Contacts of the strand formed by residues 78 - 83 (chain H) in PDB entry 3BZE
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 TYR 78 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H LEU* 4.2 10.5 - - + -
40H LEU 2.7 23.3 - - - -
41H LYS* 2.7 58.8 + - + +
42H ASN 4.7 0.2 - - - +
46H ILE* 3.3 14.6 - - + +
70H PHE* 3.0 52.1 - + + +
71H THR 4.6 11.5 + - - -
72H PRO* 5.1 2.0 - - + -
76H ASP* 4.7 8.1 - - + -
77H GLU* 1.3 91.6 - - - +
79H ALA* 1.4 58.6 + - - +
94H LYS* 3.6 7.0 + - - +
95H TRP* 2.8 55.3 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H VAL* 4.8 5.6 - - - +
23H LEU* 4.9 2.7 - - - +
39H LEU* 3.6 6.4 - - - +
40H LEU* 2.8 42.4 + - + +
78H TYR* 1.4 75.7 - - - +
80H CYS* 1.3 61.2 + - - +
92H ILE* 4.0 16.6 - - + -
93H VAL 3.3 16.6 - - - +
94H LYS* 3.5 15.9 - - + +
95H TRP* 4.0 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 80 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H VAL* 3.5 18.3 - - + +
25H CYS* 2.0 51.4 - - + -
37H VAL* 3.4 21.1 - - - -
38H ASP 3.6 2.7 - - - -
39H LEU* 4.1 5.4 - - + -
40H LEU* 5.3 0.4 - - - -
79H ALA* 1.3 74.2 - - - +
81H ARG* 1.3 61.1 + - - +
82H VAL* 3.6 9.9 - - - -
91H LYS 3.5 2.0 - - - +
92H ILE* 3.3 4.1 - - - +
93H VAL* 2.8 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H GLU 3.6 1.6 - - - +
37H VAL* 3.5 3.5 - - - -
38H ASP* 2.8 51.1 + - + +
40H LEU* 2.8 43.2 - - + +
43H GLY 4.0 9.7 + - - -
45H ARG* 5.8 1.8 - - - +
79H ALA 4.2 0.4 + - - -
80H CYS* 1.3 74.1 - - - +
82H VAL* 1.3 61.8 + - - +
83H ASN* 6.1 0.7 - - + -
90H PRO* 4.0 29.3 - - + +
91H LYS 3.5 3.1 - - - -
92H ILE* 4.1 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H PRO* 4.3 9.9 - - + -
7H ILE* 3.6 32.8 - - + -
27H VAL* 3.8 14.6 - - + -
35H ILE* 3.9 28.0 - - + -
36H GLU 3.4 4.9 - - - +
37H VAL* 4.1 4.7 - - + -
80H CYS* 3.6 23.8 - - + -
81H ARG* 1.3 79.4 - - - +
83H ASN* 1.3 67.2 + - - +
87H LEU* 3.4 6.8 - - + +
90H PRO* 3.3 3.8 - - - +
91H LYS 2.7 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 83 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H ILE* 3.2 10.7 - - - +
36H GLU* 2.9 65.1 + - + +
81H ARG* 6.1 0.9 - - + -
82H VAL* 1.3 75.4 - - - +
84H HIS* 1.3 72.3 + - - +
87H LEU* 4.2 4.6 - - - +
89H GLN* 4.2 3.3 - - - -
90H PRO* 3.8 30.4 - - + +
----------------------------------------------------------
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