Contacts of the helix formed by residues 187 - 202 (chain B) in PDB entry 2Y4T
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 ASP 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B LYS 3.4 0.4 + - - -
118B GLN 3.3 22.8 - - - +
119B GLY* 3.5 14.0 - - - +
158B ARG* 3.5 10.9 + - - -
181B LEU* 4.2 8.5 - - + -
184B CYS* 3.2 16.4 + - + +
185B VAL 3.6 1.8 + - - -
186B TRP* 1.3 72.7 - - - +
188B ALA* 1.3 64.7 + - - +
189B GLU* 3.2 16.4 + - - +
190B LEU* 3.0 40.2 + - + +
191B ARG* 3.0 27.0 + - - +
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Residues in contact with ALA 188 (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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186B TRP 3.2 7.6 + - - +
187B ASP* 1.3 70.7 + - - +
189B GLU* 1.3 65.1 + - - +
191B ARG* 3.2 9.2 - - - +
192B GLU* 3.0 34.6 + - - +
214B ALA* 4.0 11.6 - - + +
217B LEU* 4.5 12.6 - - + -
218B LYS* 3.7 37.5 - - + -
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Residues in contact with GLU 189 (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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118B GLN 5.4 0.9 - - - +
120B LYS* 6.1 1.2 - - - -
158B ARG* 5.4 7.0 - - - +
187B ASP* 3.2 11.9 + - - +
188B ALA* 1.3 81.2 + - - +
190B LEU* 1.3 58.8 + - + +
192B GLU* 3.0 21.5 + - - +
193B LEU* 3.0 23.3 + - - +
218B LYS* 3.9 21.5 + - - -
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Residues in contact with LEU 190 (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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158B ARG* 3.6 33.2 - - + +
161B ALA* 5.2 1.1 - - + -
162B LEU* 4.7 12.6 - - + -
177B LEU* 3.8 25.0 - - + +
180B ILE* 4.0 34.3 - - + -
181B LEU* 4.0 11.7 - - + +
184B CYS* 5.5 1.6 - - + -
187B ASP* 3.0 35.0 + - + +
189B GLU* 1.3 73.4 - - + +
191B ARG* 1.3 61.0 + - - +
193B LEU* 3.2 17.2 + - + +
194B ARG* 2.9 30.3 + - - +
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Residues in contact with ARG 191 (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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181B LEU* 4.1 25.0 + - + +
185B VAL* 3.4 34.5 + - - +
187B ASP 3.0 22.7 + - - +
188B ALA* 3.2 13.7 - - - +
190B LEU* 1.3 76.3 - - - +
192B GLU* 1.3 61.4 + - - +
194B ARG* 3.6 20.8 + - - +
195B ALA* 3.1 18.4 + - - +
209B SER* 4.4 5.9 + - - -
210B ASP* 3.3 52.1 + - - +
213B ALA* 4.0 24.4 - - - +
214B ALA* 4.4 3.1 - - + -
217B LEU* 4.8 4.8 - - + +
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Residues in contact with GLU 192 (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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188B ALA 3.0 20.3 + - - +
189B GLU* 3.0 21.2 + - - +
191B ARG* 1.3 76.2 - - - +
193B LEU* 1.3 53.7 + - - +
195B ALA* 3.3 8.2 - - - +
196B GLU* 2.9 29.2 + - - +
211B LEU* 4.3 13.7 - - + +
214B ALA* 4.1 16.8 - - + +
218B LYS* 3.0 36.3 + - - +
221B ASN* 5.3 0.7 + - - -
224B ALA* 5.5 2.6 - - - +
227B LYS* 6.0 4.3 - - + -
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Residues in contact with LEU 193 (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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161B ALA 4.5 5.2 - - - +
162B LEU* 4.0 27.4 - - + -
165B PHE* 4.0 50.6 - - + -
177B LEU* 4.2 22.7 - - + -
189B GLU 3.0 12.0 + - - +
190B LEU* 3.2 14.3 + - + +
192B GLU* 1.3 76.5 - - - +
194B ARG* 1.3 58.1 + - - +
196B GLU* 3.2 8.3 + - + +
197B CYS* 2.9 30.5 + - - -
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Residues in contact with ARG 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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174B ILE* 4.5 7.4 - - + -
177B LEU* 3.7 33.3 - - + +
178B ASP* 2.6 50.3 + - - +
181B LEU* 3.5 25.2 - - + +
190B LEU 2.9 15.6 + - - +
191B ARG* 3.7 22.2 - - - +
193B LEU* 1.3 73.2 - - - +
195B ALA* 1.3 64.9 + - - +
197B CYS* 3.2 4.5 + - - +
198B PHE* 2.9 44.7 + - + -
209B SER* 5.8 0.2 + - - -
210B ASP* 2.8 28.9 + - - +
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Residues in contact with ALA 195 (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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191B ARG 3.1 14.9 + - - +
192B GLU 3.3 9.9 - - - +
194B ARG* 1.3 74.6 - - - +
196B GLU* 1.3 59.5 + - - +
198B PHE* 3.0 6.8 + - - +
199B ILE* 2.9 31.5 + - - +
207B ALA* 3.5 17.4 - - + +
210B ASP* 3.9 10.8 - - + +
211B LEU* 3.6 34.8 - - + -
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Residues in contact with GLU 196 (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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165B PHE* 3.9 24.8 - - + -
192B GLU 2.9 14.2 + - - +
193B LEU* 3.2 13.0 + - + +
195B ALA* 1.3 74.3 - - - +
197B CYS* 1.3 56.9 + - - +
199B ILE* 3.4 19.4 + - - +
200B LYS* 2.9 58.0 + - + +
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Residues in contact with CYS 197 (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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165B PHE* 3.5 25.8 - - - -
170B TYR* 4.1 19.3 - - + +
173B ALA* 3.7 24.5 - - - -
174B ILE* 3.7 19.7 - - + -
177B LEU* 4.0 10.1 - - - -
193B LEU 2.9 17.9 + - - -
194B ARG* 3.3 10.1 - - - +
196B GLU* 1.3 75.9 - - - +
198B PHE* 1.3 57.5 + - - +
200B LYS* 3.7 1.9 - - - +
201B GLU* 2.9 32.1 + - - +
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Residues in contact with PHE 198 (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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174B ILE* 3.7 42.2 - - + -
178B ASP* 4.9 4.3 - - - -
194B ARG* 2.9 39.4 + - + -
195B ALA 3.0 6.5 + - - +
197B CYS* 1.3 76.5 - - - +
199B ILE* 1.3 61.3 + - - +
201B GLU* 3.3 10.0 + - + +
202B GLY 3.4 0.3 + - - -
203B GLU* 3.3 38.5 + - + +
206B LYS* 4.1 40.6 - - + -
207B ALA* 4.0 14.1 - - + +
210B ASP* 4.1 19.3 - - - -
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Residues in contact with ILE 199 (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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195B ALA 2.9 28.6 + - - +
196B GLU* 3.8 21.1 - - - +
198B PHE* 1.3 71.2 - - - +
200B LYS* 1.3 63.9 + - + +
202B GLY* 3.2 15.1 + - - -
204B PRO* 4.3 22.1 - - + +
207B ALA* 3.7 17.7 - - + -
211B LEU* 4.3 17.7 - - + -
231B LEU* 4.3 19.7 - - + -
234B GLN* 6.0 0.9 - - - +
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Residues in contact with LYS 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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165B PHE* 5.8 0.2 - - + -
170B TYR* 3.9 45.8 + - + +
196B GLU* 2.9 43.9 + - + +
197B CYS 3.7 4.3 - - - +
199B ILE* 1.3 73.3 - - + +
201B GLU* 1.3 57.3 + - - +
202B GLY* 3.1 10.5 + - - -
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Residues in contact with GLU 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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170B TYR* 3.5 25.7 - - - +
171B THR* 2.7 35.1 + - + +
174B ILE* 4.6 9.9 - - + -
197B CYS 2.9 17.0 + - - +
198B PHE* 3.3 9.3 + - - +
200B LYS* 1.3 74.5 - - - +
202B GLY* 1.3 59.3 + - - +
203B GLU* 3.6 16.5 - - + +
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Residues in contact with GLY 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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199B ILE 3.2 8.9 + - - -
200B LYS 3.1 6.3 - - - -
201B GLU* 1.3 79.5 - - - +
203B GLU* 1.3 59.8 + - - +
204B PRO* 3.2 14.9 - - - +
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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