Contacts of the helix formed by residues 209 - 219 (chain B) in PDB entry 3RIE
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 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205B GLU 4.6 2.8 + - - -
206B THR* 3.3 29.9 + - - +
208B PHE* 1.3 81.5 - - - +
210B GLN* 1.3 60.7 + - - +
211B ASN* 2.8 15.7 + - + +
212B PHE* 2.6 44.1 + - - +
213B TYR* 3.8 9.4 + - - -
246B TYR* 4.1 9.0 - - - -
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Residues in contact with GLN 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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209B ASN* 1.3 71.9 - - - +
211B ASN* 1.3 67.3 + - - +
212B PHE 3.2 0.7 - - - -
213B TYR* 3.3 4.1 + - - +
214B GLU* 3.0 18.5 + - + +
246B TYR* 3.5 61.9 + - + +
249B LYS* 3.8 24.0 - - - +
250B LEU* 3.5 24.8 - - - +
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Residues in contact with ASN 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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209B ASN* 2.8 12.9 + - - +
210B GLN* 1.3 82.1 - - - +
212B PHE* 1.3 60.1 + - - +
214B GLU* 3.2 22.6 + - - +
215B LYS* 3.0 53.7 + - - +
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Residues in contact with PHE 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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123B VAL* 4.2 16.4 - - + -
179B ALA 4.4 2.9 - - - -
180B SER* 4.4 15.0 - - - -
183B LEU* 3.7 21.1 - - + -
195B VAL* 4.1 17.7 - - + -
206B THR 4.2 6.1 - - - +
207B LEU* 3.2 58.8 - - + +
209B ASN* 2.6 25.2 + - - +
211B ASN* 1.3 72.2 + - - +
213B TYR* 1.3 68.9 + + - +
215B LYS* 3.0 14.5 + - + +
216B ILE* 2.8 56.1 + - + +
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Residues in contact with TYR 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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195B VAL* 5.2 1.8 - - + +
207B LEU 4.5 8.1 + - - -
208B PHE* 5.3 0.7 - - - -
209B ASN 3.8 13.5 - - - -
210B GLN* 3.3 10.1 + - - +
212B PHE* 1.3 88.9 - + - +
214B GLU* 1.3 61.8 + - - +
216B ILE* 3.6 11.3 - - + +
217B TYR* 2.8 30.0 + - - +
226B CYS* 4.6 13.0 - - - -
228B ALA* 3.2 25.6 - - + +
229B GLN 5.4 0.3 + - - -
243B MET* 4.8 18.5 - - + +
246B TYR* 5.0 9.9 - + + +
247B ALA* 4.5 11.2 - - + -
250B LEU* 3.5 16.1 - - + +
251B PHE* 4.2 19.8 - + + -
272B LEU* 3.7 25.0 - - + +
274B CYS* 4.2 12.3 - - - -
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Residues in contact with GLU 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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210B GLN* 3.0 16.2 + - - +
211B ASN* 3.2 27.3 + - - +
213B TYR* 1.3 77.6 - - - +
215B LYS* 1.3 62.4 + - + +
217B TYR* 3.4 2.6 + - - +
218B ASN* 3.1 43.5 + - - +
250B LEU* 3.6 25.5 - - + +
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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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180B SER* 2.9 45.3 + - - +
183B LEU* 3.9 25.9 - - + +
184B GLU* 3.5 33.8 + - - +
186B VAL 4.7 0.5 - - - +
211B ASN* 3.0 43.2 + - - +
212B PHE* 3.0 14.6 + - + +
214B GLU* 1.3 74.8 - - + +
216B ILE* 1.3 64.5 + - - +
218B ASN* 3.3 5.7 + - - +
219B ALA* 2.9 26.8 + - - +
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Residues in contact with ILE 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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183B LEU* 3.6 21.1 - - + -
193B ILE* 3.9 26.0 - - + -
195B VAL* 4.0 7.6 - - + -
212B PHE* 2.8 45.4 + - + +
213B TYR* 3.6 14.6 - - + +
214B GLU 3.3 0.2 - - - -
215B LYS* 1.3 76.9 - - - +
217B TYR* 1.3 64.1 + - - +
219B ALA* 3.0 16.7 + - - +
220B LEU* 3.1 18.7 + - + +
226B CYS* 3.6 31.6 - - + -
251B PHE* 4.0 10.5 - - + -
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Residues in contact with TYR 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 TYR 2.8 21.4 + - - +
214B GLU 3.6 4.9 - - - +
216B ILE* 1.3 76.0 - - - +
218B ASN* 1.3 80.3 + - - +
220B LEU 3.5 1.6 + - - -
250B LEU* 3.3 49.6 + - + -
251B PHE* 3.8 28.5 - + + -
276B LYS* 2.9 67.6 + - + +
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Residues in contact with ASN 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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186B VAL 4.0 6.7 - - - +
187B THR* 3.2 14.3 - - + -
188B ASN 2.9 21.0 + - - -
214B GLU* 3.1 33.5 + - - +
215B LYS* 4.0 5.1 - - - +
216B ILE 3.2 0.2 - - - -
217B TYR* 1.3 98.2 - - - +
219B ALA* 1.3 58.3 + - - +
220B LEU 3.3 2.8 + - - +
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Residues in contact with ALA 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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183B LEU* 3.6 28.9 - - + +
186B VAL* 3.5 25.1 + - + +
188B ASN 3.7 3.1 - - - +
189B THR* 2.9 25.1 + - - -
190B TYR* 2.9 11.8 + - + -
193B ILE* 3.9 10.8 - - + -
215B LYS 2.9 18.1 + - - +
216B ILE 3.0 4.2 + - - +
218B ASN* 1.3 73.2 - - - +
220B LEU* 1.3 59.6 + - - +
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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