Contacts of the helix formed by residues 148 - 165 (chain B) in PDB entry 1DUG
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 THR 148 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B MET* 4.0 19.7 - - + +
91B ILE* 3.9 25.9 - - + +
94B LEU* 5.1 1.0 - - - +
142B LEU* 3.5 16.5 + - - +
143B ASN* 4.2 6.3 - - + +
146B HIS* 3.6 27.6 + - + +
147B VAL* 1.3 85.4 - - - +
149B HIS* 1.3 67.8 + - - +
150B PRO* 3.3 17.6 - - - +
151B ASP* 2.9 24.5 + - - +
152B PHE* 4.1 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 3.9 15.0 - - + -
71B ILE* 3.9 34.2 - - + +
72B ARG* 3.9 17.4 - - + +
75B ALA* 3.9 17.7 - - + +
80B MET* 4.3 8.9 + - - +
81B LEU* 4.8 6.4 - - + +
91B ILE* 3.6 27.2 - - + +
95B GLU* 2.8 26.8 + - - -
148B THR* 1.3 70.4 - - - +
150B PRO* 1.3 71.1 - - + +
152B PHE* 3.0 24.7 + - - +
153B MET* 3.2 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ILE* 3.7 31.2 - - + +
94B LEU* 4.0 22.4 - - + +
95B GLU* 4.2 10.3 - - + +
98B VAL* 4.1 1.8 - - + +
142B LEU* 3.6 9.9 - - + +
148B THR* 3.2 21.1 - - - +
149B HIS* 1.3 105.8 - - + +
151B ASP* 1.3 55.8 + - - +
152B PHE 3.2 0.2 - - - -
153B MET* 3.5 12.9 - - + +
154B LEU* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TYR* 3.5 13.0 - - - +
142B LEU* 2.7 39.6 + - - +
147B VAL* 3.4 15.0 - - + -
148B THR* 2.9 37.2 + - - +
150B PRO* 1.3 78.5 - - - +
152B PHE* 1.3 60.9 + - + +
154B LEU 3.4 0.3 + - - -
155B TYR* 2.9 27.4 + - - +
178B PHE* 3.4 24.6 - - + -
182B ILE* 4.2 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PRO* 3.9 21.8 - - + +
18B LEU* 3.8 23.9 - - + +
19B LEU* 3.8 24.5 - - + -
22B TYR* 3.3 45.3 - + + -
71B ILE* 5.5 0.4 - - + -
147B VAL* 3.6 25.1 - - + -
148B THR 4.1 7.6 - - - -
149B HIS 3.0 7.4 + - - +
151B ASP* 1.3 74.9 - - - +
153B MET* 1.3 64.6 + - - +
155B TYR* 3.6 4.5 - - - +
156B ASP* 3.0 23.4 + - - +
182B ILE* 4.0 28.3 - - + -
185B ILE* 4.7 3.1 - - + -
188B ILE* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PRO* 3.9 25.1 - - + +
68B MET* 3.8 23.1 - - + +
71B ILE* 4.2 5.8 - - + -
95B GLU* 3.6 23.6 - - + +
98B VAL* 3.4 19.3 - - + +
99B LEU* 3.4 34.1 - - + -
102B ARG* 5.8 0.5 - - - +
149B HIS* 3.2 36.4 + - - +
150B PRO* 3.2 13.4 + - + +
152B PHE* 1.3 75.1 - - - +
154B LEU* 1.3 64.8 + - - +
156B ASP* 3.3 5.2 + - - +
157B ALA* 3.0 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B VAL* 3.6 18.3 - - + +
101B ILE* 5.0 5.2 - - + -
129B LEU* 5.4 0.7 - - + -
132B PHE* 3.9 33.2 - - + -
136B LEU* 5.2 0.4 - - + -
142B LEU* 3.8 30.7 - - + -
150B PRO 2.8 17.0 + - - +
151B ASP 3.7 3.8 - - - +
153B MET* 1.3 74.5 - - - +
155B TYR* 1.3 60.9 + - - +
157B ALA* 3.1 9.2 + - + +
158B LEU* 2.8 52.3 + - + +
175B LEU* 4.6 8.5 - - + -
178B PHE* 3.8 23.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
14B GLN* 6.3 0.2 - - - -
18B LEU* 3.6 26.2 - - + -
151B ASP 2.9 18.7 + - - +
152B PHE* 3.6 8.5 - - - +
153B MET 3.2 0.2 - - - -
154B LEU* 1.3 76.5 - - - +
156B ASP* 1.3 63.5 + - - +
158B LEU* 3.1 7.0 + - - +
159B ASP* 2.9 30.5 + - + +
178B PHE* 4.2 5.1 - - - -
179B LYS* 3.6 24.9 - - + -
182B ILE* 3.8 32.3 - - + -
183B GLU* 2.6 47.6 + - + +
188B ILE* 5.7 0.9 - - + -
192B LEU* 3.9 22.7 - - + +
222B GLN* 3.8 11.3 + - - -
225B LEU* 4.1 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS* 4.7 6.8 - - - +
11B GLY 4.4 4.3 - - - +
14B GLN* 3.5 25.6 - - + +
15B PRO* 3.6 28.9 - - + +
18B LEU* 5.0 2.0 - - + -
102B ARG* 3.1 35.1 + - - +
152B PHE 3.0 11.5 + - - +
153B MET 3.4 8.3 - - - +
155B TYR* 1.3 85.0 - - - +
157B ALA* 1.3 61.6 + - - +
159B ASP* 3.2 8.4 + - - +
160B VAL* 3.0 32.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
98B VAL* 4.1 15.0 - - + -
101B ILE* 4.1 21.5 - - + -
102B ARG* 4.2 21.1 - - + +
153B MET 3.0 13.8 + - - +
154B LEU* 3.4 13.5 - - + +
156B ASP* 1.3 76.9 + - - +
158B LEU* 1.3 58.1 + - + +
160B VAL* 3.4 1.8 + - - +
161B VAL* 3.0 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ILE* 6.6 0.4 - - + -
129B LEU* 4.1 19.1 - - + -
154B LEU* 2.8 36.8 + - + +
155B TYR* 3.5 7.0 - - - +
157B ALA* 1.3 70.3 - - + +
159B ASP* 1.3 67.3 + - - +
161B VAL* 3.4 5.5 - - + +
162B LEU* 3.0 32.2 + - - +
169B LEU* 4.0 29.2 - - + -
175B LEU* 4.0 23.3 - - + +
178B PHE* 3.9 28.5 - - + -
179B LYS* 4.4 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS* 2.6 36.0 + - - +
155B TYR* 2.9 22.1 + - + +
156B ASP* 3.4 13.6 - - - +
158B LEU* 1.3 78.6 - - - +
160B VAL* 1.3 62.1 + - - +
162B LEU* 3.5 3.1 + - - +
163B TYR* 2.9 39.3 + - - -
179B LYS* 4.3 5.1 - - - +
197B TYR* 5.3 1.1 - - - -
202B LEU* 4.3 2.9 - - - +
222B GLN* 2.9 44.6 + - - +
225B LEU* 5.0 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS* 5.7 1.6 - - + -
102B ARG* 3.5 36.8 - - - +
105B VAL* 3.8 32.8 - - + -
156B ASP* 3.0 22.2 + - - +
157B ALA 3.7 3.8 - - - +
158B LEU 3.2 0.2 - - - -
159B ASP* 1.3 79.6 - - - +
161B VAL* 1.3 64.7 + - - +
163B TYR* 3.1 19.3 + - - +
164B MET 3.4 3.8 + - - -
202B LEU* 4.2 21.5 - - + -
203B GLN* 4.4 2.5 - - - +
209B PHE* 3.8 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ILE* 4.0 22.9 - - + -
105B VAL* 4.0 19.5 - - + -
121B PHE* 4.3 5.8 - - + -
122B LEU* 5.5 0.6 - - + +
125B LEU* 4.2 18.6 - - + -
129B LEU* 5.2 5.6 - - + -
157B ALA 3.0 22.0 + - - +
158B LEU* 3.4 20.6 - - + +
160B VAL* 1.3 71.8 - - - +
162B LEU* 1.3 63.5 + - + +
164B MET* 3.1 8.5 + - + +
165B ASP* 2.8 30.0 + - - +
168B CYS* 3.7 20.0 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
158B LEU 3.0 22.4 + - - +
159B ASP 3.7 5.4 - - - +
160B VAL 3.2 0.2 - - - -
161B VAL* 1.3 76.2 - - - +
163B TYR* 1.3 58.4 + - - +
165B ASP 3.7 2.0 - - - -
166B PRO* 2.9 48.1 - - + +
168B CYS* 3.9 7.6 - - - -
169B LEU* 3.5 35.9 - - + -
179B LYS* 3.3 42.0 - - + +
221B GLN 3.4 16.6 - - - +
222B GLN* 4.0 9.4 - - + -
223B HIS* 6.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS* 4.6 0.7 + - - -
159B ASP* 2.9 47.3 + - - -
160B VAL 3.1 9.0 + - - +
162B LEU* 1.3 80.8 - - - +
164B MET* 1.3 60.3 + - - +
166B PRO* 4.2 4.7 - - - +
199B ALA 4.3 8.7 + - - -
200B TRP* 3.4 35.0 - + - -
202B LEU* 3.8 21.3 - - + -
209B PHE* 4.0 6.3 - - + -
215B PRO* 4.9 1.1 - - + -
218B SER 4.1 1.0 - - - +
219B ASP* 2.9 49.1 - - - +
220B PRO* 3.5 20.9 - - + -
221B GLN 3.9 2.0 - - - -
222B GLN* 3.6 17.1 + - + -
225B LEU* 4.3 6.8 - - - +
229B LYS* 3.5 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B VAL* 3.7 30.5 - - + -
108B ILE* 5.5 0.7 - - + -
114B PHE* 3.8 32.8 - - + -
118B LYS* 4.2 19.1 + - + +
121B PHE* 3.6 28.0 - - + -
122B LEU* 3.8 25.4 - - + +
160B VAL 3.4 3.4 + - - +
161B VAL* 3.1 9.9 + - - +
163B TYR* 1.3 80.7 - - - +
165B ASP* 1.3 60.3 + - + +
166B PRO* 4.1 2.5 - - - +
209B PHE* 3.6 33.6 - - + -
218B SER 4.9 3.1 - - - +
219B ASP* 4.6 4.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
122B LEU* 4.1 29.9 - - + +
161B VAL 2.8 8.7 + - - +
162B LEU* 3.1 3.7 - - - +
164B MET* 1.3 79.6 - - - +
166B PRO* 1.3 63.2 - - - +
167B MET* 3.0 25.6 + - - +
168B CYS* 3.0 46.3 + - + +
----------------------------------------------------------
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