Contacts of the helix formed by residues 169 - 186 (chain D) in PDB entry 2B05
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 HIS 169 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118D GLU* 4.1 10.6 - - + +
165D MET* 3.3 40.5 - - + +
166D GLN* 2.9 23.5 + - + +
167D PRO 3.3 0.4 - - - -
168D THR* 1.3 77.9 + - - +
170D PRO* 1.3 79.4 - - + +
171D ILE* 3.2 32.4 + - + -
172D ARG* 2.9 7.2 + - + +
173D LEU* 2.9 20.0 + - - +
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Residues in contact with PRO 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D THR 3.4 7.6 - - - +
169D HIS* 1.3 97.9 - - + +
171D ILE* 1.3 54.0 + - + +
173D LEU* 3.3 4.6 + - + +
174D GLY* 2.7 32.2 + - - -
215D SER* 4.2 18.4 - - - -
218D ASP* 4.3 17.0 - - + +
219D SER* 3.5 17.3 - - - +
222D ILE* 3.5 25.4 - - + +
506J LEU* 6.0 0.2 - - - +
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Residues in contact with ILE 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ARG* 3.9 24.2 - - - +
118D GLU* 4.2 20.0 - - + +
121D VAL* 3.6 27.5 - - + +
122D PHE* 4.0 29.8 - - + +
125D LYS* 4.7 7.3 - - + +
165D MET* 4.2 4.7 - - + -
169D HIS* 3.2 24.7 + - + +
170D PRO* 1.3 78.1 - - + +
172D ARG* 1.3 63.5 + - - +
174D GLY* 3.4 1.4 + - - +
175D LEU* 3.0 22.9 + - - +
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Residues in contact with ARG 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D VAL* 5.2 0.4 - - - -
158D HIS* 5.9 5.6 + - + -
161D SER* 3.6 39.5 + - - -
162D LYS* 3.8 26.1 + - - +
165D MET* 2.8 39.8 + - - -
166D GLN 3.8 15.0 - - - +
167D PRO* 3.6 39.4 + - - +
169D HIS* 2.9 12.1 + - + +
171D ILE* 1.3 79.6 - - - +
173D LEU* 1.3 64.2 + - + +
175D LEU* 3.3 7.7 + - + +
176D ALA* 3.1 22.0 + - + +
199D THR* 6.3 0.2 - - - +
200D ALA* 6.0 5.3 - - + +
203D ASP* 4.5 15.4 + - - +
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Residues in contact with LEU 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D PRO 3.4 21.3 - - - +
168D THR* 3.6 25.8 - - - +
169D HIS 2.9 9.2 + - - +
170D PRO* 3.6 7.2 - - + +
172D ARG* 1.3 78.5 - - + +
174D GLY* 1.3 57.3 + - - +
176D ALA* 3.1 7.7 + - - +
177D LEU* 2.9 28.2 + - - +
200D ALA* 4.0 10.5 - - + +
204D ALA* 3.9 15.0 - - + -
219D SER* 3.6 33.0 - - - +
222D ILE* 3.7 15.3 - - + +
223D MET* 4.0 10.1 - - + -
226D LEU* 4.0 21.8 - - + +
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Residues in contact with GLY 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D LYS* 3.7 11.3 - - - -
170D PRO 2.7 20.5 + - - -
171D ILE* 3.9 2.0 - - - -
173D LEU* 1.3 73.0 - - - +
175D LEU* 1.3 55.8 + - - +
177D LEU* 3.5 4.2 - - - +
178D ASN* 3.1 29.3 + - - +
222D ILE* 3.8 12.0 - - - +
506J LEU* 4.2 20.3 - - - +
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Residues in contact with LEU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D VAL* 4.3 4.7 - - + -
125D LYS* 3.9 29.7 - - + +
154D TYR* 3.7 30.3 - - + +
157D ALA* 3.6 20.0 - - + +
158D HIS* 3.5 43.7 - - + +
161D SER* 4.3 10.3 - - - -
171D ILE 3.0 17.6 + - - +
172D ARG* 3.6 4.3 - - - +
173D LEU 3.2 0.2 - - - -
174D GLY* 1.3 74.3 - - - +
176D ALA* 1.3 57.1 + - - +
178D ASN 3.3 0.4 + - - +
179D TYR* 2.7 43.6 + - + +
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Residues in contact with ALA 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D HIS* 5.5 5.2 - - + +
172D ARG* 3.1 14.2 + - + +
173D LEU* 3.1 9.8 + - - +
175D LEU* 1.3 75.8 - - - +
177D LEU* 1.3 63.9 + - - +
179D TYR* 4.5 0.9 - - - -
180D SER* 2.9 27.2 + - - -
196D LEU* 3.7 21.6 - - + +
200D ALA* 3.5 32.8 - - + -
226D LEU* 4.2 5.8 - - + +
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Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D LEU 2.9 12.9 + - - +
174D GLY* 3.5 9.9 - - - +
176D ALA* 1.3 75.2 - - - +
178D ASN* 1.3 63.5 + - - +
180D SER* 2.7 19.8 + - - +
181D VAL* 3.1 13.0 + - - +
222D ILE* 4.4 6.7 - - + -
225D LEU* 3.8 40.4 - - + +
226D LEU* 3.8 18.0 - - + +
229D ASN* 3.1 31.4 - - - +
504J ILE 3.5 6.1 - - - +
505J SEP 3.7 3.8 - - - -
506J LEU* 3.4 39.5 - - + +
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Residues in contact with ASN 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D LYS* 6.2 0.2 - - - +
125D LYS* 3.4 15.5 - - - +
129D ASP* 2.8 39.6 + - - +
132D ARG* 3.4 16.7 + - - +
154D TYR* 4.2 7.0 - - + +
174D GLY 3.1 13.0 + - - +
175D LEU* 4.1 2.0 - - - +
177D LEU* 1.3 76.1 - - - +
179D TYR* 1.3 60.9 + - - +
181D VAL* 3.3 7.6 + - - +
182D PHE* 2.9 27.5 + - - +
505J SEP 3.3 11.5 + - - +
506J LEU* 2.8 34.0 + - - +
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Residues in contact with TYR 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D GLU* 3.0 29.7 + - - -
154D TYR* 3.3 47.2 - + + -
155D SER* 3.8 13.0 + - - -
158D HIS* 4.2 35.2 - + + -
175D LEU* 2.7 26.2 + - + +
178D ASN* 1.3 73.1 - - - +
180D SER* 1.3 57.8 + - - +
182D PHE* 3.2 9.3 + + - +
183D TYR* 2.8 61.6 + + - -
196D LEU* 3.6 20.2 - - + -
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Residues in contact with SER 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D ALA 2.9 16.5 + - - -
177D LEU* 2.7 23.4 + - - +
179D TYR* 1.3 74.1 - - - +
181D VAL* 1.3 64.8 + - - +
183D TYR* 3.1 9.8 + - - +
184D TYR 3.0 18.4 + - - -
193D ALA* 3.4 27.8 - - - +
196D LEU* 3.5 13.6 - - - +
197D ALA* 4.2 10.2 - - - +
226D LEU* 4.7 1.0 - - - +
229D ASN* 5.0 0.7 + - - +
233D TRP* 3.7 16.8 - - - -
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Residues in contact with VAL 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ARG* 4.1 22.2 - - - +
177D LEU 3.1 13.2 + - - +
178D ASN* 3.5 9.6 - - - +
180D SER* 1.3 82.4 + - - +
182D PHE* 1.3 57.5 + - - +
185D GLU* 2.8 48.4 + - + +
229D ASN* 3.7 12.1 - - - +
233D TRP* 3.9 7.6 - - + -
503J ALA* 4.1 17.3 - - + +
504J ILE 3.7 25.8 - - - +
505J SEP 4.3 8.1 - - - +
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Residues in contact with PHE 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ARG* 4.0 14.1 - - + +
147D VAL* 3.6 23.1 - - + -
150D SER* 3.2 28.9 - - - -
151D GLU* 3.3 32.8 - - + -
154D TYR* 3.7 15.0 - + + -
178D ASN 2.9 13.3 + - - +
179D TYR* 3.2 19.1 - + - +
181D VAL* 1.3 75.4 - - - +
183D TYR* 1.3 75.0 + + - +
186D ILE* 2.9 55.4 + - + +
187D GLN* 3.2 30.7 + - + -
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Residues in contact with TYR 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D GLU* 3.6 22.1 + - - -
179D TYR* 2.8 45.6 + + - -
180D SER* 3.1 7.8 + - - +
182D PHE* 1.3 85.5 - + - +
184D TYR* 1.3 60.6 + - - +
187D GLN* 3.5 13.3 + - + +
188D ASN 3.2 6.6 + - - -
189D ALA* 2.9 28.1 + - + +
192D GLN* 3.7 55.2 + - + -
193D ALA* 3.6 14.4 - - + +
196D LEU* 4.0 24.0 - - + -
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Residues in contact with TYR 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D SER 3.0 6.7 + - - +
181D VAL 3.2 0.9 + - - +
183D TYR* 1.3 77.2 - - - +
185D GLU* 1.3 91.5 + - + +
188D ASN* 3.3 21.0 - - - +
189D ALA 4.4 2.7 - - - +
190D PRO* 3.6 36.1 - - + +
193D ALA* 3.7 8.5 - - + +
233D TRP* 3.4 73.4 + + + -
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Residues in contact with GLU 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ARG* 6.2 0.2 - - - -
143D ARG* 4.6 3.5 + - - -
181D VAL* 2.8 35.9 + - + +
184D TYR* 1.3 100.9 - - + +
186D ILE* 1.3 69.4 + - + +
188D ASN* 4.4 2.5 + - - +
502J ARG 3.6 22.6 + - - -
503J ALA* 4.5 10.7 + - + +
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Residues in contact with ILE 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ARG* 4.0 33.9 - - + +
135D ALA* 4.2 9.0 - - + -
136D GLU* 4.2 19.7 - - + +
143D ARG* 2.9 29.7 + - - +
147D VAL* 3.6 28.5 - - + -
182D PHE* 2.9 48.1 + - + +
185D GLU* 1.3 88.5 - - + +
187D GLN* 1.3 65.1 + - - +
188D ASN* 3.3 2.6 + - - +
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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) + - + + + + + -
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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