Contacts of the helix formed by residues 204 - 215 (chain B) in PDB entry 1FUU
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 PRO 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172B ASP* 4.4 7.2 - - + -
202B THR* 3.1 25.6 - - - +
203B MSE 1.3 92.4 - - - +
205B ASN* 1.3 68.4 - - - +
206B ASP* 3.0 17.5 - - + +
207B VAL* 2.9 29.3 + - + +
208B LEU* 3.1 9.0 + - - -
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Residues in contact with ASN 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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204B PRO* 1.3 72.4 - - - +
206B ASP* 1.3 58.8 + - - +
208B LEU* 3.3 25.5 - - + +
209B GLU* 2.8 32.3 + - - +
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Residues in contact with ASP 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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172B ASP* 6.1 0.4 - - - -
175B LEU* 3.5 36.3 - - + +
176B SER* 5.7 3.5 + - - -
180B LYS* 5.6 6.9 + - + +
184B TYR* 4.8 0.7 + - - -
204B PRO* 2.9 16.3 + - + +
205B ASN* 1.3 79.6 - - - +
207B VAL* 1.3 61.2 + - - +
209B GLU* 3.5 8.1 + - - +
210B VAL* 3.3 19.4 + - - +
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Residues in contact with VAL 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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171B ALA* 3.9 10.8 - - + -
172B ASP* 3.9 28.7 - - - +
175B LEU* 4.0 9.6 - - + -
198B LEU* 3.7 29.6 - - + -
200B SER* 4.0 8.5 - - - +
203B MSE 3.7 22.4 - - - -
204B PRO* 2.9 20.4 + - + +
206B ASP* 1.3 73.6 - - - +
208B LEU* 1.3 57.5 + - + +
210B VAL* 3.1 5.7 + - - +
211B THR* 2.7 42.5 + - - +
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Residues in contact with LEU 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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62B LEU* 5.8 2.5 - - + -
203B MSE 3.8 28.9 - - + +
204B PRO 3.1 12.3 + - - +
205B ASN* 3.3 36.6 - - - +
207B VAL* 1.3 76.2 - - - +
209B GLU* 1.3 58.1 + - - +
211B THR* 3.3 12.8 + - + +
212B THR* 2.8 33.2 + - - +
220B ARG* 5.7 4.7 - - - +
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Residues in contact with GLU 209 (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 LYS* 3.4 23.2 + - - -
184B TYR* 2.9 24.1 + - - +
205B ASN 2.8 18.2 + - - +
206B ASP* 3.5 8.4 - - - +
207B VAL 3.1 0.2 - - - -
208B LEU* 1.3 77.2 - - - +
210B VAL* 1.3 56.2 + - - +
212B THR* 2.9 25.0 - - + +
213B LYS* 2.9 34.1 + - + +
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Residues in contact with VAL 210 (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* 4.2 7.2 - - + -
175B LEU* 4.5 16.6 - - + -
183B ILE* 5.4 4.0 - - + -
184B TYR* 3.6 33.2 - - + +
187B PHE* 4.2 13.5 - - + -
198B LEU* 4.1 11.2 - - + -
206B ASP 3.3 10.7 + - - +
207B VAL* 3.1 9.6 + - - +
209B GLU* 1.3 76.2 - - - +
211B THR* 1.3 66.1 + - - +
213B LYS 3.2 0.2 + - - -
214B PHE* 2.8 44.2 + - + +
215B MSE 3.9 14.9 + - + +
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Residues in contact with THR 211 (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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62B LEU* 3.5 20.1 - - + +
207B VAL* 2.7 29.6 + - - +
208B LEU* 3.3 12.1 - - + +
210B VAL* 1.3 73.9 - - - +
212B THR* 1.3 59.0 + - - +
215B MSE 3.2 56.1 + - + +
218B PRO* 4.7 4.2 - - + +
220B ARG* 3.5 35.4 - - - +
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Residues in contact with THR 212 (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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208B LEU 2.8 21.2 + - - +
209B GLU* 2.9 31.0 - - + +
211B THR* 1.3 78.0 - - - +
213B LYS* 1.3 66.4 + - + +
215B MSE 4.3 6.4 - - - +
216B ARG* 5.6 1.2 + - - -
220B ARG* 6.1 0.9 - - - +
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Residues in contact with LYS 213 (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 TYR* 3.2 32.7 - - + -
209B GLU* 2.9 41.1 + - + +
212B THR* 1.3 82.2 - - + +
214B PHE* 1.3 80.2 + - + +
216B ARG* 4.0 15.7 + - - -
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Residues in contact with PHE 214 (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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60B ASP* 4.3 1.0 - - - +
184B TYR* 3.7 53.4 - + + -
187B PHE* 3.4 69.4 - + + -
188B THR* 5.2 5.6 - - + -
196B VAL* 4.2 11.3 - - - +
210B VAL* 2.8 25.1 + - + +
213B LYS* 1.3 94.8 - - + +
215B MSE 1.3 61.5 + - + +
216B ARG* 3.7 19.5 + - - +
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Residues in contact with MSE 215 (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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60B ASP* 3.4 7.9 - - + +
61B VAL 4.1 19.3 - - - +
62B LEU* 4.2 11.7 - - + -
196B VAL* 3.8 29.4 - - + +
198B LEU* 3.5 33.0 - - + -
210B VAL* 3.9 7.4 + - + -
211B THR* 3.2 58.2 + - - +
212B THR 4.3 7.3 - - - +
214B PHE* 1.3 77.8 - - - +
216B ARG* 1.3 69.5 + - - +
217B ASN 4.1 1.8 + - - -
218B PRO* 4.1 21.7 - - + +
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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