Contacts of the helix formed by residues 198 - 209 (chain B) in PDB entry 1O69
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 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B ASN* 3.8 2.2 - - - -
174B GLU* 3.3 21.1 + - - +
175B PHE* 6.4 0.2 - - - -
196B GLY 3.5 0.6 - - - -
197B LYS* 1.3 77.1 - - - +
199B LYS* 1.3 66.6 + - - +
200B GLU* 3.0 17.9 + - - +
201B LYS* 2.9 46.1 + - + +
202B ILE* 3.0 25.5 + - - +
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Residues in contact with LYS 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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49B ASN* 3.4 29.1 - - - +
197B LYS 3.8 1.4 + - - -
198B ASN* 1.3 72.4 + - - +
200B GLU* 1.3 58.0 + - - +
202B ILE* 3.3 2.6 + - - +
203B GLU* 2.9 51.9 + - + +
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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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198B ASN* 3.0 10.4 + - - +
199B LYS* 1.3 79.3 - - - +
201B LYS* 1.3 60.4 + - + +
203B GLU* 3.3 6.2 + - - +
204B LYS* 2.9 30.0 + - + +
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Residues in contact with LYS 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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66B VAL* 3.6 38.2 - - + +
67B ALA* 5.3 3.6 - - - +
151B VAL* 6.0 3.8 - - - +
174B GLU* 3.8 29.6 + - - +
175B PHE* 3.9 22.9 - - + -
198B ASN* 2.9 28.5 + - + +
200B GLU* 1.3 78.0 - - + +
202B ILE* 1.3 65.1 + - - +
204B LYS* 3.2 4.5 + - - +
205B ALA* 3.0 20.3 + - - +
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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
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49B ASN* 3.7 29.4 - - + -
50B ALA 4.3 7.9 - - - +
51B LEU* 4.1 18.7 - - + +
175B PHE* 3.8 17.3 - - + -
194B LEU* 3.7 32.3 - - + +
195B ILE* 3.7 19.1 - - - +
196B GLY* 3.8 8.7 - - - +
198B ASN 3.0 19.6 + - - +
199B LYS 4.0 2.2 - - - +
201B LYS* 1.3 76.4 - - - +
203B GLU* 1.3 69.9 + - - +
205B ALA* 3.2 4.6 + - - +
206B ARG* 2.9 27.3 + - - +
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Residues in contact with GLU 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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49B ASN* 5.1 4.0 - - - +
199B LYS* 2.9 41.3 + - + +
200B GLU* 3.9 5.8 - - - +
202B ILE* 1.3 85.0 - - - +
204B LYS* 1.3 56.8 + - - +
206B ARG* 2.9 50.2 + - - +
207B PHE* 2.9 27.5 + - - +
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Residues in contact with LYS 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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66B VAL* 4.1 12.1 - - + -
200B GLU* 2.9 18.3 + - + +
201B LYS* 3.5 8.5 - - - +
203B GLU* 1.3 75.2 - - - +
205B ALA* 1.3 66.7 + - - +
207B PHE* 3.2 33.3 + - + +
208B TYR* 2.9 57.6 + - + -
223B ASP* 5.0 1.5 + - - -
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Residues in contact with ALA 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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51B LEU* 3.6 16.6 - - + -
62B LEU* 3.5 11.6 - - + +
66B VAL* 3.8 17.3 - - + +
175B PHE* 5.8 0.4 - - + -
194B LEU* 3.7 21.5 - - + -
201B LYS 3.0 13.1 + - - +
202B ILE 3.5 8.7 - - - +
204B LYS* 1.3 76.5 - - - +
206B ARG* 1.3 56.5 + - - +
208B TYR* 3.1 8.3 + - - +
209B SER* 2.9 28.9 + - - -
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Residues in contact with ARG 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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38B GLU* 3.1 21.1 + - - -
50B ALA 3.0 26.1 + - - +
51B LEU* 3.5 21.8 - - + +
202B ILE* 2.9 15.6 + - - +
203B GLU* 2.9 46.0 + - - +
204B LYS 3.2 0.2 - - - -
205B ALA* 1.3 76.0 - - - +
207B PHE* 1.3 61.7 + - - +
209B SER* 2.7 21.2 + - - -
210B THR* 3.5 10.4 + - + +
229B ARG* 2.7 48.4 - - - +
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Residues in contact with PHE 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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203B GLU 2.9 13.6 + - - +
204B LYS* 3.3 42.4 - - + +
206B ARG* 1.3 76.1 - - - +
208B TYR* 1.3 73.9 + + - +
209B SER 3.3 0.5 + - - -
210B THR* 3.4 11.6 + - - +
212B ALA* 3.0 64.7 + - + -
213B ARG 3.6 15.9 + - - -
214B GLU* 3.4 25.8 - - - -
222B LEU* 5.6 1.3 - - + -
223B ASP* 4.5 12.6 - - + -
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Residues in contact with TYR 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* 3.8 17.7 - - + -
65B ARG* 3.4 39.7 + - + +
66B VAL* 4.0 17.9 - - + -
204B LYS* 2.9 51.9 + - + -
205B ALA* 3.1 7.8 + - - +
207B PHE* 1.3 93.0 - + - +
209B SER* 1.3 58.8 + - - +
210B THR 3.2 1.1 + - - -
211B GLN 3.4 1.9 + - - -
212B ALA* 4.3 1.8 - - + +
223B ASP* 2.9 22.5 + - - -
224B TYR 3.5 26.5 - - - -
225B GLY* 3.5 2.4 - - - -
226B TYR* 2.8 38.8 + + + -
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Residues in contact with SER 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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53B LEU* 3.5 28.9 - - - +
62B LEU* 3.9 4.9 - - - -
205B ALA 2.9 13.8 + - - -
206B ARG* 2.7 21.4 + - - -
208B TYR* 1.3 78.0 - - - +
210B THR* 1.3 56.7 + - - +
226B TYR* 3.1 5.8 - - - +
227B ASN* 3.8 2.1 - - - +
228B TYR* 3.0 32.4 + - - -
229B ARG* 3.0 29.7 + - - +
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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