Contacts of the helix formed by residues 147 - 159 (chain A) in PDB entry 2X30
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 147 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A THR* 3.6 19.7 + - - +
135A THR* 4.9 0.2 - - - +
136A LEU* 4.4 0.7 - - - -
146A GLY* 1.3 71.6 - - - -
148A LEU* 1.3 65.5 + - - +
149A TYR* 2.9 16.8 + - - +
150A GLU* 2.8 57.6 + - + +
151A THR* 2.9 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 4.2 12.1 - - + -
131A VAL* 4.0 36.3 - - + -
133A GLY 4.4 5.8 - - - +
134A THR* 2.7 26.9 + - + +
136A LEU* 4.0 18.8 - - + +
146A GLY 3.8 1.0 + - - -
147A ASP* 1.3 72.2 - - - +
149A TYR* 1.3 81.0 + - + +
151A THR* 3.4 2.1 + - - -
152A LEU* 2.9 53.5 + - + +
181A LEU* 4.3 13.2 - - + -
184A ASN* 5.8 2.7 - - + -
185A VAL* 4.6 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A THR* 4.3 22.0 - - + -
147A ASP* 2.9 14.3 + - - +
148A LEU* 1.3 88.0 - - + +
150A GLU* 1.3 65.6 + - + +
152A LEU* 3.9 6.6 - - + +
153A ASP* 3.0 24.9 + - - +
184A ASN* 4.1 29.8 + - - +
185A VAL* 6.1 0.2 - - - -
187A ALA* 6.3 0.2 - - + -
188A ALA* 4.1 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASP* 2.8 40.6 + - + +
149A TYR* 1.3 72.2 - - + +
151A THR* 1.3 61.7 + - - +
153A ASP* 3.4 7.2 + - - +
154A ARG* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ALA* 5.4 2.0 - - + +
108A LEU* 4.8 10.5 - - + +
129A LEU* 4.2 5.2 - - + -
136A LEU* 3.4 28.5 - - + +
146A GLY* 4.5 4.5 - - - -
147A ASP 2.9 23.2 + - - -
148A LEU 3.8 1.6 - - - -
150A GLU* 1.3 73.4 - - - +
152A LEU* 1.3 59.9 + - - +
154A ARG* 3.4 26.2 + - - +
155A LEU* 3.0 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 3.9 22.7 - - + -
148A LEU* 2.9 43.0 + - + +
149A TYR* 3.9 8.5 - - + +
151A THR* 1.3 72.9 - - - +
153A ASP* 1.3 56.6 + - - +
155A LEU* 4.7 1.6 - - - -
156A ASN* 2.7 46.6 + - - +
163A TYR* 3.6 36.5 + - + -
185A VAL* 4.2 17.0 - - + -
188A ALA* 3.9 24.5 - - + -
189A THR* 4.6 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A TYR 3.0 18.9 + - - +
150A GLU* 3.6 7.9 - - - +
151A THR 3.3 0.2 - - - -
152A LEU* 1.3 78.8 - - - +
154A ARG* 1.3 57.3 + - - +
156A ASN* 3.4 10.4 + - - +
157A LYS* 2.9 69.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ALA* 3.0 28.7 + - - +
108A LEU* 5.9 0.8 - - - +
111A PRO* 3.7 29.7 + - - +
114A VAL* 5.5 0.2 - - - +
150A GLU 3.1 14.4 + - - +
151A THR* 3.7 28.6 + - - +
152A LEU 3.3 0.2 - - - -
153A ASP* 1.3 78.5 + - - +
155A LEU* 1.3 81.8 + - - +
157A LYS* 3.4 6.6 + - - +
158A GLU* 2.9 57.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ALA* 4.7 1.1 - - + -
114A VAL* 4.0 20.9 - - + -
118A ILE* 4.2 5.2 - - + -
127A VAL* 3.6 33.2 - - + -
129A LEU* 4.3 4.3 - - + -
151A THR* 3.0 36.8 + - + +
152A LEU 5.0 0.2 - - - +
154A ARG* 1.3 93.7 - - - +
156A ASN* 1.3 66.4 + - - +
158A GLU* 3.0 24.9 + - - +
160A CYS* 2.9 25.6 + - + +
163A TYR* 3.3 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 2.7 31.6 + - - +
153A ASP* 3.4 11.1 + - - +
155A LEU* 1.3 71.1 - - - +
157A LYS* 1.3 63.0 + - + +
159A GLY* 3.0 10.2 + - - -
163A TYR* 2.9 16.6 + - - -
188A ALA 2.9 25.9 + - - -
189A THR* 2.7 29.8 + - - +
190A ASP* 5.3 1.3 - - - -
191A ARG* 2.8 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASP* 2.9 52.0 + - - +
154A ARG* 3.7 4.7 - - - +
156A ASN* 1.3 78.0 - - + +
158A GLU* 1.3 59.8 + - - +
159A GLY* 3.2 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A PRO 4.1 4.2 - - - +
115A ALA* 3.5 42.8 + - + +
118A ILE* 3.4 21.0 - - + +
119A ALA* 5.2 2.8 + - - +
154A ARG* 2.9 46.0 + - + +
155A LEU* 3.0 27.9 + - - +
157A LYS* 1.3 77.9 - - + +
159A GLY* 1.3 60.1 + - - +
160A CYS 3.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ILE* 3.6 10.7 - - - +
122A GLY* 6.1 0.7 - - - -
156A ASN 3.0 12.5 + - - -
157A LYS 3.2 2.2 - - - -
158A GLU* 1.3 78.9 - - - +
160A CYS* 1.3 68.2 + - - +
161A ALA* 3.3 7.1 + - - +
191A ARG* 3.5 7.1 + - - -
----------------------------------------------------------
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