Contacts of the helix formed by residues 73 - 85 (chain B) in PDB entry 5X11
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 73 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLY* 3.0 21.5 + - - +
53B PHE 2.8 33.9 + - - +
54B ILE 3.9 16.6 - - - +
55B THR* 4.2 12.6 - - - +
72B LEU* 1.3 74.9 - - - +
74B ASP* 1.3 64.9 + - - +
75B SER* 3.3 4.6 + - - -
76B GLY 3.0 8.5 + - - -
77B LYS* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B THR* 1.3 75.0 - - - +
75B SER* 1.3 66.3 + - - +
77B LYS* 3.4 5.8 + - - +
78B GLN* 3.3 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLU 5.7 0.7 - - - -
52B GLY 3.6 15.7 + - - -
53B PHE* 3.7 16.7 - - - -
73B THR* 3.3 8.7 + - - -
74B ASP* 1.3 80.1 - - - +
76B GLY* 1.3 56.8 + - - +
78B GLN* 3.3 5.6 + - - +
79B GLU* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.9 5.5 - - - +
53B PHE* 3.4 32.5 - - - -
72B LEU* 4.2 11.8 - - - +
73B THR* 3.0 9.5 + - - -
75B SER* 1.3 79.3 - - - +
77B LYS* 1.3 56.4 + - - +
79B GLU* 3.5 1.8 + - - +
80B LEU* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 4.5 15.5 - - + +
73B THR 3.1 15.2 + - - +
74B ASP* 3.8 6.1 - - - +
76B GLY* 1.3 74.8 - - - +
78B GLN* 1.3 57.0 + - - +
80B LEU* 3.3 11.5 - - + +
81B HIS* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ASP 3.3 8.8 + - - +
75B SER* 3.3 9.3 + - - +
77B LYS* 1.3 74.6 - - - +
79B GLU* 1.3 56.8 + - - +
81B HIS* 2.9 17.5 + - - +
82B ASP* 2.7 71.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LYS* 2.8 37.5 + - - +
6B TYR* 3.2 24.9 + - + -
9B LEU* 4.2 4.0 - - + -
53B PHE* 3.6 29.0 - - + -
75B SER 2.9 20.7 + - - +
76B GLY 3.7 3.8 - - - +
78B GLN* 1.3 74.2 - - - +
80B LEU* 1.3 63.0 + - - +
82B ASP* 3.5 10.3 + - - +
83B TRP 3.3 14.7 + - - -
86B ARG* 4.7 3.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
104A PHE* 5.1 2.2 - - + -
107A SER* 4.2 22.4 - - - +
6B TYR* 4.1 15.7 - - - +
9B LEU* 4.0 21.4 - - + +
10B GLY* 3.5 29.6 - - - +
13B ARG* 4.3 12.1 - - + -
72B LEU* 4.4 8.7 - - + -
76B GLY 2.9 19.4 + - - +
77B LYS* 3.3 8.7 - - + +
79B GLU* 1.3 76.3 - - - +
81B HIS* 1.3 57.7 + - - +
83B TRP* 3.2 15.6 + - + +
84B LEU* 2.9 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A SER* 4.1 15.9 + - - -
112A GLU* 3.4 37.8 + - - -
77B LYS 3.0 13.8 + - - +
78B GLN* 2.9 22.8 + - - +
80B LEU* 1.3 70.9 - - - +
82B ASP* 1.3 72.1 + - - +
84B LEU* 3.2 18.9 + - + +
85B ILE* 3.5 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLN* 2.7 54.3 + - - +
79B GLU* 3.9 9.8 + - - +
80B LEU 3.3 0.2 - - - -
81B HIS* 1.3 76.0 - - - +
83B TRP* 1.3 60.0 - - - +
85B ILE* 4.7 7.1 - - - +
86B ARG* 3.1 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLU* 2.9 41.6 + - + -
100A LEU* 3.9 22.4 - - + -
101A LYS* 2.5 66.4 + - + -
104A PHE* 4.3 11.2 - + - -
1B MET 5.6 1.0 + - - -
3B VAL* 4.9 1.8 - - + -
6B TYR* 3.5 62.9 - + + -
79B GLU 3.3 3.4 + - - -
80B LEU* 3.2 13.9 + - + +
81B HIS 3.1 0.6 - - - -
82B ASP* 1.3 78.9 - - - +
84B LEU* 1.3 80.2 + - + +
86B ARG* 3.3 33.2 + - - +
88B GLN* 3.3 8.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LYS* 3.1 45.6 + - + +
104A PHE* 4.0 18.2 - - + +
105A ILE* 5.9 0.4 - - - -
107A SER* 3.7 37.2 - - - +
116A LEU* 3.5 23.3 - - + +
80B LEU* 2.9 28.8 + - + +
81B HIS* 3.2 11.6 + - - +
83B TRP* 1.3 100.2 - - + +
85B ILE* 1.3 64.4 + - + +
86B ARG 3.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLU* 3.8 46.4 - - + +
116A LEU* 4.6 10.2 - - + +
81B HIS* 3.6 29.4 - - + +
82B ASP* 4.7 7.4 - - - +
84B LEU* 1.3 79.1 - - + +
86B ARG* 1.3 66.9 + - + +
87B HIS* 3.3 20.6 + - - -
----------------------------------------------------------
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