Contacts of the strand formed by residues 197 - 208 (chain B) in PDB entry 3AGZ
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 ILE 197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188B LYS* 3.6 32.6 + - + +
189B ARG 4.0 5.2 - - - +
190B LEU* 3.8 25.4 - - + +
196B SER* 1.3 75.4 + - - +
198B ARG* 1.3 59.9 + - - +
226B GLN 3.5 18.4 - - - +
227B THR* 3.4 31.2 - - + +
228B SER 5.8 0.7 - - - +
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Residues in contact with ARG 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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188B LYS* 3.3 11.5 + - - +
189B ARG* 3.0 33.0 + - - +
190B LEU 4.1 9.5 + - - -
191B ASN* 3.9 24.8 + - - +
192B PRO* 3.7 34.7 - - - +
196B SER* 3.5 5.1 + - - +
197B ILE* 1.3 74.7 - - - +
199B ASN* 1.3 78.0 + - - +
200B GLU* 2.5 42.3 + - - +
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Residues in contact with ASN 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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186B SER* 3.8 23.8 + - - -
187B HIS 3.5 18.2 + - - -
188B LYS* 3.0 29.6 + - - +
198B ARG* 1.3 89.0 - - - +
200B GLU* 1.3 69.0 + - - +
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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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185B ILE 3.5 1.2 - - - +
186B SER* 3.1 5.5 - - - -
187B HIS* 3.0 49.3 + - + +
189B ARG* 3.4 25.8 - - + +
198B ARG* 2.5 38.7 + - - +
199B ASN* 1.3 80.8 - - - +
201B ASP* 1.3 67.3 + - - +
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Residues in contact with ASP 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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184B LYS* 2.9 33.6 + - - +
185B ILE 3.4 3.0 - - - +
186B SER* 2.9 28.8 + - - -
187B HIS* 5.3 0.2 + - - -
200B GLU* 1.3 77.4 - - - +
202B LYS* 1.3 64.6 + - - +
203B ILE* 5.9 1.3 - - + -
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Residues in contact with LYS 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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183B MET 3.6 0.2 - - - +
184B LYS* 3.3 4.8 - - - +
185B ILE* 3.0 44.2 + - + +
187B HIS* 4.2 11.4 - - + +
201B ASP* 1.3 78.8 - - - +
203B ILE* 1.3 72.3 + - - +
204B LEU* 4.0 14.5 - - + +
223B GLU* 2.9 41.1 + - - +
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Residues in contact with ILE 203 (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 LYS* 4.5 15.5 - - + +
183B MET 3.7 2.5 - - - +
184B LYS* 4.2 28.0 - - + -
201B ASP* 6.1 0.4 - - + -
202B LYS* 1.3 84.0 + - - +
204B LEU* 1.3 70.4 + - - +
205B THR* 3.6 22.1 + - - +
640D VAL* 4.6 15.7 - - + -
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Residues in contact with LEU 204 (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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181B LYS 3.5 1.4 - - - +
182B LYS* 3.5 0.7 - - - -
183B MET* 2.7 47.2 + - - +
185B ILE* 3.5 40.6 - - + -
202B LYS* 4.0 23.1 - - + +
203B ILE* 1.3 81.2 - - - +
205B THR* 1.3 59.9 + - - +
206B ILE* 4.0 0.6 + - - -
220B PHE* 3.7 39.7 - - + -
223B GLU* 4.4 9.6 - - + -
235B ILE* 4.8 3.4 - - + -
237B PHE* 3.9 28.5 - - + -
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Residues in contact with THR 205 (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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180B THR* 3.7 17.7 - - + -
181B LYS 3.4 4.9 - - - +
182B LYS* 4.1 12.1 - - + +
203B ILE* 3.6 21.3 + - - +
204B LEU* 1.3 69.9 - - - +
206B ILE* 1.3 62.3 + - - +
207B GLU* 3.4 26.8 + - - +
220B PHE* 3.8 14.3 - - - -
634F GLY* 5.1 1.4 + - - -
635F PRO* 4.3 7.6 - - - +
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Residues in contact with ILE 206 (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 LEU* 3.7 28.9 - - + -
180B THR* 3.5 2.3 - - - +
181B LYS* 2.8 47.1 + - + +
183B MET* 4.4 6.5 - - + -
204B LEU 4.6 3.4 - - - +
205B THR* 1.3 75.2 - - - +
207B GLU* 1.3 72.6 + - - +
208B VAL* 3.5 10.6 + - + +
212B TRP* 4.6 1.3 - - + -
218B ILE* 3.8 28.9 - - + -
220B PHE* 3.8 17.0 - - + -
237B PHE* 3.5 42.8 - - + -
635F PRO* 5.3 1.8 - - + -
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Residues in contact with GLU 207 (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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179B CYS 3.7 4.0 - - - +
180B THR* 2.5 32.8 + - - +
205B THR* 3.4 26.0 + - + +
206B ILE* 1.3 71.9 - - - +
208B VAL* 1.3 59.9 + - - +
209B LYS* 3.2 11.8 + - + +
212B TRP* 3.6 15.9 - - - -
635F PRO* 6.0 1.0 - - - +
637F ILE* 5.6 0.7 - - - +
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Residues in contact with VAL 208 (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 LEU* 4.3 16.8 - - + -
170B VAL* 4.4 9.2 - - + -
174B GLU 4.9 3.6 - - - +
175B ILE* 4.2 13.2 - - + -
178B GLY* 3.3 2.6 - - - -
179B CYS* 2.8 53.9 + - - +
181B LYS* 4.4 9.6 - - + -
206B ILE* 3.5 16.4 + - + +
207B GLU* 1.3 69.2 - - - +
209B LYS* 1.3 77.5 + - - +
212B TRP* 4.0 7.9 - - + -
218B ILE* 6.0 0.2 - - + -
239B LEU* 4.2 21.8 - - + -
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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