Contacts of the helix formed by residues 192 - 202 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A ILE* 3.0 43.5 + - + +
184A ASN* 3.0 41.4 + - - -
187A MET* 3.2 25.8 + - - +
188A ASP 3.4 3.0 + - - -
189A ALA* 3.3 13.8 + - - +
190A ASP 3.2 1.6 - - - -
191A MET* 1.3 76.5 - - - +
193A GLN* 1.3 64.7 + - - +
194A PRO* 3.2 4.3 - - - -
195A ILE* 2.9 27.3 + - + +
196A LEU 3.9 0.9 + - - -
333A PHE* 3.8 4.7 - - - -
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Residues in contact with GLN 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ALA 4.4 1.6 + - - -
190A ASP 3.6 13.0 + - - +
191A MET 3.3 0.8 - - - -
192A ASN* 1.3 77.3 - - - +
194A PRO* 1.4 68.4 - - + +
196A LEU* 2.9 42.8 + - - +
197A ASP* 2.9 39.2 + - - +
200A ASP* 5.3 2.8 + - - -
206A TYR* 5.5 0.4 + - - -
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Residues in contact with PRO 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ASP 5.1 0.2 - - - +
191A MET* 3.4 13.7 - - - +
192A ASN 3.3 4.7 - - - -
193A GLN* 1.4 91.7 - - + +
195A ILE* 1.3 55.5 + - - +
196A LEU 3.3 0.2 - - - -
197A ASP* 3.6 14.9 - - + +
198A GLU* 2.9 34.0 + - - +
331A TYR* 3.7 37.9 - - + -
333A PHE* 3.9 7.6 - - + -
387A VAL* 4.0 15.7 - - + -
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Residues in contact with ILE 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LEU* 3.9 24.9 - - + -
176A LEU* 5.5 0.9 - - + -
183A ILE* 4.0 17.3 - - + -
184A ASN* 3.6 25.1 - - + +
192A ASN* 2.9 37.5 + - - +
194A PRO* 1.3 78.2 - - - +
196A LEU* 1.3 63.4 + - + +
198A GLU 3.3 0.2 + - - -
199A LEU* 3.1 31.1 + - + +
326A VAL* 6.0 0.2 - - + -
328A PHE* 3.5 31.8 - - + -
333A PHE* 3.5 22.4 - - + -
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU* 5.7 1.1 - - + -
183A ILE* 3.9 28.3 - - + -
192A ASN 4.6 1.6 - - - +
193A GLN* 2.9 33.6 + - - +
195A ILE* 1.3 73.7 - - + +
197A ASP* 1.3 61.3 + - - +
199A LEU* 3.2 15.3 + - + +
200A ASP* 2.9 35.6 + - - +
206A TYR* 3.6 48.9 - - + +
208A LEU* 4.4 15.7 - - + -
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Residues in contact with ASP 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLN* 2.9 44.4 + - - +
194A PRO* 3.6 19.2 - - + +
196A LEU* 1.3 76.6 - - - +
198A GLU* 1.3 60.1 + - + +
200A ASP* 3.3 9.7 + - - +
201A LYS* 2.8 30.7 + - - +
331A TYR* 5.7 4.5 + - + +
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Residues in contact with GLU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A PRO 2.9 21.2 + - - +
195A ILE 3.7 4.3 - - - +
196A LEU 3.3 0.2 - - - -
197A ASP* 1.3 75.4 - - - +
199A LEU* 1.3 67.8 + - - +
201A LYS* 3.5 13.7 + - - +
202A ARG* 3.0 55.8 + - - +
328A PHE* 4.0 8.7 - - + +
329A PHE* 3.2 22.1 - - + +
330A ASP* 2.9 38.0 + - - +
331A TYR* 3.7 25.3 - - + -
389A LYS* 5.9 0.2 - - - -
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Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 3.8 13.5 - - + -
176A LEU* 4.0 23.8 - - + -
195A ILE* 3.1 25.2 + - + +
196A LEU* 3.5 16.2 - - + +
198A GLU* 1.3 75.5 - - - +
200A ASP* 1.3 63.3 + - - +
202A ARG* 3.2 3.3 + - - -
203A GLU 3.1 3.6 + - - -
204A ILE* 3.0 66.3 + - + +
206A TYR* 3.8 26.9 - - + -
328A PHE* 3.7 23.6 - - + -
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Residues in contact with ASP 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLN* 5.3 2.1 + - - -
196A LEU* 2.9 21.5 + - - +
197A ASP* 3.6 10.2 - - - +
199A LEU* 1.3 77.6 - - - +
201A LYS* 1.3 61.6 + - - +
203A GLU* 3.1 19.4 + - - +
204A ILE 5.1 1.5 - - - +
206A TYR* 3.5 27.1 + - - -
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Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ASP 2.8 20.2 + - - +
198A GLU* 3.8 20.5 + - - +
199A LEU 3.3 0.4 - - - -
200A ASP* 1.3 73.8 - - - +
202A ARG* 1.3 75.3 + - + +
203A GLU* 3.4 4.4 + - - +
330A ASP* 4.1 16.6 + - - -
389A LYS* 5.2 8.1 - - - +
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Residues in contact with ARG 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A TYR* 3.6 35.2 + - + +
169A GLU* 5.1 0.6 + - - -
198A GLU* 3.0 63.9 + - - +
199A LEU 3.2 1.8 + - - -
200A ASP 3.1 0.8 - - - -
201A LYS* 1.3 95.8 - - + +
203A GLU* 1.3 72.2 + - - +
204A ILE* 3.2 14.1 + - + +
329A PHE* 3.3 47.7 - - - +
330A ASP* 3.4 19.2 + - - -
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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