Contacts of the helix formed by residues 188 - 205 (chain B) in PDB entry 1YA8
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 188 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B GLY 3.7 8.2 + - - -
177B PHE* 4.0 11.6 + - - +
187B GLY* 1.3 71.8 - - - +
189B TRP* 1.3 65.9 + - - +
190B GLY 3.2 2.2 - - - -
191B HIS* 3.2 7.2 + - + -
192B LEU* 3.0 24.2 + - + +
320B GLY 4.1 1.4 - - - +
321B THR* 3.2 14.0 - - - +
322B VAL* 3.0 53.0 + - - +
324B ASP* 3.4 25.1 + - - +
327B LEU* 4.1 24.2 - - + +
328B LEU* 5.1 0.4 - - - +
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Residues in contact with TRP 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 3.1 35.3 - + - +
66B THR* 3.2 20.9 - - - -
67B PRO* 3.4 28.5 - - + -
171B ARG* 3.6 25.2 + - - +
175B TRP 3.7 10.5 - - - -
176B GLY* 2.7 26.7 + - - +
177B PHE 4.0 2.5 - - - -
178B PHE 3.3 18.6 + - - -
185B SER* 3.7 15.7 - - - -
186B ARG* 4.0 12.3 - - + -
187B GLY* 3.3 33.1 - - - -
188B ASN* 1.3 69.2 - - - +
190B GLY* 1.3 68.0 + - - +
192B LEU* 3.1 13.9 + - + +
193B ASP* 2.9 28.4 + - - +
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Residues in contact with GLY 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B TYR* 3.5 10.2 - - - +
171B ARG* 3.4 26.2 - - - -
176B GLY* 2.8 11.5 + - - -
177B PHE* 3.7 10.5 - - - -
189B TRP* 1.3 76.4 - - - +
191B HIS* 1.3 60.4 + - - +
193B ASP* 3.1 25.9 + - - +
194B GLN* 3.3 8.5 + - - -
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Residues in contact with HIS 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 4.6 5.7 - - + +
177B PHE* 3.5 28.5 - + - -
188B ASN* 3.2 16.4 + - - +
189B TRP 3.2 0.6 - - - -
190B GLY* 1.3 72.6 - - - +
192B LEU* 1.3 64.6 + - - +
194B GLN* 3.0 36.7 + - - +
195B VAL* 3.2 18.8 + - - +
225B GLU* 3.6 14.1 + - - -
226B SER* 3.6 25.2 + - - -
229B VAL* 4.3 7.1 - - + +
230B LEU* 4.6 2.6 - - + +
321B THR* 2.7 30.4 + - + +
327B LEU* 3.3 31.6 - - + -
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Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PRO* 3.8 23.3 - - + -
68B PRO* 3.7 14.7 - - + +
187B GLY 4.5 4.0 - - - +
188B ASN* 3.0 17.0 + - + +
189B TRP* 3.1 35.9 + - + +
191B HIS* 1.3 77.7 - - - +
193B ASP* 1.3 56.6 + - - +
195B VAL* 3.4 7.3 + - + +
196B ALA* 2.9 28.1 + - - +
235B LEU* 3.8 28.5 - - + -
324B ASP* 5.1 4.5 - - - +
326B MET* 5.7 5.8 - - + -
327B LEU* 4.5 13.7 - - + -
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Residues in contact with ASP 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PHE* 3.3 14.0 - - + -
68B PRO* 3.2 14.6 - - - +
117B LEU* 3.5 15.4 - - + +
169B GLN 5.3 0.2 - - - -
170B TYR* 3.9 14.1 - - + -
171B ARG* 2.7 64.7 + - - +
189B TRP 2.9 13.2 + - - +
190B GLY 3.1 9.8 + - - +
192B LEU* 1.3 76.4 - - - +
194B GLN* 1.3 53.4 + - - +
196B ALA* 3.1 6.0 + - - -
197B ALA* 2.8 30.0 + - - +
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Residues in contact with GLN 194 (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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139B ILE* 3.9 9.1 - - + +
168B ILE* 4.0 25.7 - - + +
170B TYR* 3.2 44.4 - - + -
190B GLY 3.3 9.5 + - - +
191B HIS* 3.0 32.9 + - - +
193B ASP* 1.3 78.2 - - - +
195B VAL* 1.3 56.9 + - - +
197B ALA* 3.2 3.1 + - - +
198B LEU* 2.9 35.0 + - + +
226B SER* 3.5 28.5 + - - -
230B LEU* 4.3 18.1 - - + +
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B HIS 3.2 16.1 + - - +
192B LEU* 3.7 10.8 - - + +
194B GLN* 1.3 75.7 - - - +
196B ALA* 1.3 61.1 + - - +
198B LEU* 3.7 7.2 - - - -
199B ARG* 3.2 32.8 + - - +
230B LEU* 3.5 23.8 - - + -
235B LEU* 3.4 35.0 - - + +
236B ALA* 4.4 2.9 - - + -
239B LEU* 3.4 14.2 - - + +
327B LEU* 4.2 14.8 - - + -
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Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PHE* 4.0 15.7 - - + +
56B ALA* 5.3 2.0 - - + -
68B PRO* 3.6 25.4 - - + +
192B LEU 2.9 18.2 + - - +
193B ASP* 3.3 6.5 - - - +
194B GLN 3.1 0.2 - - - -
195B VAL* 1.3 76.3 - - - +
197B ALA* 1.3 64.6 + - - +
199B ARG* 3.4 12.9 + - - +
200B TRP* 3.3 19.1 + - - +
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Residues in contact with ALA 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PHE* 3.5 30.9 - - + -
119B LEU* 4.5 2.6 - - + +
168B ILE* 3.9 31.9 - - + -
193B ASP 2.8 16.8 + - - +
194B GLN 3.5 5.2 - - - +
196B ALA* 1.3 78.6 - - - +
198B LEU* 1.3 62.1 + - - +
200B TRP* 3.2 6.7 + - - +
201B VAL* 3.1 25.1 + - - +
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B VAL* 4.1 28.3 - - + -
168B ILE* 5.8 2.0 - - + -
194B GLN* 2.9 19.7 + - + +
195B VAL* 3.7 9.0 - - - +
196B ALA 3.2 0.2 - - - -
197B ALA* 1.3 76.4 - - - +
199B ARG* 1.3 61.0 + - - +
201B VAL* 3.1 9.0 + - + +
202B GLN* 3.0 25.0 + - - +
215B VAL* 4.5 3.6 - - + -
217B ILE* 3.8 32.5 - - + -
230B LEU* 4.3 20.4 - - + -
236B ALA* 5.2 0.9 - - + -
239B LEU* 3.8 37.1 - - + +
240B PHE* 4.5 8.5 - - + -
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Residues in contact with ARG 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B VAL* 3.2 21.1 + - - +
196B ALA* 3.7 11.4 - - - +
197B ALA 3.3 0.4 - - - -
198B LEU* 1.3 73.9 - - - +
200B TRP* 1.3 67.2 + - - +
202B GLN* 3.0 11.0 + - - +
203B ASP* 2.9 31.7 + - - +
235B LEU* 3.9 22.8 + - - +
239B LEU* 4.0 22.8 - - + +
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Residues in contact with TRP 200 (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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28B THR* 4.6 9.5 + - + -
30B HIS* 4.4 18.2 - + - -
53B ILE* 3.7 24.8 - - + +
54B PRO 3.8 10.3 + - - -
55B PHE* 3.8 36.3 - - + +
74B TRP* 5.8 1.2 - + - -
119B LEU* 3.8 18.6 - - + -
121B ILE* 3.7 23.1 - - + -
166B VAL* 6.0 0.2 - - + -
196B ALA 3.3 6.8 + - - +
197B ALA 3.2 10.2 + - - +
199B ARG* 1.3 78.7 - - - +
201B VAL* 1.3 67.2 + - + +
203B ASP* 3.3 3.8 + - - -
204B ASN* 2.9 60.2 + - + +
205B ILE* 4.5 6.3 - - + -
208B PHE* 3.6 30.1 - + - -
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Residues in contact with VAL 201 (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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119B LEU* 4.8 1.8 - - + -
135B VAL* 4.6 4.0 - - + -
137B VAL* 4.2 19.3 - - + -
166B VAL* 4.6 18.8 - - + -
168B ILE* 5.7 0.4 - - + -
197B ALA 3.1 13.2 + - - +
198B LEU* 3.1 14.1 + - + +
200B TRP* 1.3 90.6 - - + +
202B GLN* 1.3 62.7 + - - +
205B ILE* 2.9 50.1 + - + +
215B VAL* 4.0 33.9 - - + -
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Residues in contact with GLN 202 (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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198B LEU 3.0 15.3 + - - +
199B ARG* 3.0 11.3 + - - +
201B VAL* 1.3 77.7 - - - +
203B ASP* 1.3 65.0 + - - +
204B ASN 5.4 0.2 - - - -
206B ALA* 5.8 1.2 + - - +
212B PRO* 2.7 52.6 + - - +
215B VAL* 3.3 21.2 - - - +
238B ASN 4.1 12.3 - - - +
239B LEU* 3.6 34.2 + - + +
241B HIS* 4.5 2.6 + - - -
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Residues in contact with ASP 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 3.9 15.8 - - + +
199B ARG* 2.9 24.3 + - - +
200B TRP* 4.9 1.4 - - - -
202B GLN* 1.3 82.5 - - - +
204B ASN* 1.3 75.8 + - - +
206B ALA* 5.5 1.7 - - - +
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Residues in contact with ASN 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B THR* 3.2 12.3 + - - -
29B VAL* 3.0 39.3 + - - +
30B HIS* 5.3 2.6 + - - -
200B TRP* 2.9 68.0 + - + +
201B VAL 3.3 0.4 + - - -
202B GLN 3.5 0.2 - - - -
203B ASP* 1.3 89.0 - - - +
205B ILE* 1.3 52.8 + - - +
206B ALA* 2.7 19.6 + - - +
207B SER* 2.7 27.8 + - - -
208B PHE* 3.8 6.0 - - + -
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Residues in contact with ILE 205 (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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121B ILE* 4.2 10.3 - - + -
135B VAL* 3.8 27.6 - - + -
164B VAL* 4.0 11.9 - - + -
166B VAL* 3.9 25.6 - - + -
200B TRP* 4.2 5.3 + - + -
201B VAL* 2.9 35.4 + - + +
204B ASN* 1.3 70.7 - - - +
206B ALA* 1.3 60.2 + - - +
207B SER 3.1 0.2 - - - -
208B PHE* 2.9 35.0 + - + -
210B GLY* 2.9 23.8 + - - -
212B PRO* 3.7 31.0 - - + -
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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
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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