Contacts of the helix formed by residues 70 - 81 (chain A) in PDB entry 4BU2
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 ASP 70 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 2.5 36.4 + - - -
68A ARG* 3.9 10.6 - - + +
69A ASP* 1.3 80.5 + - - +
71A PRO* 1.3 63.5 - - - +
72A ALA* 3.0 13.3 + - - +
73A LEU* 2.9 29.5 + - + +
74A ALA* 2.9 28.6 + - - +
227A LYS* 5.8 1.4 - - - +
229A GLY* 5.4 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ASP* 4.2 11.7 - - - +
70A ASP* 1.3 87.2 - - - +
72A ALA* 1.3 53.5 + - - +
74A ALA* 3.5 7.2 + - + +
75A THR* 2.7 37.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 5.4 2.2 - - - +
70A ASP* 3.0 10.0 + - - +
71A PRO* 1.3 76.4 - - + +
73A LEU* 1.3 60.8 + - - +
75A THR* 3.0 7.9 + - - -
76A TYR* 2.8 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 3.8 30.9 + - - +
32A ALA* 5.4 2.5 - - - +
33A LEU* 5.3 4.7 - - + -
44A SER 5.9 1.1 - - - +
68A ARG* 3.4 46.9 - - - +
70A ASP* 2.9 24.2 + - + +
72A ALA* 1.3 76.4 - - - +
74A ALA* 1.3 53.2 + - - +
76A TYR* 3.0 18.2 + - + -
77A TYR* 2.7 64.5 + - + +
229A GLY* 3.9 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASP 2.9 18.8 + - - +
71A PRO* 3.6 9.6 - - + +
73A LEU* 1.3 76.6 - - - +
75A THR* 1.3 58.7 + - - +
77A TYR* 3.6 2.4 + - - +
78A GLY* 3.1 21.1 + - - -
190A LEU 4.7 0.2 - - - +
227A LYS* 6.0 1.8 - - - +
228A PRO* 3.5 33.8 - - + +
229A GLY* 3.9 13.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PRO 2.7 21.0 + - - -
72A ALA* 3.0 6.9 + - - -
74A ALA* 1.3 75.6 - - - +
76A TYR* 1.3 67.8 + - - +
78A GLY* 3.3 8.8 + - - -
79A SER* 3.3 12.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA* 6.1 1.1 - - - -
33A LEU* 3.2 45.7 - - + +
35A PHE* 3.8 4.0 - + - -
72A ALA 2.8 13.0 + - - +
73A LEU* 3.0 28.7 + - + +
75A THR* 1.3 75.0 - - - +
77A TYR* 1.3 65.1 + + - +
79A SER* 2.5 38.6 + - - -
80A LEU* 3.4 12.7 + - + +
146A GLU* 2.6 47.9 + - + +
150A ILE* 4.0 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 5.6 6.1 - - + -
45A LEU* 4.3 3.7 + - + +
68A ARG* 3.2 17.5 + - - -
73A LEU* 2.7 50.7 + - + +
74A ALA 3.7 5.4 - - - +
76A TYR* 1.3 81.6 - + - +
78A GLY* 1.3 62.0 + - - +
79A SER 3.0 1.4 + - - -
80A LEU* 3.0 19.9 + - + +
188A LEU* 3.5 39.3 - - + +
189A GLN 3.0 28.0 - - - +
190A LEU* 3.2 21.4 - - + +
229A GLY* 3.5 21.1 - - - +
230A ASP 3.2 21.3 - - - -
231A LEU* 3.7 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA 3.1 11.7 + - - -
75A THR* 3.3 6.3 + - - -
76A TYR 3.2 0.4 - - - -
77A TYR* 1.3 77.9 - - - +
79A SER* 1.3 57.2 + - - +
80A LEU 3.4 0.2 - - - -
81A PHE 3.9 5.5 - - - +
82A LYS* 3.3 30.2 - - - +
190A LEU* 3.5 22.2 + - - -
191A GLU* 4.6 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A THR 3.3 9.2 + - - -
76A TYR* 2.5 35.0 + - - -
78A GLY* 1.3 75.9 - - - +
80A LEU* 1.3 66.9 + - - +
81A PHE* 3.0 5.4 + - - -
82A LYS* 3.9 21.6 + - - +
85A ASP* 4.5 0.9 - - - +
144A LYS* 4.4 12.3 + - - -
146A GLU* 5.4 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 5.9 0.2 - - + -
76A TYR* 3.9 16.2 - - + +
77A TYR* 3.0 24.9 + - + +
79A SER* 1.3 78.7 + - - +
81A PHE* 1.3 63.4 + - - +
144A LYS* 3.7 22.3 - - - +
146A GLU* 3.5 39.7 - - + -
147A LEU* 4.0 28.5 - - + +
150A ILE* 3.9 16.6 - - + -
188A LEU* 3.9 27.6 - - + -
190A LEU* 4.1 14.4 - - + -
254A VAL* 5.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR 4.2 0.2 + - - -
78A GLY 3.9 6.7 + - - +
79A SER 3.0 2.4 + - - -
80A LEU* 1.3 79.9 - - - +
82A LYS* 1.3 78.3 + - - +
85A ASP* 3.4 20.2 - - + -
86A LEU* 4.5 9.4 - - + -
89A LEU* 4.8 3.6 - - + -
137A PHE* 3.9 32.1 - + + -
140A PRO* 3.7 27.1 - - + -
144A LYS* 3.8 24.5 - - + -
147A LEU* 5.0 2.7 - - + -
166A VAL* 3.8 29.4 - - + -
168A ILE* 4.4 11.9 - - + -
190A LEU* 3.8 27.0 - - + +
191A GLU* 4.0 3.8 - - - -
252A THR* 3.9 12.1 - - + +
----------------------------------------------------------
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