Contacts of the helix formed by residues 147 - 160 (chain B) in PDB entry 5BZZ
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 LYS 147 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 3.7 10.5 - - - +
145B PHE* 3.6 0.4 - - - +
146B LEU* 1.3 92.1 - - + +
148B ALA* 1.3 66.8 + - - +
149B GLN* 3.1 9.7 + - + +
150B GLU* 3.2 37.8 + - + +
151B ALA* 3.3 9.0 + - - +
179B SER* 4.7 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 4.0 12.6 - - - -
147B LYS* 1.3 72.1 - - - +
149B GLN* 1.3 57.5 + - - +
151B ALA* 3.5 3.1 + - - +
152B LEU* 3.1 35.0 + - + +
175B VAL* 4.0 10.0 - - + +
176B TYR* 3.3 55.3 - - + +
179B SER* 3.9 12.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LYS* 3.1 6.8 - - + +
148B ALA* 1.3 77.8 - - - +
150B GLU* 1.3 60.8 + - + +
152B LEU* 3.4 5.2 + - - +
153B ASP* 2.9 50.1 + - - +
172B ARG* 4.4 15.7 - - - +
176B TYR* 3.3 26.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 3.9 16.0 - - + +
157A GLU* 3.9 3.8 - - - +
161A ARG* 2.3 49.6 + - - +
145B PHE* 4.2 6.4 - - + +
146B LEU* 3.3 22.1 + - - +
147B LYS* 3.2 34.4 + - + +
149B GLN* 1.3 77.9 - - + +
151B ALA* 1.3 59.2 + - - +
153B ASP* 3.4 7.5 + - - +
154B PHE* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B CYS* 3.3 29.5 - - + +
139B LEU* 6.0 0.5 - - - +
140B LEU* 4.1 13.2 - - + -
145B PHE* 3.7 34.3 - - + -
147B LYS 3.3 7.2 + - - +
148B ALA 3.7 7.9 - - - +
149B GLN 3.3 0.4 - - - -
150B GLU* 1.3 79.6 - - - +
152B LEU* 1.3 57.4 + - - +
154B PHE* 3.3 2.1 + - - +
155B TYR* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B CYS* 3.9 8.3 - - - -
148B ALA 3.1 31.4 + - - +
149B GLN* 3.8 4.7 - - - +
150B GLU 3.3 0.2 - - - -
151B ALA* 1.3 76.0 - - - +
153B ASP* 1.3 59.8 + - - +
155B TYR* 3.5 3.3 + - - +
156B GLY* 3.0 24.6 + - - -
165B GLY 5.6 0.2 + - - -
166B VAL* 3.5 43.6 + - + -
172B ARG* 3.8 49.1 + - + +
175B VAL* 4.1 23.6 - - + -
176B TYR* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLU* 3.7 8.5 - - - +
163A LYS* 3.2 32.7 + - - +
149B GLN* 2.9 41.9 + - - +
150B GLU* 3.7 6.4 + - - +
152B LEU* 1.3 76.2 - - - +
154B PHE* 1.3 63.8 + - - +
156B GLY* 4.0 1.0 - - - -
157B GLU* 3.1 26.3 + - - +
163B LYS* 6.0 0.3 - - - +
172B ARG* 4.7 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG 3.4 21.1 - - - -
15A ARG* 4.3 11.9 - - + -
157A GLU* 3.5 13.9 + - + +
158A VAL* 3.9 28.7 - - + -
15B ARG* 6.3 0.4 - - - -
28B ILE* 3.6 28.0 - - + -
29B TYR* 3.5 39.0 - + - -
139B LEU* 5.1 0.7 - - + -
145B PHE* 3.4 23.8 - + + -
150B GLU 2.9 17.3 + - - +
151B ALA 3.6 2.5 - - - +
152B LEU 3.3 0.2 - - - -
153B ASP* 1.3 75.5 - - - +
155B TYR* 1.3 66.8 + - + +
157B GLU* 4.0 0.3 - - - +
158B VAL* 3.0 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 3.9 26.7 - - + -
34B ALA* 4.2 0.6 - - + +
127B GLY 2.8 28.4 + - - -
128B LYS* 2.9 21.9 + - - -
131B THR* 3.9 4.0 - - - +
132B GLY* 3.4 27.9 + - - -
135B ILE* 4.2 18.8 - - + -
136B CYS* 3.6 11.2 - - - -
139B LEU* 6.4 1.1 - - + -
151B ALA 2.9 17.8 + - - +
152B LEU* 3.7 2.7 - - - +
154B PHE* 1.3 82.1 - - + +
156B GLY* 1.3 56.5 + - - +
158B VAL* 4.9 1.1 - - - -
159B ARG* 2.8 59.6 + - + +
165B GLY* 3.9 24.7 - - - -
166B VAL* 4.3 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU 3.0 15.4 + - - -
153B ASP* 4.0 0.9 - - - -
155B TYR* 1.3 76.7 - - - +
157B GLU* 1.3 55.9 + - - +
160B THR* 2.4 39.6 + - - +
163B LYS* 3.7 11.7 - - - -
165B GLY* 3.7 27.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A GLU* 3.8 3.3 - - - +
153A ASP* 3.6 13.9 - - - +
154A PHE* 3.3 26.7 + - + +
157A GLU* 3.7 30.4 - - + +
14B ARG* 2.5 49.9 + - - +
153B ASP 3.1 17.5 + - - +
154B PHE 4.0 0.7 - - - +
156B GLY* 1.3 76.9 - - - +
158B VAL* 1.3 55.6 + - + +
160B THR 2.9 7.2 - - - +
161B ARG 5.5 1.7 - - - +
163B LYS* 2.9 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A PHE* 3.8 6.7 - - + -
158A VAL* 3.5 32.3 - - + -
15B ARG* 3.0 57.4 - - - +
26B THR* 3.5 3.6 - - + +
27B TYR 3.9 10.5 - - - +
28B ILE* 4.0 17.7 - - + +
154B PHE* 3.0 38.0 + - + +
155B TYR* 4.1 2.0 - - - +
157B GLU* 1.3 79.1 - - + +
159B ARG* 1.3 59.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG 2.4 22.1 - - - +
16B TYR* 3.0 25.6 + - - +
24B ASP* 2.9 24.2 + - - -
25B LEU 3.9 6.1 - - - +
26B THR* 2.8 40.6 + - - -
28B ILE* 4.4 3.1 - - + -
34B ALA* 3.9 19.6 - - - +
35B MET* 3.7 15.2 - - - +
126B ALA 3.1 23.6 + - - -
127B GLY 2.9 16.3 + - - +
128B LYS* 5.4 0.7 - - - -
155B TYR* 2.8 50.3 + - + +
158B VAL* 1.3 75.6 - - - +
160B THR* 1.3 64.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ARG* 3.1 8.4 - - - -
15B ARG 4.0 1.8 - - - -
16B TYR* 3.7 14.4 - - + +
128B LYS* 5.0 7.0 - - + -
156B GLY 2.4 30.6 + - - +
157B GLU* 2.9 22.9 - - - +
159B ARG* 1.3 92.4 - - + +
161B ARG* 1.3 60.0 + - - +
162B ASP* 3.4 10.8 - - - +
163B LYS 3.2 2.3 + - - -
164B LYS 3.0 40.2 + - - +
165B GLY* 4.2 5.4 - - - -
----------------------------------------------------------
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