Contacts of the helix formed by residues 147 - 167 (chain B) in PDB entry 3WOO
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ALA 4.4 6.3 - - - +
145B GLY 3.3 2.7 + - - +
146B ASP* 1.3 79.0 + - - +
148B ALA* 1.3 66.2 + - - +
149B LEU* 3.8 7.2 + - - +
150B ALA* 2.9 41.2 + - + +
151B ARG* 3.1 22.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
146B ASP 4.1 1.0 + - - -
147B ASP* 1.3 71.9 + - - +
149B LEU* 1.3 59.2 + - - +
151B ARG* 2.9 38.8 + - - +
152B THR 3.2 5.7 + - - -
544B THR* 3.5 31.9 - - + +
547B GLY* 3.4 9.3 - - - -
548B GLU* 3.5 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ASP* 4.0 6.3 - - - +
148B ALA* 1.3 76.8 - - - +
150B ALA* 1.3 63.5 + - - +
152B THR* 3.2 7.1 + - - -
153B LYS* 3.0 43.3 + - + +
540B GLN* 3.5 33.2 - - + +
543B LYS* 3.7 27.8 - - + -
544B THR* 3.7 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ALA* 3.6 14.6 - - + +
147B ASP* 2.9 32.7 + - + +
149B LEU* 1.3 77.7 - - - +
151B ARG* 1.3 58.5 + - - +
153B LYS* 3.8 12.4 - - - +
154B ALA* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ILE* 3.6 43.3 + - + +
144B ALA* 3.8 9.4 - - + +
145B GLY* 5.6 0.4 - - - -
146B ASP* 3.4 39.4 + - - +
147B ASP 3.1 13.9 + - - +
148B ALA* 2.9 24.2 + - - +
150B ALA* 1.3 75.1 - - - +
152B THR* 1.3 63.9 + - - +
154B ALA* 3.3 3.8 + - - +
155B LEU* 3.2 22.0 + - - +
547B GLY 2.8 42.1 + - - +
548B GLU* 3.8 10.1 + - - +
550B LEU* 4.0 11.2 - - + +
551B ALA* 3.9 20.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ALA 3.2 0.6 + - - -
149B LEU* 3.2 9.1 + - + -
151B ARG* 1.3 77.2 - - - +
153B LYS* 1.4 63.8 + - + +
155B LEU* 3.2 5.7 + - - +
156B GLU* 3.0 45.8 + - + +
543B LYS* 2.4 50.4 + - + +
546B ALA* 3.9 7.3 - - + +
547B GLY* 3.2 15.4 + - - -
550B LEU* 4.3 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 3.0 39.2 + - + +
150B ALA* 3.8 8.5 - - - +
152B THR* 1.4 76.0 - - + +
154B ALA* 1.3 56.6 + - - +
156B GLU* 3.5 16.9 - - - +
157B ALA* 2.8 30.9 + - - +
540B GLN* 3.6 27.1 + - - +
543B LYS* 5.7 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ALA* 3.5 28.8 - - + +
141B ILE* 4.9 0.4 - - - -
144B ALA* 4.0 11.0 - - + -
150B ALA 3.0 19.0 + - - +
151B ARG 3.7 4.5 - - - +
152B THR 3.2 0.4 - - - -
153B LYS* 1.3 76.0 - - - +
155B LEU* 1.3 60.5 + - - +
157B ALA* 3.9 5.7 - - - +
158B PHE* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ALA* 4.8 3.4 - - + +
140B ALA* 5.5 0.7 - - - -
141B ILE* 4.1 25.0 - - + +
151B ARG 3.2 10.9 + - - +
152B THR* 3.2 8.6 + - - +
154B ALA* 1.3 72.8 - - - +
156B GLU* 1.3 57.7 + - + +
158B PHE* 3.1 19.8 + - + +
159B GLU* 2.7 42.9 + - - +
176B LEU* 4.5 8.7 - - + -
185B TYR* 4.2 25.1 - - + +
550B LEU* 3.8 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B THR* 3.0 31.9 + - + +
153B LYS* 3.5 16.8 - - - +
155B LEU* 1.3 78.1 - - + +
157B ALA* 1.3 64.2 + - - +
159B GLU* 3.3 11.6 + - - +
160B LYS* 2.9 50.5 + - - +
426B GLU* 4.5 4.7 - - - +
427B SER* 6.0 1.3 - - - +
543B LYS* 2.3 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LYS 2.8 18.9 + - - +
154B ALA* 3.9 6.5 - - - +
156B GLU* 1.3 78.3 - - - +
158B PHE* 1.3 63.1 + - - +
160B LYS* 3.4 9.8 + - - +
161B LYS* 3.2 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL* 4.2 7.2 - - + -
136B ASP* 3.8 24.0 - - + -
137B ALA* 3.6 35.4 - - + -
140B ALA* 3.9 22.7 - - + -
154B ALA 2.9 20.3 + - - +
155B LEU* 3.1 15.5 + - + +
157B ALA* 1.3 78.3 - - - +
159B GLU* 1.3 66.7 + - - +
161B LYS* 3.3 5.0 + - - +
162B LEU* 3.0 61.1 + - + +
176B LEU* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU* 2.7 24.1 + - - +
156B GLU* 3.6 11.2 - - - +
158B PHE* 1.3 78.6 - - - +
160B LYS* 1.3 60.8 + - + +
162B LEU* 3.2 4.9 + - - +
163B ILE* 2.8 54.5 + - + +
176B LEU* 3.7 35.7 + - + +
427B SER* 4.6 12.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLU* 2.9 46.3 + - - +
157B ALA* 3.8 8.0 - - - +
158B PHE 3.3 0.2 - - - -
159B GLU* 1.3 77.4 - - + +
161B LYS* 1.3 58.7 + - - +
163B ILE* 3.8 4.6 - - - +
164B ALA* 2.7 33.1 + - - +
423B ALA* 3.5 26.8 + - + +
424B GLU* 4.1 5.9 + - - +
425B ARG 2.8 29.9 + - - -
426B GLU* 4.3 2.0 + - - +
427B SER* 4.0 23.5 - - - +
430B GLN* 3.8 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ALA 3.2 14.2 + - - +
158B PHE* 3.8 4.9 - - + +
160B LYS* 1.3 79.0 - - - +
162B LEU* 1.3 66.2 + - - +
164B ALA* 3.7 6.7 - - + +
165B ASP* 3.0 51.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL* 3.9 39.0 - - + -
136B ASP* 6.2 0.4 - - + -
158B PHE* 3.0 44.5 + - + +
159B GLU* 3.5 4.0 - - - +
161B LYS* 1.3 79.4 - - - +
163B ILE* 1.3 58.0 + - - +
165B ASP* 3.3 8.2 + - + +
166B CYS* 2.9 28.8 + - - +
176B LEU* 4.3 9.0 - - + -
187B LEU* 4.0 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B GLU* 2.8 51.9 + - + +
160B LYS* 3.9 4.5 - - - +
162B LEU* 1.3 71.3 - - + +
164B ALA* 1.3 59.1 + - - +
166B CYS* 3.1 5.8 + - - -
167B GLU* 2.7 64.0 + - + +
174B CYS* 4.1 16.6 - - + +
175B ARG* 4.5 0.9 - - - -
176B LEU* 4.3 9.9 - - + +
187B LEU* 4.4 16.6 - - + -
432B ARG* 3.6 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LYS 2.7 23.0 + - - +
161B LYS* 3.7 8.5 - - + +
163B ILE* 1.3 75.1 - - - +
165B ASP* 1.3 64.6 + - - +
167B GLU* 3.5 5.5 + - - +
168B ALA* 3.3 20.1 + - - +
432B ARG* 6.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LYS* 3.0 51.5 + - - +
162B LEU* 3.6 7.8 - - + +
164B ALA* 1.3 78.1 - - - +
166B CYS* 1.3 64.6 + - - +
168B ALA* 3.3 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU 2.9 17.5 + - - +
163B ILE 3.5 2.7 - - - +
165B ASP* 1.3 77.2 - - - +
167B GLU* 1.3 59.4 + - - +
168B ALA 3.3 1.1 + - - -
169B GLU* 4.0 7.1 + - - +
172B PHE* 4.8 0.9 - - - +
174B CYS* 2.1 49.2 - - + -
187B LEU* 4.0 20.4 - - + -
189B LYS* 3.6 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ILE* 2.7 30.1 + - - +
164B ALA* 3.8 6.0 - - - +
166B CYS* 1.3 68.3 - - - +
168B ALA* 1.3 64.0 + - - +
169B GLU 3.1 14.5 + - - +
170B ALA* 4.3 1.6 + - - -
172B PHE 3.4 24.8 - - - +
173B ARG* 3.4 6.4 - - - +
174B CYS* 2.9 27.5 + - - +
432B ARG* 2.7 53.3 + - - +
----------------------------------------------------------
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