Contacts of the helix formed by residues 60 - 70 (chain A) in PDB entry 2BZN
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 60 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASP 3.8 19.3 - - - +
58A VAL 3.0 13.6 + - - -
59A GLY* 1.3 75.9 - - - -
61A PHE* 1.3 65.9 + - - +
62A GLU* 3.5 10.1 + - - +
63A MET* 3.0 15.3 + - - +
64A ALA* 3.0 22.6 + - - +
74A THR* 4.1 1.9 - - - +
76A VAL* 5.5 1.1 - - - -
77A HIS* 4.2 2.0 - - + +
80A TYR* 3.4 14.1 - - - +
250A GLU 2.8 22.0 + - - +
252A GLY* 3.7 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 1.3 72.8 - - - +
62A GLU* 1.3 68.4 + - - +
64A ALA* 3.4 5.5 + - + +
65A LYS* 3.1 28.1 + - - +
76A VAL* 4.1 19.1 - - + -
80A TYR* 3.0 57.1 + + - +
84A GLN* 3.8 20.2 - - + -
85A TRP* 3.7 40.6 - + - -
88A PHE* 3.5 50.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 3.1 16.1 - - - -
61A PHE* 1.3 84.9 + - - +
63A MET* 1.3 61.2 + - - +
65A LYS* 3.5 23.9 + - - +
66A VAL* 3.5 10.2 + - - +
80A TYR* 3.8 5.6 + - - -
249A SER 6.0 0.2 - - - +
250A GLU* 3.7 37.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA* 4.0 16.6 - - + -
58A VAL* 3.3 29.8 - - - +
59A GLY 4.9 0.2 - - - -
60A THR* 3.0 15.9 + - - +
62A GLU* 1.3 76.1 - - - +
64A ALA* 1.3 63.1 + - - +
66A VAL* 3.2 3.7 + - - +
67A LEU* 2.9 53.3 + - + +
74A THR* 4.3 1.1 - - - +
245A LEU* 3.4 35.2 - - + +
250A GLU* 3.9 8.0 + - + -
251A SER* 3.7 24.5 - - - +
301A VAL* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR 3.0 12.7 + - - +
61A PHE* 3.6 13.7 - - + +
63A MET* 1.3 78.0 - - - +
65A LYS* 1.3 56.5 + - - +
67A LEU 4.5 0.2 - - - +
68A CYS* 2.9 38.7 + - - -
74A THR* 3.3 24.1 + - + +
76A VAL* 5.4 0.2 - - + -
88A PHE* 4.3 8.3 - - + -
95A CYS* 5.0 0.4 - - - -
99A LEU* 3.8 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 3.1 20.1 + - - +
62A GLU* 3.8 19.7 - - - +
63A MET 3.2 0.2 - - - -
64A ALA* 1.3 77.6 - - - +
66A VAL* 1.3 64.0 + - + +
68A CYS* 3.9 4.9 + - - +
69A LYS* 3.4 29.2 + - - +
88A PHE* 3.8 12.1 - - + -
92A ASN* 3.1 35.4 + - - +
95A CYS* 4.2 12.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU 3.5 11.6 + - - +
63A MET 3.2 6.1 + - - +
65A LYS* 1.3 77.0 - - + +
67A LEU* 1.3 69.1 - - + +
69A LYS* 3.0 35.2 + - + +
70A PHE* 3.5 14.2 - - + -
250A GLU* 3.6 26.9 - - + +
301A VAL* 3.6 22.2 - - + -
302A GLU* 4.1 23.8 - - + +
305A ILE* 5.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA* 3.7 31.9 - - + +
63A MET* 2.9 39.0 + - + +
64A ALA 4.1 2.2 - - - +
66A VAL* 1.3 78.5 - - - +
68A CYS* 1.3 63.1 + - - +
70A PHE* 2.9 17.9 + - - +
72A LEU* 3.0 51.0 + - + +
73A PHE 3.9 8.5 - - - +
74A THR* 3.9 13.0 - - - +
245A LEU* 4.5 7.2 - - + -
301A VAL* 4.2 7.4 - - + -
305A ILE* 3.8 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ALA* 2.9 29.9 + - - +
65A LYS 4.0 6.3 - - - +
67A LEU* 1.3 76.9 - - - +
69A LYS* 1.3 57.3 + - + +
71A SER* 3.0 20.1 + - - +
72A LEU 4.1 11.6 + - - +
74A THR* 5.7 1.1 - - - -
94A ASP 4.7 4.7 - - - +
95A CYS* 3.7 46.9 - - - -
98A HIS* 5.1 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LYS* 3.4 30.7 + - - +
66A VAL* 3.0 26.5 + - + +
68A CYS* 1.3 75.8 - - + +
70A PHE* 1.3 69.4 + - + +
71A SER* 3.8 2.0 + - - -
302A GLU* 6.0 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 3.6 10.2 - - - +
66A VAL* 3.5 28.9 - - + -
67A LEU* 2.9 7.6 + - - +
69A LYS* 1.3 84.2 - - + +
71A SER* 1.3 69.9 + - - +
72A LEU* 3.2 26.1 + - + +
302A GLU* 3.7 41.3 - - + -
305A ILE* 3.7 22.0 - - + -
306A ARG* 3.8 37.2 - - + -
309A LEU* 4.1 14.3 - - + +
----------------------------------------------------------
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