Contacts of the helix formed by residues 192 - 201 (chain B) in PDB entry 1YYH
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 THR 192 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B HIS* 3.7 2.2 - - - -
183B LYS 4.7 2.2 - - - -
184B ASP* 3.7 20.9 - - - +
185B MET 3.4 1.8 - - - -
186B GLN* 3.9 4.9 - - + -
190B GLU 3.8 0.4 + - - +
191B GLU* 1.3 75.2 - - - +
193B PRO* 1.3 76.8 - - - +
194B LEU* 3.5 9.7 + - - +
195B PHE* 3.1 23.2 + - - +
196B LEU* 3.1 21.1 + - - +
215B ASN 4.9 4.9 + - - +
218B ILE* 3.6 45.5 + - + +
226B PRO* 4.7 2.1 - - - +
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Residues in contact with PRO 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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159B SER* 4.8 0.4 - - - +
161B LEU* 3.9 39.5 - - + +
162B HIS* 3.6 25.3 - - + +
165B ALA* 3.2 17.0 - - + +
182B ASN 4.5 3.8 - - - +
183B LYS 3.5 19.1 - - - +
185B MET 3.3 15.0 - - - +
192B THR* 1.3 87.0 - - - +
194B LEU* 1.3 55.5 + - - +
196B LEU* 3.2 2.1 + - + +
197B ALA* 2.9 25.1 + - - +
209B LEU* 3.7 14.1 - - + -
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Residues in contact with LEU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LYS 5.1 0.6 + - - +
192B THR* 3.2 8.8 + - - +
193B PRO* 1.3 76.3 - - - +
195B PHE* 1.3 67.5 + - - +
197B ALA* 3.2 1.6 + - - +
198B ALA* 2.9 24.1 + - + +
206B ALA* 4.0 29.4 - - + +
209B LEU* 3.7 15.5 - - + +
210B LEU* 3.6 35.7 - - + -
214B ALA* 4.5 14.6 - - + -
215B ASN 4.2 6.5 - - - +
216B ARG* 3.7 28.7 - - + +
226B PRO* 4.0 14.1 - - + -
238B ILE* 6.1 0.2 - - + -
242B LEU* 4.4 9.4 - - + -
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Residues in contact with PHE 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 GLU* 3.6 35.0 - - + -
192B THR* 3.1 29.0 + - - +
194B LEU* 1.3 77.5 - - - +
196B LEU* 1.3 61.0 + - + +
198B ALA* 3.3 3.1 + - - +
199B ARG* 2.9 35.9 + - - +
218B ILE 5.0 2.2 - - - +
220B ASP* 3.3 28.5 - - + -
224B ARG* 3.3 31.0 - - + -
225B LEU 3.7 10.1 - - - -
226B PRO* 3.8 25.5 - - + +
229B ILE* 3.7 32.5 - - + +
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Residues in contact with LEU 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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158B LYS* 4.4 10.8 - - + +
162B HIS* 3.5 52.0 - - + +
165B ALA 4.6 1.6 - - - -
166B ALA* 4.4 13.7 - - + +
187B ASN* 4.4 6.5 - - - +
191B GLU* 3.5 32.8 - - + +
192B THR 3.1 9.9 + - - +
193B PRO 3.2 5.8 + - - +
195B PHE* 1.3 76.7 - - + +
197B ALA* 1.3 65.4 + - - +
199B ARG* 3.3 30.3 + - - +
200B GLU* 2.9 31.1 + - - +
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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
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165B ALA* 3.7 24.3 - - + +
193B PRO 2.9 14.8 + - - +
194B LEU* 3.6 9.0 - - - +
196B LEU* 1.3 75.7 - - - +
198B ALA* 1.3 57.2 + - - +
200B GLU 3.4 0.2 + - - -
201B GLY* 2.9 10.2 + - - -
202B SER* 2.8 35.4 + - - +
205B THR 4.6 0.4 - - - -
206B ALA* 3.8 31.0 - - + +
209B LEU* 4.4 1.8 - - + -
238B ILE* 4.2 2.3 - - - +
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Residues in contact with ALA 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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194B LEU* 2.9 19.0 + - + +
195B PHE 3.6 4.3 - - - +
197B ALA* 1.3 72.1 - - - +
199B ARG* 1.3 65.9 + - - +
201B GLY* 3.5 1.7 + - - -
206B ALA* 5.1 0.6 - - - +
226B PRO* 3.3 36.1 - - + +
229B ILE* 3.9 2.5 - - + -
230B ALA* 3.8 9.0 - - + +
235B HIS* 3.2 19.9 - - - +
238B ILE* 3.8 25.6 - - + -
242B LEU* 4.9 0.2 - - + -
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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
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158B LYS* 4.6 11.3 - - - +
166B ALA* 5.9 2.2 - - - +
189B ARG* 4.5 9.7 - - - +
191B GLU* 3.0 27.5 + - - -
195B PHE* 2.9 24.0 + - + +
196B LEU* 3.5 27.7 - - - +
198B ALA* 1.3 76.6 - - - +
200B GLU* 1.3 81.1 + - - +
229B ILE* 3.6 29.5 - - + +
233B ARG* 3.2 47.3 + - - +
235B HIS* 2.9 18.9 + - - -
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Residues in contact with GLU 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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166B ALA* 3.4 37.3 - - + +
196B LEU* 2.9 20.2 + - - +
199B ARG* 1.3 115.0 + - - +
201B GLY* 1.3 61.5 + - - +
202B SER* 3.6 6.4 + - - +
233B ARG* 4.2 10.4 + - - -
235B HIS* 3.7 8.8 + - - -
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Residues in contact with GLY 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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168B ASN* 5.4 0.3 + - - -
197B ALA 2.9 5.8 + - - -
199B ARG 3.3 3.6 - - - -
200B GLU* 1.3 79.0 - - - +
202B SER* 1.3 59.8 + - - +
203B TYR* 3.0 11.1 + - - +
235B HIS* 3.4 30.3 + - - -
238B ILE* 4.1 11.4 - - - +
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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