Contacts of the helix formed by residues 168 - 182 (chain B) in PDB entry 2P0R
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 PHE 168 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PRO* 3.8 37.9 - - + -
73B ILE* 4.1 29.6 - - + -
74B VAL* 4.6 3.6 - - + -
77B PRO* 4.2 11.7 - - + -
78B GLU 3.1 12.6 + - - +
123B PHE* 4.5 4.3 - - + -
150B LEU* 3.9 18.8 - - + -
157B LEU* 3.7 27.8 - - + -
165B HIS 3.6 25.4 - - - -
166B ASN* 3.6 15.9 - - - -
167B GLU* 1.3 77.6 - - - +
169B TRP* 1.3 59.7 + - - +
170B SER 3.3 2.9 - - - -
171B ALA* 3.3 5.1 + - + +
172B LEU* 2.9 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.0 56.0 + - + +
80B ILE* 4.0 11.7 - - + -
84B ALA* 3.7 21.0 - - + +
85B THR 3.7 20.4 - - - -
88B ASP* 3.1 26.1 + - + +
89B ILE* 3.7 17.7 - - + -
103B ILE* 3.8 11.4 - - + -
107B THR* 3.8 12.6 - - + -
113B LEU* 4.5 2.9 - - + -
117B ILE* 3.3 31.9 - - + -
133B PHE* 3.6 4.0 - - - -
167B GLU* 3.2 24.8 + - + -
168B PHE* 1.3 76.2 - - - +
170B SER* 1.3 69.1 + - - +
172B LEU* 3.3 2.4 + - - +
173B LEU* 2.8 44.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ASP 2.9 18.5 + - - -
89B ILE* 3.5 31.0 - - - -
103B ILE* 5.5 0.2 - - - -
160B LEU* 3.2 21.9 - - - +
162B SER* 3.8 14.2 + - - -
167B GLU 5.3 0.7 + - - -
168B PHE 3.3 0.5 - - - -
169B TRP* 1.3 94.4 - - - +
171B ALA* 1.3 62.6 + - - +
173B LEU* 3.4 4.0 + - - +
174B GLU 3.0 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LEU* 3.6 24.9 - - + +
157B LEU* 4.0 20.2 - - + -
160B LEU* 3.1 30.7 + - - +
161B HIS* 4.7 2.0 - - - -
167B GLU 5.3 0.4 - - - +
168B PHE* 3.3 13.1 + - - +
170B SER* 1.3 81.6 + - - +
172B LEU* 1.3 60.6 - - - +
174B GLU* 3.6 4.3 + - - +
175B LYS 3.1 16.8 + - - -
184B TYR* 4.2 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PRO* 5.4 0.4 - - + -
79B PHE* 3.5 28.5 - - + -
123B PHE* 4.8 2.0 - - + -
131B PHE* 3.8 20.4 - - + -
133B PHE* 3.6 14.4 - - + -
146B ILE* 3.4 22.3 - - + +
148B ASP* 3.6 31.4 - - + -
150B LEU* 3.9 19.7 - - + -
168B PHE* 2.9 30.0 + - + +
169B TRP 3.5 4.7 - - - +
171B ALA* 1.3 74.1 - - - +
173B LEU* 1.3 66.4 + - - +
175B LYS* 3.0 6.0 + - - +
176B ALA* 2.9 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.9 0.4 - - + -
103B ILE* 3.7 34.5 - - + -
106B LEU* 5.3 4.9 - - + -
116B VAL* 4.4 11.4 - - + -
117B ILE* 4.1 17.3 - - + -
133B PHE* 3.4 23.5 - - + -
135B PHE* 4.3 9.0 - - + -
169B TRP* 2.8 42.5 + - + +
170B SER* 3.4 7.4 + - - +
172B LEU* 1.3 72.0 - - - +
174B GLU* 1.3 59.9 + - - +
176B ALA* 3.2 3.3 + - - +
177B TYR* 2.8 28.9 + - + +
199B PHE* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLY 5.7 0.9 + - - -
94B LEU* 4.0 6.9 - - - +
96B ASP* 2.4 34.4 - - - +
99B LEU* 4.2 7.6 - - + -
100B LEU* 4.6 0.9 - - - +
103B ILE* 5.3 0.2 - - + -
159B PHE* 3.2 12.1 - - - +
160B LEU* 3.0 47.0 + - + +
170B SER 3.0 16.8 + - - +
171B ALA 3.8 4.3 - - - +
172B LEU 3.2 0.2 - - - -
173B LEU* 1.3 77.7 - - - +
175B LYS* 1.3 59.2 + - - +
177B TYR* 3.7 6.0 - - - +
178B ALA* 2.8 27.5 + - - +
184B TYR* 3.5 16.4 + - + -
187B LEU* 4.0 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP* 6.5 0.2 - - - -
48B PHE* 3.9 33.8 + - + -
50B ALA* 5.7 1.0 - - - +
67B TRP* 4.0 14.6 - - + -
146B ILE* 4.1 15.0 - - + -
147B ASP* 2.6 42.6 + - - +
149B ARG* 2.5 34.1 + - - +
150B LEU* 3.9 12.6 - - + -
171B ALA 3.1 11.4 + - - +
172B LEU 3.0 9.2 + - - +
174B GLU* 1.3 74.2 - - - +
176B ALA* 1.3 53.5 + - - +
178B ALA* 2.9 6.6 + - - +
179B LYS* 2.8 32.1 + - - +
184B TYR* 3.2 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 3.6 30.3 - - + -
135B PHE* 3.7 10.4 - - + -
144B VAL* 3.5 20.3 - - + +
146B ILE* 3.6 24.0 - - + -
172B LEU 2.9 7.3 + - - +
173B LEU 3.5 7.9 - - - +
175B LYS* 1.3 76.7 - - - +
177B TYR* 1.3 56.7 + - - +
179B LYS* 3.4 5.2 - - - +
180B LEU 3.2 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TRP* 3.7 26.3 - + - -
99B LEU* 3.6 42.4 - - + -
135B PHE* 3.8 27.3 - + + -
173B LEU* 2.8 18.4 + - + +
174B GLU* 3.8 4.3 - - - +
175B LYS 3.1 0.2 - - - -
176B ALA* 1.3 72.6 - - - +
178B ALA* 1.3 63.0 + - - +
180B LEU* 3.4 14.8 + - + +
181B ASN* 2.6 51.0 + - - -
187B LEU* 3.7 4.0 - - + -
194B GLU* 4.5 4.2 + - - +
195B ALA* 3.8 13.0 + - - -
198B ASP* 2.6 39.9 + - + -
199B PHE* 4.2 7.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE* 4.2 5.2 - - + -
174B GLU 2.8 15.1 + - - +
175B LYS* 3.2 12.3 - - - +
177B TYR* 1.3 76.3 - - - +
179B LYS* 1.3 55.8 + - - +
181B ASN 3.0 2.8 + - - -
182B GLY 2.8 25.3 + - - -
183B SER 3.1 32.7 + - - +
184B TYR* 3.9 17.3 - - + +
187B LEU* 3.8 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 5.6 5.9 - - - +
23B HIS* 4.3 6.9 - - - +
45B ASP* 2.8 25.6 + - - +
47B ASP* 4.1 17.5 + - - +
48B PHE* 3.6 40.0 - - + -
144B VAL* 4.1 10.3 - - + +
145B VAL* 2.4 47.9 + - - +
146B ILE* 4.0 6.5 - - + -
175B LYS 2.8 15.1 + - - +
176B ALA* 3.4 12.6 - - - +
178B ALA* 1.3 72.3 - - - +
180B LEU* 1.3 62.6 + - - +
182B GLY* 3.0 14.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PHE* 3.8 22.7 - - + -
137B GLN* 3.9 41.0 + - + +
142B LEU* 4.0 20.4 - - + -
144B VAL* 4.3 17.2 - - + +
176B ALA 3.2 10.6 + - - +
177B TYR* 3.5 32.3 - - + +
179B LYS* 1.3 77.6 - - - +
181B ASN* 1.3 65.2 + - - +
182B GLY 3.5 0.2 - - - -
198B ASP* 4.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TRP* 5.3 3.5 - - - -
177B TYR* 2.6 49.5 + - - +
178B ALA 3.0 7.8 + - - +
180B LEU* 1.3 86.4 - - - +
182B GLY* 1.3 57.5 + - - +
183B SER 3.5 0.9 - - - -
186B ALA* 3.3 31.9 - - + +
187B LEU* 3.8 10.3 - - + +
194B GLU* 5.4 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE* 3.8 15.2 - - - -
53B SER 4.1 7.1 - - - +
54B SER* 4.7 0.3 - - - -
178B ALA 2.8 5.2 + - - -
179B LYS 3.0 10.7 + - - -
180B LEU 3.5 0.4 - - - -
181B ASN* 1.3 76.7 - - - +
183B SER* 1.3 64.1 + - - +
----------------------------------------------------------
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