - +
56C GLU* 1.3 76.4 - - - +
58C ARG* 1.3 55.9 + - - +
60C SER* 3.3 4.9 + - - -
61C LEU* 2.9 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 3.7 7.7 + - - -
29B LYS* 5.5 0.4 - - - +
54C GLU* 2.4 58.5 + - - +
55C THR* 3.8 7.7 + - - +
57C ALA* 1.3 69.1 - - - +
59C ILE* 1.3 61.6 + - + +
61C LEU* 3.8 7.6 - - - +
62C GLU* 2.9 30.3 + - - +
78C ALA* 2.9 31.6 + - + +
79C GLY* 3.8 17.0 + - - -
80C VAL* 3.6 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C THR* 3.2 30.9 + - + +
56C GLU* 3.0 13.5 + - + +
58C ARG* 1.3 76.1 - - + +
60C SER* 1.3 64.1 + - - +
62C GLU* 3.4 10.9 + - + +
63C ALA* 3.3 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ASP 5.4 1.8 - - - -
44C HIS* 3.9 15.6 + - - -
45C ALA* 4.1 15.3 - - - -
48C LEU* 3.7 13.9 - - - +
56C GLU* 2.9 16.0 + - - +
57C ALA* 3.4 10.1 - - - -
59C ILE* 1.3 78.8 - - - +
61C LEU* 1.3 62.1 + - - +
63C ALA* 3.2 15.7 + - - +
64C LEU* 3.4 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 4.2 12.3 - - + -
45C ALA* 3.7 23.8 - - + -
49C LEU* 4.5 5.2 - - + -
57C ALA 2.9 23.1 + - - +
58C ARG* 3.2 6.0 + - - +
60C SER* 1.3 76.4 - - - +
62C GLU* 1.3 58.7 + - - +
64C LEU* 2.9 26.6 + - + +
65C LYS* 3.3 11.3 + - - +
70C ALA* 3.8 20.9 - - + +
73C VAL* 4.0 18.2 - - + -
74C ALA* 3.8 23.9 - - + +
78C ALA* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS* 5.0 11.2 - - - +
58C ARG 2.9 17.3 + - - +
59C ILE* 3.7 9.2 - - + +
60C SER 3.2 0.2 - - - -
61C LEU* 1.3 77.6 - - - +
63C ALA* 1.3 61.7 + - + +
64C LEU 3.1 0.7 + - - -
65C LYS* 3.3 51.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ILE* 3.3 11.1 + - + +
60C SER* 3.2 12.9 + - - +
61C LEU 3.2 1.0 - - - -
62C GLU* 1.3 78.0 - - - +
64C LEU* 1.3 63.6 + - + +
65C LYS* 3.4 1.1 + - - +
66C MSE 6.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ASP* 3.8 52.5 - - + +
42C LEU* 3.9 11.7 - - + +
45C ALA* 5.0 0.4 - - + -
60C SER* 3.4 17.3 - - - +
61C LEU* 2.9 20.1 + - + +
63C ALA* 1.3 85.8 - - + +
65C LYS* 1.3 55.1 + - - +
66C MSE 3.2 3.4 - - - -
67C ASP* 2.9 26.4 - - + +
70C ALA* 3.4 27.5 - - + +
----------------------------------------------------------
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