Contacts of the helix formed by residues 81 - 92 (chain D) 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 SER 81 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D HIS 4.2 0.4 + - - -
80D TYR* 1.3 76.3 - - - +
82D LEU* 1.3 63.7 + - - +
83D VAL* 3.5 9.4 + - - +
84D GLN* 2.8 41.3 + - - +
85D TRP* 3.1 20.5 + - - -
116D ILE* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D TYR 4.1 0.2 + - - -
81D SER* 1.3 70.3 - - - +
83D VAL* 1.3 61.7 + - + +
85D TRP* 3.2 10.2 + - + +
86D GLN* 2.8 47.8 + - + +
115D GLN* 3.5 50.9 - - + +
116D ILE* 3.6 21.4 - - + +
119D ALA* 3.6 16.4 - - + -
120D ILE* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D SER* 3.3 8.8 + - - +
82D LEU* 1.3 78.4 - - + +
84D GLN* 1.3 63.6 + - + +
86D GLN* 3.4 19.1 + - - +
87D GLU* 3.0 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D PHE* 3.9 6.8 - - + -
79D HIS 4.4 1.9 - - - +
80D TYR* 3.4 30.8 - - + -
81D SER* 2.8 47.5 + - - +
83D VAL* 1.3 78.8 - - + +
85D TRP* 1.3 61.6 - - - +
87D GLU* 3.4 5.9 + - - +
88D PHE* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D PHE* 3.8 18.4 - + - -
76D VAL* 3.5 39.9 - - + +
77D HIS 4.9 4.2 + - - -
80D TYR* 3.7 24.0 + - + +
81D SER 3.1 21.8 + - - +
82D LEU* 3.4 10.1 - - + +
84D GLN* 1.3 75.1 - - - +
86D GLN* 1.3 60.1 + - - +
88D PHE* 3.2 6.2 + + - +
89D ALA* 2.9 27.3 + - + +
96D LEU* 5.7 0.9 - - + -
99D LEU* 4.1 15.5 - - + -
100D ALA 4.2 7.9 - - - -
101D ALA* 4.2 22.2 - - + -
102D SER 5.4 0.9 - - - -
116D ILE* 3.3 44.2 - - + +
120D ILE* 3.4 27.2 - - + +
123D VAL* 3.9 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D LEU* 2.8 44.6 + - + +
83D VAL* 3.4 24.2 - - - +
84D GLN 3.4 0.2 - - - -
85D TRP* 1.3 71.6 - - - +
87D GLU* 1.3 58.7 + - - +
89D ALA* 3.4 1.8 + - - +
90D GLY* 2.9 26.9 + - - -
119D ALA* 4.1 22.1 - - + +
120D ILE* 3.9 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D VAL* 3.0 20.5 + - + +
84D GLN* 3.7 6.7 - - - +
86D GLN* 1.3 77.9 - - - +
88D PHE* 1.3 64.9 + - - +
90D GLY* 3.4 1.2 + - - -
91D GLN* 3.0 52.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D PHE* 3.4 65.7 - + + -
64D ALA* 4.3 8.1 - - + -
65D LYS* 4.1 9.2 - - + -
84D GLN 3.0 16.3 + - - +
85D TRP* 3.7 7.2 - + - +
87D GLU* 1.3 81.1 + - - +
89D ALA* 1.3 61.0 + - + +
92D ASN* 2.8 64.3 + - + +
95D CYS* 3.9 21.8 - - + -
96D LEU* 3.5 25.1 - - + -
99D LEU* 3.6 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D TRP 2.9 17.2 + - - +
86D GLN* 3.7 4.0 - - - +
88D PHE* 1.3 79.1 - - + +
90D GLY* 1.3 67.2 + - - +
92D ASN 3.3 7.8 + - - -
93D PRO* 3.3 17.2 - - - +
96D LEU* 4.1 18.1 - - + +
120D ILE* 3.8 31.0 - - + -
122D GLN* 5.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D GLN 2.9 17.3 + - - -
87D GLU* 3.9 1.6 - - - -
88D PHE 3.3 0.2 - - - -
89D ALA* 1.3 78.7 - - - +
91D GLN* 1.3 60.4 + - - +
92D ASN 3.6 0.3 + - - -
93D PRO* 3.7 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D LYS* 6.2 0.2 - - - +
87D GLU* 3.0 44.8 + - - +
90D GLY* 1.3 75.1 - - - +
92D ASN* 1.3 75.9 + - - +
93D PRO* 3.4 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D LYS* 3.5 34.1 + - - +
88D PHE* 2.8 51.2 + - + +
89D ALA 3.3 3.8 + - - -
91D GLN* 1.3 92.5 + - - +
93D PRO* 1.4 60.6 - - - +
94D ASP 3.2 2.7 - - - -
95D CYS* 3.1 29.9 + - - +
96D LEU* 3.6 13.2 - - - +
----------------------------------------------------------
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