Contacts of the helix formed by residues 197 - 202 (chain B) in PDB entry 2YZ2
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 197 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B LEU* 4.7 8.5 - - + -
174B LYS* 3.2 26.9 + - - +
195B SER* 3.0 18.4 + - - +
196B HIS* 1.3 75.3 - - - +
198B ILE* 1.3 62.3 + - - +
199B GLU* 3.1 7.5 + - - +
200B THR* 2.9 38.5 + - - -
201B VAL* 3.2 9.4 + - - +
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Residues in contact with ILE 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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37B LEU* 3.7 28.7 - - + -
39B ALA* 3.6 30.7 - - + -
40B GLY 5.5 0.4 - - - +
46B LYS* 5.8 1.3 - - - +
195B SER 3.0 26.7 - - - +
196B HIS* 2.9 17.9 + - - +
197B ASP* 1.3 69.3 - - - +
199B GLU* 1.3 63.1 + - - +
201B VAL* 3.1 2.1 + - - +
202B ILE* 3.0 30.2 + - + +
225B PHE* 3.9 30.3 - - + -
238B MET* 4.5 14.8 - - + -
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Residues in contact with GLU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLU* 4.9 8.7 - - - +
235A THR* 5.6 4.9 - - - -
236A SER* 4.8 2.6 + - - -
197B ASP* 3.1 6.4 - - - +
198B ILE* 1.3 80.5 - - - +
200B THR* 1.3 64.1 + - - +
202B ILE* 3.4 15.0 - - - +
203B ASN* 4.3 8.0 + - - -
235B THR* 3.5 34.5 + - + +
237B LYS* 2.9 42.6 - - + +
238B MET* 3.8 19.2 - - + +
241B MET* 4.7 1.7 - - + +
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Residues in contact with THR 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 LEU* 4.0 11.4 - - + -
171B ARG* 2.8 39.7 + - - +
174B LYS* 4.6 3.3 - - + +
178B LEU* 3.3 27.6 - - + -
197B ASP* 2.9 36.0 + - - -
199B GLU* 1.3 78.0 - - - +
201B VAL* 1.3 60.7 + - - +
203B ASN* 3.9 8.5 + - - +
204B HIS* 3.8 13.7 + - + -
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.0 24.0 - - + -
165B PRO* 6.0 1.1 - - + -
166B LEU* 3.9 19.7 - - + -
178B LEU* 3.7 25.1 - - + -
193B LEU* 3.2 37.2 - - + -
195B SER* 4.2 8.5 - - - +
197B ASP 3.2 9.4 + - - +
198B ILE 3.1 3.0 + - - +
200B THR* 1.3 74.2 - - - +
202B ILE* 1.3 58.1 + - - +
203B ASN 3.0 2.9 - - - -
204B HIS* 2.7 35.1 + - + +
205B VAL* 3.4 6.4 + - + -
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Residues in contact with ILE 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 5.1 2.0 - - + +
198B ILE* 3.0 18.3 + - + +
199B GLU* 3.4 21.3 - - - +
201B VAL* 1.3 77.4 - - - +
203B ASN* 1.3 62.3 + - - +
204B HIS 3.1 1.4 + - - -
205B VAL* 3.4 12.5 + - - +
208B VAL* 3.9 10.8 - - + -
222B ARG* 3.1 51.2 - - + +
225B PHE* 3.5 35.7 - - + -
226B LEU* 4.9 4.7 - - + -
238B MET* 5.3 2.2 - - + -
241B MET* 4.2 21.3 - - + -
252B PHE* 3.6 20.6 - - + -
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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