Contacts of the helix formed by residues 148 - 165 (chain A) in PDB entry 1WUR
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 VAL 148 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLU* 3.3 33.2 - - + +
110A HIS* 3.9 20.4 - - + +
115A PHE* 4.2 2.2 - - - -
147A GLN* 1.3 76.2 + - - +
149A GLN* 1.3 65.9 + - - +
150A GLU* 4.1 6.5 - - + +
151A ARG* 3.0 44.7 + - + +
152A LEU* 3.1 9.9 + - - +
821A 8DG 3.2 15.3 - - + +
89B PHE* 6.2 1.1 - - + -
92B GLU* 3.8 12.3 - - + +
129B ILE* 5.3 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PHE* 3.8 23.0 - - + -
148A VAL* 1.3 70.4 - - - +
150A GLU* 1.3 63.6 + - - +
151A ARG 3.3 0.5 + - - -
152A LEU* 3.4 4.3 + - + +
153A ALA 3.3 13.9 + - - -
173A VAL* 2.9 41.1 + - + +
175A GLY* 3.8 9.9 + - - +
177A HIS* 2.8 31.5 + - + -
192A THR* 2.8 35.1 + - + +
194A THR* 3.0 32.9 + - + +
821A 8DG 2.6 18.2 + - + +
132B LEU* 5.3 0.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
148A VAL* 4.0 3.9 - - + +
149A GLN* 1.3 76.0 + - - +
151A ARG* 1.3 59.9 + - - +
153A ALA* 3.9 3.8 + - - +
154A VAL* 3.4 23.9 + - - +
194A THR* 3.9 16.8 - - + -
195A SER 5.0 2.1 - - - +
821A 8DG 2.6 47.1 + - - -
92B GLU* 3.9 21.4 - - + +
93B GLY 5.3 1.3 + - - +
97B VAL* 3.7 38.1 - - + +
123B TYR* 4.5 1.6 + - - -
129B ILE* 3.9 19.8 - - + +
132B LEU* 4.1 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLU* 2.8 41.2 + - - -
146A LEU 4.1 8.1 + - - -
147A GLN* 3.4 20.9 + - - +
148A VAL* 3.0 26.8 + - + +
150A GLU* 1.3 77.6 - - - +
152A LEU* 1.3 59.0 + - - +
153A ALA 3.2 0.4 - - - -
154A VAL* 3.1 5.3 + - + +
155A GLN* 2.9 57.3 + - + +
92B GLU* 2.9 44.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
104A PHE* 3.6 40.6 - - + -
106A SER* 4.7 0.7 - - - -
115A PHE* 4.2 13.2 - - + -
119A VAL* 5.4 0.2 - - + -
142A PHE* 3.7 41.1 - - + +
143A ALA* 3.8 9.6 - - + +
147A GLN* 3.7 13.4 + - + +
148A VAL 3.1 9.3 + - - +
149A GLN* 3.4 9.8 + - - +
151A ARG* 1.3 79.2 - - - +
153A ALA* 1.3 60.5 + - - +
155A GLN* 3.6 2.2 + - - +
156A ILE* 3.1 46.4 + - + +
173A VAL* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A GLN 3.3 4.1 + - - +
150A GLU 4.0 4.9 - - - +
151A ARG 3.2 0.6 - - - -
152A LEU* 1.3 79.5 - - - +
154A VAL* 1.3 63.5 - - - +
156A ILE 3.5 0.2 + - - -
157A ALA* 3.1 23.9 + - - +
171A VAL* 3.8 12.2 - - - +
173A VAL* 3.7 25.0 - - + +
194A THR* 3.8 14.6 - - - +
195A SER* 3.8 28.0 - - - +
196A ALA* 3.6 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A GLU 3.4 16.2 - - - +
151A ARG* 3.1 9.5 + - + +
153A ALA* 1.3 77.0 - - - +
155A GLN* 1.3 61.5 + - + +
157A ALA* 3.3 2.8 + - - +
158A GLU* 2.9 53.4 + - + +
195A SER 4.8 4.3 - - - +
196A ALA* 3.6 19.3 - - + -
92B GLU 3.6 27.8 - - - +
93B GLY* 4.2 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PHE* 3.5 36.0 - - + -
145A ARG* 4.4 11.0 + - - +
147A GLN* 2.8 31.0 + - - -
151A ARG* 2.9 41.3 + - + +
152A LEU 4.2 2.0 - - - +
154A VAL* 1.3 73.6 - - + +
156A ILE* 1.3 64.6 + - - +
158A GLU* 3.9 10.1 - - - +
159A ALA* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL* 4.1 17.0 - - + -
121A ILE* 4.2 11.0 - - + -
138A ILE* 4.3 13.9 - - + +
139A VAL* 4.0 32.5 - - + -
142A PHE* 4.4 8.3 - - + -
152A LEU* 3.1 44.3 + - + +
153A ALA 3.8 3.8 - - - +
155A GLN* 1.3 75.7 - - - +
157A ALA* 1.3 63.2 + - - +
159A ALA* 3.3 3.5 + - - +
160A ILE* 3.1 34.6 + - + +
171A VAL* 3.9 20.6 - - + -
173A VAL* 4.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ALA 3.1 17.5 + - - +
154A VAL 3.6 4.3 - - - +
156A ILE* 1.3 77.8 - - - +
158A GLU* 1.3 57.0 + - - +
160A ILE* 3.4 1.2 + - - +
161A GLN* 3.0 22.7 + - - +
169A VAL* 3.6 12.6 - - + +
171A VAL* 3.6 20.0 - - + -
196A ALA* 3.7 21.3 - - + +
198A LEU* 3.4 22.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
154A VAL* 2.9 39.5 + - + +
155A GLN* 4.0 10.1 - - - +
156A ILE 3.3 0.2 - - - -
157A ALA* 1.3 72.1 - - - +
159A ALA* 1.3 61.6 + - - +
161A GLN* 3.4 3.7 + - - +
162A GLU* 3.0 30.6 + - - +
198A LEU* 4.0 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.9 21.5 - - + -
138A ILE* 3.8 12.8 - - + -
142A PHE* 3.6 24.0 - - + -
155A GLN 3.0 18.8 + - - +
156A ILE 3.5 5.6 - - - +
158A GLU* 1.3 77.0 - - - +
160A ILE* 1.3 56.5 + - - +
162A GLU* 3.4 4.7 + - - +
163A VAL* 3.0 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 3.5 38.8 - - + -
123A TYR* 5.0 4.5 - - + -
130A LEU* 5.2 1.1 - - + -
135A PHE* 3.7 30.3 - - + -
138A ILE* 4.2 14.8 - - + -
156A ILE* 3.1 23.2 + - + +
157A ALA 3.7 5.8 - - - +
158A GLU 3.3 0.2 - - - -
159A ALA* 1.3 73.3 - - - +
161A GLN* 1.3 60.6 + - - +
163A VAL* 3.3 4.9 + - - +
164A LEU* 2.9 44.8 + - + +
166A PRO* 4.1 2.2 - - + +
169A VAL* 3.9 23.6 - - + -
171A VAL* 4.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ALA 3.0 18.1 + - - +
158A GLU* 3.6 6.5 - - - +
160A ILE* 1.3 77.6 - - - +
162A GLU* 1.3 55.5 + - - +
165A GLU* 2.8 49.1 + - - +
166A PRO* 3.7 31.1 + - - +
167A GLN 5.3 0.2 - - - -
168A GLY* 4.6 3.8 - - - -
169A VAL* 3.9 10.9 - - + +
198A LEU* 3.9 22.3 - - + +
199A GLY* 5.1 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.8 23.9 - - + +
158A GLU 3.0 17.8 + - - +
159A ALA* 3.6 6.3 - - - +
161A GLN* 1.3 79.9 - - - +
163A VAL* 1.3 62.0 + - + +
165A GLU* 4.1 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.7 20.9 - - + -
84A VAL* 3.5 46.7 - - + -
88A VAL* 4.1 12.8 - - + +
128A LYS* 4.7 7.8 + - - -
130A LEU* 4.0 15.7 - - + -
138A ILE* 4.9 3.1 - - + -
159A ALA 3.0 17.7 + - - +
160A ILE* 3.3 5.4 + - - +
162A GLU* 1.3 78.8 - - + +
164A LEU* 1.3 64.1 + - + +
165A GLU* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.7 21.5 - - + -
123A TYR* 3.6 34.1 - - + -
126A ASP 4.9 2.6 + - - +
128A LYS* 3.7 32.2 + - - +
129A ILE 3.7 22.9 - - - -
130A LEU* 3.6 25.4 - - + -
135A PHE* 4.5 1.6 - - + -
160A ILE* 2.9 28.1 + - + +
163A VAL* 1.3 86.0 - - + +
165A GLU* 1.3 74.4 + - - +
166A PRO* 3.9 10.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASP* 3.5 19.1 - - - +
128A LYS* 4.2 16.1 + - - +
161A GLN* 2.8 32.8 + - - +
162A GLU* 4.1 12.1 - - - +
163A VAL 5.3 0.7 - - - +
164A LEU* 1.3 75.7 - - - +
166A PRO* 1.3 70.0 - - - +
----------------------------------------------------------
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