Contacts of the helix formed by residues 208 - 226 (chain B) in PDB entry 3URZ
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 SER 208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B ILE* 6.5 0.2 - - - -
202B VAL* 4.6 3.3 - - - +
203B ILE* 3.3 10.0 - - - +
206B PHE* 3.1 26.7 + - - -
207B PRO* 1.3 71.7 - - - +
209B THR* 1.3 59.6 + - - +
210B GLU* 3.8 7.6 + - - +
211B ALA* 3.3 28.0 + - - +
212B GLN* 3.1 24.1 + - - +
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Residues in contact with THR 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B PRO 4.3 0.2 - - - -
208B SER* 1.3 68.6 - - - +
210B GLU* 1.3 57.1 + - - +
212B GLN* 3.4 5.3 + - + +
213B LYS* 2.8 39.7 + - + +
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Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ASN* 5.4 11.3 - - - +
208B SER* 3.4 6.9 + - - +
209B THR* 1.3 79.4 - - - +
211B ALA* 1.3 58.2 + - - +
213B LYS* 3.6 26.2 + - - +
214B THR* 3.1 33.9 + - - +
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Residues in contact with ALA 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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149B ASN* 6.0 0.2 - - - -
199B LEU* 4.3 25.3 - - + +
202B VAL* 4.4 9.4 - - + -
203B ILE* 3.4 27.4 - - + -
208B SER* 3.3 17.1 + - - +
209B THR 3.3 0.2 - - - -
210B GLU* 1.3 77.2 - - - +
212B GLN* 1.3 57.7 + - - +
214B THR* 3.3 5.1 + - - -
215B LEU* 3.1 31.1 + - - +
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Residues in contact with GLN 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE* 3.8 34.3 - - + +
208B SER 3.1 13.5 + - - +
209B THR* 3.4 6.3 + - + +
211B ALA* 1.3 73.4 - - - +
213B LYS* 1.3 62.6 + - - +
215B LEU* 3.4 19.0 + - - +
216B ASP* 3.0 31.0 + - - +
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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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209B THR* 2.8 24.7 + - + +
210B GLU* 3.6 26.9 + - - +
211B ALA 3.3 0.2 - - - -
212B GLN* 1.3 72.3 - - - +
214B THR* 1.3 61.4 + - - +
216B ASP* 2.9 29.6 - - - +
217B LYS* 3.5 29.8 - - + +
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Residues in contact with THR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ASN* 4.3 11.1 + - - +
152B TYR* 3.6 40.8 - - + -
199B LEU* 3.4 25.1 - - + -
210B GLU* 3.1 19.1 + - - -
211B ALA* 3.7 8.1 - - - -
212B GLN 3.3 0.2 - - - -
213B LYS* 1.3 78.1 - - - +
215B LEU* 1.3 63.4 + - - +
217B LYS* 3.3 15.9 + - - +
218B ILE* 3.1 22.9 + - + +
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Residues in contact with LEU 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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196B ARG* 3.6 38.3 + - + +
199B LEU* 3.7 30.1 - - + +
200B GLN* 4.2 12.1 - - + +
203B ILE* 3.9 29.2 - - + -
211B ALA 3.1 16.4 + - - +
212B GLN* 3.4 23.3 + - - +
214B THR* 1.3 77.0 - - - +
216B ASP* 1.3 56.1 + - - +
218B ILE* 3.5 7.0 + - + +
219B LEU* 3.1 25.5 + - - +
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Residues in contact with ASP 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 GLN* 3.0 18.3 + - - +
213B LYS* 2.9 20.3 - - - +
215B LEU* 1.3 76.5 - - - +
217B LYS* 1.3 80.9 + - - +
219B LEU* 3.2 14.3 + - + +
220B ARG* 2.9 33.6 + - - +
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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
----------------------------------------------------------
152B TYR* 3.3 38.5 + - + +
213B LYS* 3.5 39.4 - - + +
214B THR* 3.3 16.4 + - - +
216B ASP* 1.3 81.2 + - - +
218B ILE* 1.3 60.4 + - - +
220B ARG* 3.3 37.8 + - - +
221B ILE* 2.9 36.6 + - + +
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Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TYR* 3.9 17.5 - - + -
188B PHE* 3.6 27.0 - - + -
192B TYR* 3.9 30.5 - - + +
195B ALA* 4.1 12.1 - - + -
196B ARG* 4.0 32.1 - - + +
199B LEU* 4.4 3.8 - - + -
214B THR* 3.1 26.7 + - + +
215B LEU* 3.7 9.6 - - - +
216B ASP 3.3 0.2 - - - -
217B LYS* 1.3 74.5 - - - +
219B LEU* 1.3 52.7 + - - +
221B ILE* 3.3 6.1 + - - -
222B GLU* 2.8 32.8 + - - +
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Residues in contact with LEU 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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196B ARG* 4.8 7.1 - - - +
215B LEU 3.1 14.5 + - - +
216B ASP* 3.2 15.9 + - + +
218B ILE* 1.3 73.8 - - - +
220B ARG* 1.3 63.1 + - - +
222B GLU* 3.3 27.1 - - - +
223B LYS* 3.2 21.8 + - - +
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Residues in contact with ARG 220 (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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216B ASP* 2.9 18.9 + - - +
217B LYS* 3.4 40.9 - - - +
218B ILE 3.3 0.2 - - - -
219B LEU* 1.3 75.3 - - - +
221B ILE* 1.3 64.9 + - - +
223B LYS* 3.2 9.0 + - - +
224B GLU* 3.2 45.1 + - + +
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Residues in contact with ILE 221 (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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152B TYR* 4.6 5.6 - - + +
156B GLU* 3.6 13.5 - - - +
159B LYS* 4.2 18.2 - - + +
188B PHE* 4.1 10.3 - - + -
192B TYR* 3.4 52.0 - - + +
217B LYS* 2.9 24.1 + - + +
218B ILE* 3.8 5.8 - - - +
220B ARG* 1.3 77.2 - - + +
222B GLU* 1.3 63.9 + - - +
224B GLU* 3.5 9.5 + - - +
225B VAL* 3.1 34.8 + - + +
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Residues in contact with GLU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B PHE* 3.5 26.4 - - + -
196B ARG* 3.2 34.2 + - - -
218B ILE 2.8 20.6 + - - +
219B LEU* 3.3 24.3 - - - +
220B ARG 3.3 0.2 - - - -
221B ILE* 1.3 73.9 - - - +
223B LYS* 1.3 60.8 + - - +
225B VAL* 4.1 1.1 - - - +
226B ASN* 3.2 27.2 + - - +
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Residues in contact with LYS 223 (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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219B LEU 3.2 9.7 + - - +
220B ARG* 3.2 11.3 + - - +
222B GLU* 1.3 80.4 - - - +
224B GLU* 1.3 67.7 + - + +
226B ASN* 3.0 23.1 + - - +
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Residues in contact with GLU 224 (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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159B LYS* 4.8 13.5 + - - -
181B ARG* 3.8 19.8 + - - -
220B ARG* 3.2 39.0 + - + +
221B ILE* 4.0 9.5 - - - +
222B GLU 3.4 0.2 - - - -
223B LYS* 1.3 87.0 - - + +
225B VAL* 1.3 59.6 + - + +
226B ASN* 3.1 11.8 - - - +
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Residues in contact with VAL 225 (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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174A LYS* 5.2 4.5 + - - -
159B LYS* 5.1 4.9 - - - -
181B ARG* 4.2 18.5 + - - +
184B LEU* 3.5 33.2 - - + +
185B SER* 3.5 40.5 - - - +
188B PHE* 4.8 9.0 - - + -
221B ILE* 3.1 31.8 + - + +
222B GLU* 4.4 3.8 - - - +
224B GLU* 1.3 76.0 - - + +
226B ASN* 1.3 71.6 + - - +
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Residues in contact with ASN 226 (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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174A LYS* 5.3 10.2 - - - +
181B ARG* 3.8 16.8 + - - +
185B SER* 5.4 3.6 + - - -
222B GLU* 3.2 20.4 + - - +
223B LYS* 3.0 17.2 - - - +
224B GLU* 3.1 10.1 - - - +
225B VAL* 1.3 86.3 - - - +
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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