Contacts of the helix formed by residues 201 - 219 (chain B) in PDB entry 1YYO
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 SER 201 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B PHE* 3.5 9.1 - - - -
199B GLY 4.2 0.5 - - - -
200B LYS* 1.3 80.5 - - - +
202B LYS* 1.3 68.1 + - - +
203B LYS* 4.2 6.2 + - - +
204B GLU* 3.2 22.6 + - - +
205B ALA* 3.1 22.9 + - - +
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Residues in contact with LYS 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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170B TYR 4.8 9.3 + - - -
172B LEU* 4.3 33.9 - - + +
184B PHE* 3.6 25.2 - - + -
186B VAL* 4.8 5.5 - - + +
201B SER* 1.3 73.9 - - - +
203B LYS* 1.3 64.3 + - - +
205B ALA* 3.3 3.2 + - - +
206B GLU* 3.0 46.8 + - + +
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Residues in contact with LYS 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LYS* 4.9 9.2 - - + +
201B SER* 3.3 7.0 + - - +
202B LYS* 1.3 77.8 - - - +
204B GLU* 1.3 66.2 + - - +
206B GLU* 3.2 17.0 + - - +
207B GLN* 3.0 44.1 + - + +
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Residues in contact with GLU 204 (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 GLU 4.5 0.7 - - - +
199B GLY* 3.1 10.1 - - - -
200B LYS* 2.8 48.6 + - - +
201B SER* 3.2 22.0 + - - +
203B LYS* 1.3 78.2 - - - +
205B ALA* 1.3 63.0 + - - +
207B GLN* 3.1 19.8 + - - +
208B ARG* 3.2 19.6 + - + +
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Residues in contact with ALA 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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184B PHE* 4.1 13.7 - - + +
186B VAL* 3.5 20.1 - - + +
197B GLY* 3.6 15.1 - - - +
198B GLU* 4.0 12.8 - - - -
199B GLY* 3.9 12.0 - - - +
201B SER 3.1 9.7 + - - +
202B LYS* 3.6 7.0 - - - +
204B GLU* 1.3 77.6 - - - +
206B GLU* 1.3 64.2 + - - +
208B ARG* 2.8 16.5 + - - +
209B ALA 3.0 9.9 + - - -
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Residues in contact with GLU 206 (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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153B LYS* 3.2 32.9 + - + -
170B TYR* 3.4 38.9 - - + +
186B VAL* 3.7 19.1 - - + -
202B LYS* 3.0 42.6 - - + +
203B LYS* 3.2 15.3 + - - +
205B ALA* 1.3 75.4 - - - +
207B GLN* 1.3 53.3 + - - +
209B ALA* 3.1 3.7 + - - +
210B ALA* 2.7 35.5 + - - +
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Residues in contact with GLN 207 (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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151B ASP* 3.2 26.9 + - - +
152B TYR* 3.6 20.2 + - + +
153B LYS* 3.2 44.9 + - + +
203B LYS* 3.0 30.4 + - + +
204B GLU* 3.1 11.2 + - - +
206B GLU* 1.3 73.9 - - - +
208B ARG* 1.3 67.8 + - + +
210B ALA* 3.2 2.0 + - - +
211B GLU* 2.9 24.9 + - - +
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Residues in contact with ARG 208 (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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152B TYR* 4.6 9.5 - - - -
196B LEU 5.1 0.2 - - - +
197B GLY* 3.7 12.3 - - - -
198B GLU 3.4 25.8 - - - +
204B GLU* 3.5 19.7 - - + +
205B ALA 2.8 8.0 + - - +
207B GLN* 1.3 81.3 - - - +
209B ALA* 1.3 61.9 + - - +
211B GLU* 2.7 33.5 + - - +
212B GLU* 3.1 34.6 + - + +
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Residues in contact with ALA 209 (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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170B TYR* 4.9 0.2 - - + -
186B VAL* 4.2 7.2 - - + +
188B ALA* 3.4 28.9 - - + +
195B THR* 2.9 23.4 + - - +
196B LEU 4.0 4.9 - - - -
197B GLY* 3.7 23.9 - - - +
205B ALA 3.0 6.2 + - - +
206B GLU* 3.5 8.1 - - - +
208B ARG* 1.3 78.3 - - - +
210B ALA* 1.3 59.2 + - - +
212B GLU* 3.4 1.6 + - - -
213B LEU* 2.9 16.6 + - - +
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Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TYR 4.0 2.5 - - - -
153B LYS* 3.9 24.2 - - + +
156B LEU* 3.5 28.1 - - + +
170B TYR* 3.7 10.5 - - - +
188B ALA* 4.1 1.1 - - - +
206B GLU 2.7 20.3 + - - +
207B GLN 3.5 4.0 - - - +
209B ALA* 1.3 72.6 - - - +
211B GLU* 1.3 61.8 + - - +
213B LEU* 3.3 2.1 + - - +
214B ILE* 2.9 32.0 + - - +
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Residues in contact with GLU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TYR* 3.0 53.1 + - + +
207B GLN 2.9 12.3 + - - +
208B ARG* 2.7 39.4 + - - +
210B ALA* 1.3 76.9 - - - +
212B GLU* 1.3 74.2 + - - +
214B ILE* 3.0 15.4 + - + +
215B LYS* 3.2 30.7 + - + +
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Residues in contact with GLU 212 (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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176A GLU* 4.6 9.2 - - - +
183A LYS* 4.6 8.9 + - - -
195B THR* 3.7 20.0 - - + +
196B LEU 4.3 11.2 - - - +
208B ARG* 3.1 22.9 + - + +
209B ALA 3.9 2.5 - - - +
211B GLU* 1.3 88.2 - - - +
213B LEU* 1.3 61.9 + - - +
215B LYS* 2.7 43.0 + - - +
216B LEU* 3.1 21.8 + - - +
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LEU* 3.7 33.0 - - + -
168B PRO* 4.9 0.9 - - + -
188B ALA* 3.9 16.4 - - + -
189B LYS* 4.1 13.9 - - - +
190B ILE* 4.1 13.7 - - + +
193B TYR* 3.9 32.1 - - + +
195B THR* 3.2 21.0 + - + +
209B ALA 2.9 12.3 + - - +
210B ALA 3.7 4.9 - - - +
212B GLU* 1.3 73.8 - - - +
214B ILE* 1.3 65.0 + - - +
216B LEU* 3.5 9.0 + - + -
217B LEU* 3.2 27.8 + - + +
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Residues in contact with ILE 214 (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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152B TYR* 3.8 38.8 - - + +
155B ILE* 3.8 25.4 - - + -
156B LEU* 4.0 16.6 - - + +
159B ILE* 4.0 19.9 - - + +
210B ALA 2.9 25.4 + - - +
211B GLU* 3.0 7.1 + - - +
213B LEU* 1.3 76.4 - - - +
215B LYS* 1.3 66.6 + - + +
217B LEU* 3.0 16.2 + - - +
218B GLU* 3.0 33.9 + - + +
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Residues in contact with LYS 215 (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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176A GLU* 5.0 8.4 + - - +
183A LYS* 4.3 13.9 - - - +
211B GLU* 3.2 26.2 + - + +
212B GLU* 2.7 43.4 + - - +
214B ILE* 1.3 77.2 - - + +
216B LEU* 1.3 57.9 + - - +
218B GLU* 2.8 43.4 + - - +
219B GLU* 3.8 9.8 + - - +
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Residues in contact with LEU 216 (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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193B TYR* 3.5 47.0 - - + -
194B ARG 4.5 7.6 - - - +
195B THR* 4.5 12.3 - - + -
212B GLU 3.1 10.2 + - - +
213B LEU* 3.7 15.5 - - + +
215B LYS* 1.3 79.6 - - - +
217B LEU* 1.3 59.6 + - - +
219B GLU* 3.7 26.5 - - - +
220B SER* 3.9 10.0 - - - -
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Residues in contact with LEU 217 (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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156B LEU* 4.1 12.1 - - + -
159B ILE* 4.3 17.0 - - + -
160B THR* 4.0 26.5 - - + -
163B ARG* 3.7 22.1 + - - +
164B TRP* 3.8 27.1 - - + -
190B ILE* 4.2 8.3 - - + -
193B TYR* 3.8 26.9 - - + -
213B LEU* 3.2 21.9 + - + +
214B ILE* 3.0 8.3 + - - +
215B LYS 3.0 1.4 - - - -
216B LEU* 1.3 76.5 - - - +
218B GLU* 1.3 62.1 + - - +
219B GLU 3.4 1.3 - - - -
220B SER* 3.7 19.6 + - - +
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Residues in contact with GLU 218 (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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159B ILE* 6.2 0.7 - - + -
214B ILE* 3.0 31.5 - - + +
215B LYS* 2.8 21.8 + - - +
217B LEU* 1.3 79.7 - - - +
219B GLU* 1.3 60.6 + - - +
220B SER 3.6 1.9 + - - -
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Residues in contact with GLU 219 (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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177A GLY* 5.9 2.4 - - - -
178A PRO* 6.2 0.3 - - - +
215B LYS 4.2 8.4 - - - +
216B LEU* 3.7 25.8 - - - +
218B GLU* 1.3 78.4 - - - +
220B SER* 1.3 63.4 + - - +
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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
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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