Contacts of the helix formed by residues 210 - 219 (chain B) in PDB entry 1OFU
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 210 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B ILE 6.0 1.1 - - - -
201B ILE* 6.0 1.3 - - - -
208B ASN 4.2 0.4 - - - -
209B VAL* 1.3 76.1 - - - +
211B PHE* 1.3 65.5 + - - +
212B ALA* 3.2 15.4 + - - +
213B ASP* 2.6 51.4 + - - +
214B VAL* 3.3 14.3 + - - +
90Y GLU* 5.1 0.9 - - - +
93Y ARG* 3.9 32.5 + - - +
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Residues in contact with PHE 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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12B ALA* 4.3 15.3 - - + -
14B ILE* 5.6 0.2 - - + -
97B ASP* 3.6 33.9 - - + -
98B MET* 4.2 13.2 - - + -
127B LEU* 4.1 8.1 - - + -
201B ILE* 3.6 48.9 - - + +
210B ASP* 1.3 74.8 - - - +
212B ALA* 1.3 64.8 + - - +
214B VAL* 3.0 9.8 + - + +
215B LYS* 2.9 52.7 + - + +
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Residues in contact with ALA 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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210B ASP* 3.2 15.1 + - - +
211B PHE* 1.3 82.6 - - - +
213B ASP* 1.3 60.2 + - - +
215B LYS* 3.4 9.8 + - - +
216B THR* 2.9 26.8 + - - -
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Residues in contact with ASP 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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208B ASN 3.5 8.3 - - - +
209B VAL* 3.4 20.6 - - + -
210B ASP* 2.6 47.6 + - - +
212B ALA* 1.3 70.5 - - - +
214B VAL* 1.3 66.2 + - - +
216B THR* 3.1 21.4 + - - -
217B VAL* 3.3 11.3 + - - +
294B LYS* 3.1 33.5 + - + +
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Residues in contact with VAL 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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98B MET* 4.9 3.6 - - + -
127B LEU* 5.1 2.0 - - + -
197B ILE* 4.2 9.2 - - + -
200B ILE* 3.8 28.7 - - + -
201B ILE* 4.0 32.1 - - + -
209B VAL* 4.2 5.2 - - + -
210B ASP 3.7 11.4 - - - +
211B PHE* 3.0 7.8 + - + +
213B ASP* 1.3 77.2 - - - +
215B LYS* 1.3 62.6 + - - +
217B VAL* 3.0 9.3 + - - +
218B MET* 2.9 28.2 + - + +
262B LEU* 4.1 26.9 - - + -
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Residues in contact with LYS 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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125B GLY 5.5 4.4 + - - -
127B LEU* 3.7 33.5 - - + +
211B PHE* 2.9 43.8 + - + +
212B ALA* 3.6 11.7 - - - +
214B VAL* 1.3 76.1 - - - +
216B THR* 1.3 60.0 + - - +
218B MET 3.0 0.4 + - - +
219B SER* 2.6 53.7 + - - +
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Residues in contact with THR 216 (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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212B ALA 2.9 14.9 + - - -
213B ASP* 3.1 13.1 + - - -
215B LYS* 1.3 79.2 - - - +
217B VAL* 1.3 61.4 + - - +
219B SER* 4.4 5.1 + - - +
221B MET* 4.3 9.5 - - - +
292B THR* 3.9 27.6 + - + +
294B LYS* 5.3 3.6 - - - +
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Residues in contact with VAL 217 (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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213B ASP 3.7 11.9 - - - +
214B VAL* 3.0 8.8 + - - +
216B THR* 1.3 76.6 - - - +
218B MET* 1.3 61.0 + - - +
221B MET* 3.4 11.3 - - - +
260B GLY* 4.1 2.9 - - - -
261B ILE 3.9 12.8 - - - +
262B LEU* 3.9 26.5 - - + +
292B THR* 4.1 22.0 - - + +
294B LYS* 4.1 27.1 - - + -
314B THR* 2.7 46.3 + - + +
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Residues in contact with MET 218 (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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98B MET* 4.3 6.5 - - + -
127B LEU* 4.1 17.5 - - + -
129B VAL* 3.6 28.5 - - + -
159B ASP* 3.4 11.6 - - - +
160B SER* 2.8 35.9 + - - +
162B ILE* 5.2 1.6 - - + -
197B ILE* 3.9 21.1 - - + -
214B VAL* 2.9 18.7 + - + +
215B LYS 4.0 0.4 - - - +
217B VAL* 1.3 82.4 - - - +
219B SER* 1.3 64.3 + - - +
221B MET* 3.6 1.3 - - - +
224B ALA* 5.0 1.3 - - + -
262B LEU* 4.3 18.4 - - - -
312B VAL* 3.9 16.8 - - + -
314B THR* 3.3 29.6 - - + -
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Residues in contact with SER 219 (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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127B LEU* 4.0 8.5 - - - +
159B ASP* 3.3 14.4 + - - -
215B LYS* 2.6 39.4 + - - -
216B THR* 4.4 4.3 + - - +
217B VAL 3.8 0.2 - - - -
218B MET* 1.3 68.7 - - - +
220B GLU* 1.3 79.9 + - - +
221B MET* 2.7 16.0 + - - +
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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