Contacts of the helix formed by residues 184 - 195 (chain B) in PDB entry 1YXJ
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 184 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B ILE* 3.4 7.8 - - - +
183B ASN* 1.3 81.7 - - - +
185B THR* 1.3 64.6 + - - +
186B ALA* 3.5 11.3 + - - +
187B ASP* 3.1 27.1 + - - +
188B LEU* 3.1 18.0 + - - +
227B LEU* 3.6 13.7 - - - +
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Residues in contact with THR 185 (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 SER* 1.3 75.4 - - - +
186B ALA* 1.3 52.8 + - - +
188B LEU* 3.2 12.3 + - + +
189B ASP* 2.8 58.0 + - - +
226B HIS 4.5 8.3 + - - -
227B LEU* 3.7 15.3 + - - +
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Residues in contact with ALA 186 (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 HIS* 4.5 7.1 + - + +
184B SER* 3.1 10.7 - - - +
185B THR* 1.3 79.3 - - - +
187B ASP* 1.3 63.7 + - - +
189B ASP* 3.4 10.7 + - - +
190B PHE* 3.0 23.2 + - - +
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Residues in contact with ASP 187 (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 HIS* 4.6 10.4 + - - -
156B TYR* 4.6 13.9 + - + -
180B LEU* 6.1 1.6 - - + -
181B LYS 3.8 7.7 - - - +
182B ILE* 3.8 15.7 - - + -
183B ASN* 3.0 29.3 + - - +
184B SER* 3.1 20.5 + - - +
186B ALA* 1.3 78.4 - - - +
188B LEU* 1.3 63.8 + - - +
190B PHE* 3.3 9.0 + - - +
191B ILE* 3.1 28.5 + - + +
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Residues in contact with LEU 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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182B ILE* 3.7 29.7 - - + +
184B SER 3.1 12.5 + - - +
185B THR* 3.2 14.6 + - + +
187B ASP* 1.3 76.7 - - - +
189B ASP* 1.3 59.2 + - - +
191B ILE* 3.3 4.4 + - + +
192B GLN* 2.9 63.2 + - + +
227B LEU* 3.5 26.5 - - + +
228B PHE* 4.3 15.7 - - + -
246B ILE* 4.1 13.9 - - + -
249B GLY 4.8 1.8 - - - +
251B VAL* 5.0 3.6 - - + -
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Residues in contact with ASP 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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185B THR* 2.8 43.3 + - - +
186B ALA* 3.7 9.0 - - - +
187B ASP 3.3 0.2 - - - -
188B LEU* 1.3 74.9 - - - +
190B PHE* 1.3 63.2 + - - +
192B GLN* 3.4 17.2 + - - +
193B GLN* 2.9 41.5 + - - +
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Residues in contact with PHE 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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150A TRP* 3.4 31.2 - + - -
149B ILE* 3.8 17.3 - - + -
151B HIS* 3.5 44.6 - + + +
156B TYR* 3.5 38.4 - + + -
158B PHE* 4.9 2.2 - + - -
186B ALA 3.0 13.2 + - - +
187B ASP* 3.5 8.3 - - - +
189B ASP* 1.3 77.4 - - - +
191B ILE* 1.3 76.7 + - + +
193B GLN* 3.3 9.3 + - - +
194B ALA* 2.8 31.5 + - + +
2001B EDO 3.6 17.9 - - - -
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Residues in contact with ILE 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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156B TYR* 4.3 4.3 - - + -
158B PHE* 4.3 13.9 - - + -
180B LEU* 3.8 40.8 - - + -
182B ILE* 4.9 3.6 - - + -
187B ASP* 3.1 16.2 + - + +
188B LEU* 3.3 8.7 + - - +
190B PHE* 1.3 97.3 - - + +
192B GLN* 1.3 64.1 + - - +
194B ALA* 3.2 10.7 + - - +
195B ILE* 3.1 27.4 + - + +
246B ILE* 3.9 23.1 - - + -
263B ILE* 3.9 21.5 - - + -
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Residues in contact with GLN 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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271A ARG* 6.3 1.3 - - - +
188B LEU* 2.9 44.2 + - + +
189B ASP* 3.7 22.8 - - - +
191B ILE* 1.3 74.8 - - - +
193B GLN* 1.3 58.9 + - + +
195B ILE* 3.3 5.8 - - - -
196B SER* 2.8 33.6 + - - -
246B ILE* 4.4 4.0 - - + -
249B GLY* 2.9 41.8 + - - +
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Residues in contact with GLN 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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143A PRO* 3.8 2.8 - - - +
150A TRP* 3.7 19.9 - - + -
152A GLY 4.9 3.1 - - - +
270A LEU* 3.7 37.6 - - + +
271A ARG 5.9 2.7 - - - +
189B ASP* 2.9 32.3 + - - +
190B PHE* 3.6 7.2 - - - +
192B GLN* 1.3 73.4 - - + +
194B ALA* 1.3 67.9 + - - +
195B ILE 3.1 0.9 + - - -
196B SER* 3.2 22.8 + - - -
2001B EDO 5.1 3.1 + - - -
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Residues in contact with ALA 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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142A MSE 3.6 19.9 - - - +
143A PRO* 3.8 11.6 - - - +
150A TRP* 3.7 23.0 - - + -
158B PHE* 3.4 34.1 - - + -
190B PHE* 2.8 20.5 + - + +
191B ILE* 3.2 5.8 + - - +
193B GLN* 1.3 76.3 - - - +
195B ILE* 1.3 62.6 + - - +
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Residues in contact with ILE 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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142A MSE 4.2 9.4 - - + -
158B PHE* 3.7 28.3 - - + -
191B ILE* 3.1 31.9 - - + +
192B GLN* 3.3 4.5 - - - +
193B GLN 3.1 0.4 - - - -
194B ALA* 1.3 81.5 - - - +
196B SER* 1.3 62.3 + - - +
197B TYR 3.0 5.3 + - - -
198B SER* 3.2 29.5 + - - +
200B PHE 5.6 0.2 - - - +
202B PHE* 3.7 37.5 - - + -
246B ILE* 4.3 15.5 - - + +
247B GLN* 6.3 0.2 - - - -
248B ARG* 5.7 4.3 - - - +
249B GLY 5.7 4.4 + - - +
263B ILE* 4.5 0.2 - - + -
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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