Contacts of the helix formed by residues 73 - 82 (chain B) in PDB entry 2XJZ
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 CYS 73 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B CYS* 3.5 4.8 - - - +
53B CYS* 4.2 0.7 - - - -
55B CYS* 3.7 22.0 - - - -
57B LEU* 3.8 12.1 - - + -
63B ARG 4.5 4.3 - - - +
65B TYR* 4.0 2.5 - - - -
72B LEU* 1.3 75.0 - - - +
74B ARG* 1.3 58.3 + - - +
75B ARG* 3.8 11.2 - - - -
76B ASP* 3.4 15.9 - - - -
77B TYR* 2.9 28.6 + - - +
203B ZN 2.3 36.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 3.3 53.7 + - + +
65B TYR* 3.7 34.0 - - + +
73B CYS* 1.3 71.7 - - - +
75B ARG* 1.4 54.1 + - - +
77B TYR* 3.3 1.4 + - - +
78B LEU* 2.8 55.2 + - + +
97B TYR* 4.4 8.1 + - + +
66C TYR* 5.5 4.0 - - - -
68C LEU* 3.7 17.0 - - - +
69C GLY* 3.5 29.9 - - - +
345J LEU* 3.9 26.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B CYS* 4.2 14.5 - - - +
73B CYS* 3.4 9.2 - - - -
74B ARG* 1.4 77.7 - - - +
76B ASP* 1.4 83.0 + - - +
78B LEU* 3.4 1.6 + - - +
79B ARG* 2.9 63.9 + - + +
97B TYR* 3.5 49.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B CYS* 3.5 5.3 - - - -
52B LEU* 3.8 24.7 - - + +
53B CYS* 3.2 12.9 - - - +
72B LEU* 4.5 4.5 - - + -
73B CYS* 3.4 6.1 - - - +
75B ARG* 1.4 89.9 + - - +
77B TYR* 1.3 67.9 + - - +
79B ARG* 2.8 32.6 + - - +
80B LEU* 3.2 26.7 + - - +
203B ZN 1.9 37.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TYR* 3.6 45.3 - + + -
67B LYS* 4.3 9.6 - - + -
72B LEU* 4.0 13.6 - - + +
73B CYS 2.9 19.7 + - - +
74B ARG 3.5 3.6 - - - +
76B ASP* 1.3 76.7 - - - +
78B LEU* 1.3 76.7 + - + +
80B LEU 3.2 2.1 + - - -
81B PHE* 2.8 62.7 + + + -
347J GLY 5.9 0.2 - - - -
350J PHE* 3.2 24.3 - + - -
351J GLY* 4.1 9.9 - - - -
354J ASP* 2.7 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 5.0 1.7 + - - +
65B TYR* 5.8 2.0 - - + -
74B ARG* 2.8 41.9 + - + +
75B ARG 3.8 3.1 - - - +
77B TYR* 1.3 94.1 - - + +
79B ARG* 1.3 61.6 + - - +
82B GLY* 3.0 32.0 + - - +
96B ALA* 3.5 30.2 - - + +
97B TYR* 3.7 28.5 - - + -
345J LEU* 4.1 12.6 - - + -
347J GLY* 4.1 21.3 - - - +
348J GLY* 5.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A HIS* 4.2 20.3 - - - +
122A PHE 3.1 23.8 + - - +
123A CYS* 3.4 32.7 - - - +
124A VAL* 3.1 26.3 + - - +
52B LEU* 4.5 11.1 - - - +
75B ARG* 2.9 50.7 + - + +
76B ASP* 2.8 26.4 + - - +
77B TYR 3.3 0.2 - - - -
78B LEU* 1.3 75.8 - - - +
80B LEU* 1.3 79.4 + - - +
97B TYR* 5.3 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A MET* 4.2 5.4 - - + -
101A MET* 5.7 2.0 - - + -
110A LEU* 4.1 22.9 - - + -
122A PHE 5.3 0.7 - - - +
124A VAL* 3.1 17.5 - - - +
52B LEU* 3.4 28.5 - - + -
72B LEU* 4.3 3.8 - - + -
76B ASP 3.2 14.3 + - - +
77B TYR 3.2 0.4 + - - -
79B ARG* 1.3 113.0 - - - +
81B PHE* 1.3 82.2 + - + +
341I GLY 4.1 0.3 - - - +
342I GLU* 3.5 3.8 - - - -
343I PRO* 3.4 35.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A MET* 3.9 5.4 - - + -
124A VAL* 4.6 0.4 - - - -
67B LYS* 3.7 39.5 - - + -
68B LEU* 3.8 14.6 - - + -
72B LEU* 4.0 9.2 - - + -
77B TYR* 2.8 47.4 + + + +
80B LEU* 1.3 95.4 - - + +
82B GLY* 1.3 61.3 + - - +
342I GLU* 3.5 32.0 - - - +
343I PRO* 3.7 39.0 - - + -
350J PHE* 3.0 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 3.2 25.8 - - - +
77B TYR 3.7 1.4 + - - -
78B LEU* 3.0 35.6 + - - +
80B LEU 3.8 0.2 - - - -
81B PHE* 1.3 80.9 - - - +
83B GLN* 1.3 60.3 + - - -
96B ALA* 3.5 12.3 - - - -
347J GLY* 4.8 0.9 - - - -
350J PHE* 4.6 4.9 - - - -
----------------------------------------------------------
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