Contacts of the strand formed by residues 211 - 217 (chain B) in PDB entry 6O81
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 ARG 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B VAL* 3.4 1.9 - - - -
206B ASP* 3.0 40.0 + - + +
209B THR* 3.1 19.8 + - + -
210B ASN* 1.3 74.2 - - - +
212B VAL* 1.3 66.3 + - - +
213B LEU* 3.4 28.8 + - + +
233B GLY 5.2 4.0 + - - -
234B SER* 4.4 17.8 - - - -
280B GLU* 4.0 17.0 + - - -
286B GLN* 2.6 42.2 + - + +
287B ILE 3.4 8.7 - - - +
288B HIS* 3.5 20.4 - - + +
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B MET* 4.5 13.0 - - + -
185B PHE* 5.8 0.2 - - + -
203B VAL* 4.9 4.0 - - + -
205B VAL* 3.7 13.7 - - + -
211B ARG* 1.3 76.8 + - - +
213B LEU* 1.3 66.1 + - - +
214B HIS 3.6 24.0 - - - +
215B PHE* 4.3 8.1 - - + -
273B VAL* 5.4 0.4 - - + -
277B LEU* 3.4 23.5 - - + +
280B GLU* 5.4 0.9 - - - +
286B GLN* 5.6 0.7 - - - -
287B ILE* 2.5 39.8 + - + +
288B HIS 4.0 6.3 - - - +
289B MET* 3.8 31.4 - - + -
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ALA 2.9 11.3 + - - +
205B VAL 4.4 7.6 - - - -
206B ASP* 4.6 4.0 - - + +
211B ARG* 3.4 49.8 - - + +
212B VAL* 1.3 79.5 - - - +
214B HIS* 1.3 64.1 + - - +
230B LEU* 3.4 57.3 - - + +
234B SER* 4.8 8.5 - - - -
237B GLY 5.1 0.2 - - - +
238B VAL* 4.1 23.1 - - + -
277B LEU* 3.4 23.9 - - - +
280B GLU* 5.7 1.8 - - - +
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Residues in contact with HIS 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 3.3 5.9 - - - +
204B ALA* 2.9 38.6 + - + +
212B VAL* 3.6 3.9 - - - +
213B LEU* 1.3 78.6 + - - +
215B PHE* 1.3 75.9 + - - +
216B GLN* 3.3 35.4 + - + +
225B ALA 4.0 4.1 + - - -
226B PHE* 3.5 23.8 - + + -
227B PRO* 3.4 33.0 - - + +
230B LEU* 3.8 14.6 - - + +
274B ARG* 6.4 0.9 - - + -
277B LEU* 3.8 8.3 - - - +
278B VAL* 6.0 6.8 - - + +
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Residues in contact with PHE 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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183B MET* 3.8 23.6 - - + -
185B PHE* 4.3 2.7 - + - -
201B VAL* 3.6 24.7 - - + -
202B VAL 3.8 3.8 - - - -
203B VAL* 3.7 19.1 - - + -
212B VAL* 4.3 5.8 - - + -
214B HIS* 1.3 85.1 + - - +
216B GLN* 1.3 67.9 + - - +
217B LYS* 4.7 13.9 - - + -
246B ASP* 4.7 7.0 - - - -
269B ARG* 4.8 5.2 - - - -
270B ASP* 3.7 41.1 - - + -
273B VAL* 3.7 24.5 - - + -
274B ARG* 3.5 19.8 - - + +
277B LEU* 3.8 16.5 - - + +
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Residues in contact with GLN 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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201B VAL* 3.5 8.1 - - - +
202B VAL* 2.9 45.0 + - + +
214B HIS* 3.3 20.4 + - + +
215B PHE* 1.3 81.5 - - - +
217B LYS* 1.3 70.8 - - - +
224B PHE* 4.0 18.4 - - - +
225B ALA 3.5 20.9 + - - +
226B PHE* 3.8 24.0 - - + -
274B ARG* 5.0 9.6 - - - +
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Residues in contact with LYS 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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198B GLU 4.9 12.1 - - - +
199B ASP* 4.9 13.9 + - - +
200B ASN 3.3 14.1 - - - +
201B VAL* 3.5 22.6 - - + +
202B VAL* 4.9 1.4 - - - +
215B PHE* 4.7 8.3 - - + -
216B GLN* 1.3 88.3 - - - +
218B THR* 1.3 62.9 + - - +
219B GLN* 3.4 16.1 + - + +
221B LEU* 5.0 4.2 - - - +
224B PHE* 4.9 3.1 - - - -
246B ASP* 5.0 4.8 + - - +
248B HIS* 5.0 10.3 + - - -
269B ARG* 5.9 0.2 - - - +
270B ASP* 3.6 34.7 - - - +
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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