Contacts of the helix formed by residues 67 - 77 (chain D) in PDB entry 2OZB
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 LEU 67 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LYS* 4.0 34.1 - - + +
63D LEU* 3.7 39.5 - - + +
64D GLU* 3.2 22.3 + - + +
66D ILE* 1.3 76.6 - - - +
68D HIS* 1.3 63.1 + - - +
69D LEU 3.2 0.9 - - - -
70D PRO* 3.3 20.1 - - + +
71D LEU* 4.0 7.6 - - - +
82D PHE* 3.9 23.6 - - + -
308E PHE* 3.2 32.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ALA* 4.7 2.7 - - + -
43D THR* 2.8 31.2 + - + -
64D GLU 4.2 0.8 + - - -
65D ILE 3.6 10.6 + - - -
66D ILE* 3.8 1.7 - - - -
67D LEU* 1.3 78.8 - - - +
69D LEU* 1.3 82.7 + - + +
71D LEU* 3.2 11.8 + - + +
72D LEU* 3.1 38.7 + - + +
242E SER* 3.4 36.3 - - - +
243E LYS* 5.0 4.4 - - + +
244E MET 5.7 0.2 + - - -
304E ARG* 3.3 43.6 + - + -
308E PHE* 3.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ALA* 4.0 2.9 - - + +
42D ALA* 4.0 9.0 - - + -
43D THR* 3.5 39.3 - - - +
46D LEU* 3.8 21.0 - - + +
54D ILE* 4.6 8.3 - - + -
56D MET* 3.9 15.5 - - + -
66D ILE* 3.0 24.1 + - + +
68D HIS* 1.3 89.0 - - + +
70D PRO* 1.4 66.5 - - + +
72D LEU* 2.9 7.1 + - + +
73D CYS* 2.9 24.9 + - - -
101D ALA* 3.6 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D MET* 4.0 14.1 - - + -
66D ILE 3.4 10.5 - - - +
67D LEU* 3.3 28.3 - - + +
69D LEU* 1.4 89.2 - - + +
71D LEU* 1.3 61.8 + - + +
73D CYS* 3.1 12.4 + - + +
74D GLU* 3.2 13.7 + - - +
80D TYR* 3.7 45.8 + - + +
82D PHE* 4.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LEU 4.0 8.3 - - - +
68D HIS* 3.2 13.4 + - + +
69D LEU 3.1 0.6 - - - -
70D PRO* 1.3 78.4 - - + +
72D LEU* 1.3 63.0 + - - +
74D GLU* 3.1 19.1 + - + +
75D ASP* 3.1 14.3 - - - +
239E THR* 5.6 5.6 - - + -
242E SER* 5.6 4.0 - - - +
243E LYS* 4.5 21.5 - - - +
308E PHE* 3.8 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D THR* 3.9 28.0 - - + -
46D LEU* 3.8 27.2 - - + +
47D ASN* 3.5 22.2 - - - +
68D HIS* 3.1 25.0 + - + +
69D LEU* 2.9 8.5 + - - +
71D LEU* 1.3 78.6 - - - +
73D CYS* 1.3 61.3 + - - +
74D GLU 3.6 0.2 + - - -
75D ASP* 3.6 10.5 - - - +
76D LYS* 3.2 37.8 + - - +
243E LYS* 4.1 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D LEU* 4.0 20.2 - - - -
54D ILE* 4.0 17.9 - - - -
69D LEU 2.9 17.1 + - - +
70D PRO 3.4 9.6 - - - +
71D LEU 3.1 0.2 - - - -
72D LEU* 1.3 77.5 - - - +
74D GLU* 1.3 58.0 + - - +
76D LYS 3.5 0.3 + - - -
77D ASN* 2.9 11.1 + - - -
78D VAL* 2.8 55.1 + - - +
80D TYR* 3.6 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D PRO 3.2 9.1 + - - +
71D LEU* 3.1 14.3 + - + +
73D CYS* 1.3 72.8 - - - +
75D ASP* 1.3 72.6 + - - +
77D ASN* 3.0 17.0 + - - +
80D TYR* 5.6 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D LEU 3.1 17.0 - - - +
72D LEU* 3.6 19.2 - - - +
74D GLU* 1.3 82.2 - - - +
76D LYS* 1.3 75.0 + - + +
77D ASN* 3.6 0.7 + - - +
243E LYS* 5.0 9.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D LEU* 3.3 31.0 + - + +
47D ASN* 4.1 21.6 + - - +
49D GLY* 4.8 11.7 - - - +
72D LEU* 3.2 28.7 + - + +
73D CYS 3.5 0.8 + - - +
74D GLU 3.1 0.4 - - - -
75D ASP* 1.3 92.3 + - + +
77D ASN* 1.3 64.8 + - - +
78D VAL* 3.7 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D CYS 2.9 7.9 + - - -
74D GLU* 3.0 10.6 + - - +
75D ASP 3.3 0.8 - - - -
76D LYS* 1.3 79.2 - - - +
78D VAL* 1.3 60.1 + - - +
79D PRO* 4.0 4.7 - - - +
124D GLU* 4.8 11.7 + - - -
----------------------------------------------------------
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