Contacts of the helix formed by residues 192 - 202 (chain B) in PDB entry 1YQZ
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 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B ILE* 3.0 43.9 + - + +
184B ASN* 2.9 40.7 + - - +
187B MET* 3.3 16.3 + - - +
188B ASP 3.7 13.3 + - - -
189B ALA* 3.8 13.6 + - - +
190B ASP 3.5 0.8 - - - -
191B MET* 1.3 76.9 - - - +
193B GLN* 1.3 65.2 + - - +
194B PRO* 3.1 4.9 - - - -
195B ILE* 2.9 26.0 + - + +
196B LEU 3.9 1.2 + - - -
333B PHE* 3.8 5.2 - - - -
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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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189B ALA 5.1 1.0 + - - -
190B ASP 4.9 6.4 + - - +
191B MET 3.5 1.2 - - - +
192B ASN* 1.3 74.7 - - - +
194B PRO* 1.3 69.4 - - + +
196B LEU* 3.0 32.0 + - - +
197B ASP* 2.9 48.5 + - - +
200B ASP* 5.5 2.0 + - - -
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Residues in contact with PRO 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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191B MET 3.6 12.6 - - - +
192B ASN 3.2 5.4 - - - -
193B GLN* 1.3 94.5 - - + +
195B ILE* 1.3 60.5 + - - +
197B ASP* 3.6 14.0 - - + +
198B GLU* 2.9 31.2 + - - +
331B TYR* 3.7 44.0 - - + +
333B PHE* 3.9 7.4 - - + -
387B VAL* 4.1 11.9 - - + -
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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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161B LEU* 4.0 24.7 - - + -
176B LEU* 5.4 1.6 - - + -
183B ILE* 3.9 21.1 - - + -
184B ASN* 3.6 35.9 - - + +
192B ASN* 2.9 24.6 + - - +
194B PRO* 1.3 78.0 - - - +
196B LEU* 1.3 65.6 + - + +
198B GLU 3.3 0.2 + - - -
199B LEU* 3.1 31.7 + - + +
328B PHE* 3.5 29.9 - - + -
333B PHE* 3.5 22.9 - - + -
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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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176B LEU* 5.7 2.0 - - + -
183B ILE* 4.1 25.8 - - + -
192B ASN 4.8 1.8 - - - +
193B GLN* 3.0 31.8 + - - +
195B ILE* 1.3 79.2 - - + +
197B ASP* 1.3 62.2 + - - +
199B LEU* 3.3 15.4 + - + +
200B ASP* 3.0 30.0 + - - +
206B TYR* 3.7 46.6 - - + +
208B LEU* 4.3 18.8 - - + -
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Residues in contact with ASP 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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193B GLN* 2.9 48.1 + - - +
194B PRO* 3.7 15.5 - - + +
196B LEU* 1.3 76.8 - - - +
198B GLU* 1.3 59.8 + - + +
200B ASP* 3.3 9.3 + - - +
201B LYS* 2.8 31.2 + - - +
331B TYR* 5.5 5.8 + - + +
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Residues in contact with GLU 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 PRO 2.9 20.8 + - - +
195B ILE 3.7 4.5 - - - +
197B ASP* 1.3 76.3 - - + +
199B LEU* 1.3 64.6 + - - +
201B LYS* 3.8 16.2 + - - +
202B ARG* 3.0 54.6 + - - +
328B PHE* 4.0 17.9 - - + +
329B PHE* 3.3 13.8 - - + +
330B ASP* 2.9 37.1 + - - +
331B TYR* 3.7 27.1 - - + -
389B LYS* 5.4 0.7 - - - -
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Residues in contact with LEU 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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164B LEU* 4.0 13.5 - - + -
176B LEU* 4.0 23.8 - - + -
195B ILE* 3.1 21.7 + - + +
196B LEU* 3.6 16.8 - - + +
197B ASP 3.3 0.2 - - - -
198B GLU* 1.3 76.8 - - - +
200B ASP* 1.3 63.0 + - - +
202B ARG* 3.2 3.1 + - - -
203B GLU 3.0 3.5 + - - -
204B ILE* 2.9 68.2 + - + +
205B PRO 5.3 0.2 - - - +
206B TYR* 3.9 24.7 - - + -
328B PHE* 3.8 21.3 - - + -
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Residues in contact with ASP 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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193B GLN* 5.5 1.4 + - - -
196B LEU* 3.0 22.3 + - - +
197B ASP* 3.6 10.0 - - - +
199B LEU* 1.3 78.5 - - - +
201B LYS* 1.3 63.2 + - - +
203B GLU* 2.9 21.6 + - - +
204B ILE 5.1 1.3 - - - +
206B TYR* 3.4 27.4 + - - -
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Residues in contact with LYS 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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197B ASP 2.8 17.9 + - - +
198B GLU* 3.8 21.7 + - - +
199B LEU 3.3 0.2 - - - -
200B ASP* 1.3 76.3 - - - +
202B ARG* 1.3 70.9 + - + +
203B GLU* 3.4 4.0 + - - +
330B ASP* 4.2 15.8 + - - -
389B LYS* 4.7 12.3 - - - +
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Residues in contact with ARG 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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168B TYR* 3.8 31.3 + - - +
169B GLU* 5.4 0.2 + - - -
198B GLU* 3.0 56.9 + - - +
199B LEU 3.2 2.0 + - - -
200B ASP 3.1 0.4 - - - -
201B LYS* 1.3 95.4 - - + +
203B GLU* 1.3 70.5 + - - +
204B ILE* 3.2 16.2 + - + +
329B PHE* 3.3 43.8 - - - +
330B ASP* 3.3 29.3 + - - -
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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