Contacts of the helix formed by residues 166 - 183 (chain B) in PDB entry 1YWT
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 ASN 166 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B GLU* 3.6 28.7 + - - -
162B MET* 3.2 26.2 - - + +
163B PRO* 3.1 32.5 + - + +
165B THR* 1.3 79.6 + - - +
167B PRO* 1.3 73.4 - - - +
168B ILE* 2.9 26.3 + - - +
169B ARG* 3.1 13.4 + - + +
170B LEU* 3.1 19.1 + - - +
212B SER* 5.0 1.1 - - - -
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Residues in contact with PRO 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLU* 5.9 0.7 - - - +
165B THR 3.1 6.0 - - - +
166B ASN* 1.3 89.2 - - - +
168B ILE* 1.3 64.8 + - + +
170B LEU* 4.3 1.6 - - + -
171B GLY* 2.9 23.7 + - - -
212B SER* 3.3 36.3 - - - +
215B ASP* 3.6 28.5 - - + +
216B SER* 3.8 11.0 - - - +
219B ILE* 3.2 17.8 - - + +
7D TYR* 5.4 1.7 - - + -
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Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B CYS* 5.7 4.0 - - - -
41B ARG* 4.2 12.6 - - - +
115B GLU* 2.9 48.5 - - + +
118B VAL* 4.0 22.2 - - + -
119B PHE* 4.1 30.5 - - + +
122B LYS* 4.6 6.8 - - + +
162B MET* 3.8 4.9 - - + -
166B ASN* 2.9 12.7 + - - +
167B PRO* 1.3 75.4 - - + +
169B ARG* 1.3 61.8 - - - +
171B GLY* 3.1 1.8 + - - -
172B LEU* 2.8 31.1 + - - +
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Residues in contact with ARG 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 5.2 0.2 - - - -
155B MET* 5.3 1.5 - - - +
158B SER* 3.6 37.8 + - - +
159B LYS* 3.9 38.4 + - - +
162B MET* 2.5 36.7 + - - -
163B PRO 3.6 13.0 - - - -
164B PRO* 3.6 36.3 + - + +
166B ASN* 3.1 18.1 + - + +
168B ILE* 1.3 80.6 - - - +
170B LEU* 1.3 57.2 + - + +
172B LEU* 3.4 8.3 + - - +
173B ALA* 2.8 29.8 + - + +
197B THR* 6.4 0.9 - - + -
200B GLU* 4.3 13.1 + - - -
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B PRO 3.8 17.9 - - - +
165B THR* 3.4 29.8 - - - +
166B ASN 3.1 11.5 + - - +
167B PRO* 3.8 3.8 - - + +
169B ARG* 1.3 76.1 - - + +
171B GLY* 1.3 57.6 + - - +
173B ALA* 3.8 4.3 - - - +
174B LEU* 2.7 35.9 + - - +
197B THR* 3.6 26.9 - - + +
201B ALA* 4.0 13.2 - - + -
216B SER* 3.4 31.0 - - - +
219B ILE* 3.5 13.4 - - + +
220B MET* 4.5 8.1 - - + -
223B LEU* 4.3 11.1 - - + +
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Residues in contact with GLY 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LYS* 3.4 20.0 - - - -
167B PRO 2.9 18.2 + - - -
168B ILE* 3.6 1.3 - - - -
170B LEU* 1.3 75.8 - - - +
172B LEU* 1.3 62.0 + - - +
174B LEU* 3.3 2.8 + - - +
175B ASN* 3.0 23.9 + - - +
219B ILE* 3.9 16.5 - - - +
7D TYR* 4.5 10.3 - - - -
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 3.7 10.3 - - + -
122B LYS* 3.5 23.6 - - + +
151B TYR* 3.7 29.6 - - + +
154B ALA* 3.3 50.5 - - + +
155B MET* 3.4 23.6 - - + +
158B SER* 3.8 7.2 - - - +
168B ILE 2.8 17.5 + - - +
169B ARG* 3.4 4.0 - - - +
171B GLY* 1.3 77.8 - - - +
173B ALA* 1.3 58.3 + - - +
175B ASN* 3.4 1.1 + - - +
176B PHE* 2.8 26.9 + - + +
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B MET* 3.9 22.4 - - + -
169B ARG* 2.8 22.1 + - + +
170B LEU 3.9 0.9 - - - +
172B LEU* 1.3 74.0 - - - +
174B LEU* 1.3 63.0 + - - +
176B PHE* 3.8 1.8 - - - +
177B SER* 3.1 23.4 + - - -
193B LEU* 4.0 7.9 - - + +
194B ALA* 5.8 0.2 - - - -
197B THR* 3.5 36.1 - - + +
223B LEU* 4.9 2.5 - - - +
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU 2.7 21.6 + - - +
171B GLY 3.4 2.9 - - - +
172B LEU 3.2 0.2 - - - -
173B ALA* 1.3 72.2 - - - +
175B ASN* 1.3 65.3 + - - +
177B SER* 2.4 25.3 + - - +
178B VAL* 3.1 7.3 + - - +
219B ILE* 4.1 8.5 - - + -
222B LEU* 3.6 17.5 - - + -
223B LEU* 3.7 35.8 - - + +
226B ASN* 3.2 30.3 - - - +
5D HIS 3.8 4.0 - - - +
6D SEP 3.6 7.2 - - - -
7D TYR* 3.4 40.4 - - + +
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Residues in contact with ASN 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LYS* 3.1 9.2 - - - +
126B ASP* 2.9 32.8 + - - +
129B ARG* 3.4 17.8 + - - +
151B TYR* 4.0 6.9 + - + +
171B GLY 3.0 14.0 + - - +
172B LEU 4.0 2.2 - - - +
174B LEU* 1.3 76.4 - - - +
176B PHE* 1.3 62.7 + - - +
178B VAL* 3.2 10.4 + - - +
179B PHE* 3.0 21.3 + - - +
6D SEP 3.4 9.8 + - - -
7D TYR 2.7 46.5 + - - +
8D PRO* 5.2 0.2 - - - +
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Residues in contact with PHE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ARG* 4.4 13.9 - - + -
151B TYR* 3.6 40.1 - + + -
152B GLN* 3.8 33.4 - - - -
155B MET* 3.4 30.5 - - + -
172B LEU 2.8 22.3 + - - +
173B ALA 3.8 4.0 - - - +
174B LEU 3.3 0.2 - - - -
175B ASN* 1.3 72.7 - - - +
177B SER* 1.3 59.8 + - - +
179B PHE* 3.1 33.7 - + - +
180B HIS* 3.1 37.7 + + - -
193B LEU* 4.2 10.3 - - + -
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Residues in contact with SER 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ALA 3.1 11.9 + - - -
174B LEU* 2.4 32.1 + - - +
176B PHE* 1.3 75.8 - - - +
178B VAL* 1.3 64.3 + - - +
180B HIS* 3.2 6.4 + - - -
181B TYR 3.0 18.9 + - - -
190B ALA* 3.3 24.9 - - - +
193B LEU* 4.0 12.8 - - - +
194B ALA* 4.2 11.1 - - - +
223B LEU* 4.7 0.2 - - - +
230B TRP* 3.5 22.4 - - - -
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG* 4.0 24.2 - - - +
174B LEU 3.1 12.5 + - - +
175B ASN* 3.5 13.0 - - - +
177B SER* 1.3 77.3 + - - +
179B PHE* 1.3 58.6 + - - +
182B GLU* 2.9 46.0 + - + +
183B ILE* 4.8 0.3 - - - +
226B ASN* 4.2 7.0 - - - +
230B TRP* 4.1 8.3 - - + -
4D SER* 3.5 22.9 - - - +
5D HIS 3.2 28.7 - - - +
6D SEP 4.5 7.6 - - - +
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Residues in contact with PHE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG* 3.9 13.7 - - + +
144B ILE* 3.6 37.2 - - + -
147B ALA* 3.9 13.0 - - + -
148B ARG* 3.7 39.9 - - + -
151B TYR* 3.9 22.9 - + + -
175B ASN 3.0 12.6 + - - +
176B PHE* 3.1 27.8 - + - +
178B VAL* 1.3 78.0 - - - +
180B HIS* 1.3 66.1 + + - +
183B ILE* 2.9 47.3 + - + +
184B ALA* 3.0 20.3 + - + -
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Residues in contact with HIS 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ARG* 3.8 19.0 + - - -
176B PHE* 3.1 44.1 + + - -
177B SER* 3.2 7.8 + - - +
179B PHE* 1.3 90.8 - + - +
181B TYR* 1.3 60.1 + - - +
184B ALA* 4.1 1.6 - - - -
185B ASN 3.3 7.6 + - - -
186B SER* 2.8 40.9 + - - +
189B GLU* 3.3 27.6 + - + -
190B ALA* 3.6 22.0 + - + +
193B LEU* 3.9 23.3 - - + +
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Residues in contact with TYR 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B SER 3.0 10.8 + - - +
178B VAL 4.0 1.3 - - - +
180B HIS* 1.3 80.7 - - - +
182B GLU* 1.3 73.6 + - + +
183B ILE 3.8 0.2 + - - -
185B ASN* 4.0 14.4 - - - +
186B SER 4.4 2.9 + - - -
187B PRO* 3.4 40.4 - - + +
190B ALA* 3.6 12.6 - - + -
191B ILE* 5.0 1.1 - - + -
229B LEU 4.9 1.2 + - - -
230B TRP* 3.4 71.9 + + + -
1D MET* 5.9 7.4 - - - -
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Residues in contact with GLU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ARG* 5.6 2.3 + - - -
129B ARG* 5.6 0.5 + - - -
133B GLU* 5.2 5.7 - - - +
178B VAL* 2.9 27.5 + - + +
181B TYR* 1.3 89.5 - - + +
183B ILE* 1.3 70.5 + - + +
185B ASN* 4.8 3.4 + - - +
1D MET 6.0 0.2 - - - -
3D ARG* 3.6 26.7 + - - +
4D SER* 3.4 33.0 + - - +
6D SEP 5.6 1.0 + - - -
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Residues in contact with ILE 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG* 3.8 31.4 - - + +
132B ALA* 4.0 9.0 - - + +
133B GLU* 3.9 36.3 - - + +
140B LYS* 5.5 7.1 - - - +
144B ILE* 3.6 39.0 - - + +
179B PHE* 2.9 30.7 + - + +
181B TYR 3.5 0.2 - - - -
182B GLU* 1.3 92.8 - - + +
184B ALA* 1.3 58.4 + - - +
185B ASN* 3.1 17.0 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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