Contacts of the helix formed by residues 208 - 221 (chain B) in PDB entry 3RKR
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 GLU 208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B ALA 3.7 7.1 + - - +
207B ILE* 1.3 77.1 - - - +
209B PRO* 1.3 68.0 - - + +
210B ASP* 4.2 9.0 - - + +
211B ASP* 2.5 41.5 + - + +
212B ILE 3.5 2.4 + - - -
235B PRO* 5.3 1.2 - - + +
236B THR* 5.9 3.6 - - - +
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Residues in contact with PRO 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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17B GLY* 3.8 28.0 - - - +
18B ILE* 4.1 20.0 - - + +
21B ALA* 3.8 22.2 - - + +
207B ILE 3.5 6.7 - - - +
208B GLU* 1.3 89.4 - - + +
210B ASP* 1.3 58.6 + - - +
212B ILE* 3.1 7.0 + - + +
213B ALA* 2.9 26.5 + - - +
241B SO4 5.2 0.2 - - - +
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Residues in contact with ASP 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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21B ALA* 3.6 17.8 - - - +
24B ARG* 4.9 4.3 + - - -
208B GLU* 2.7 11.5 + - + +
209B PRO* 1.3 77.6 - - - +
211B ASP* 1.3 55.4 - - - +
213B ALA* 3.9 7.7 - - - +
214B ASP* 3.1 33.4 + - - +
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Residues in contact with ASP 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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207B ILE* 3.7 9.3 - - + +
208B GLU* 2.5 26.8 + - + +
210B ASP* 1.3 71.8 - - - +
212B ILE* 1.3 61.1 + - - +
214B ASP* 3.3 9.3 + - - +
215B VAL* 3.1 25.9 + - - +
233B VAL* 3.8 17.4 - - - +
234B ARG 2.9 24.8 - - - +
235B PRO* 3.8 3.1 - - - +
236B THR* 3.6 30.4 + - - +
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Residues in contact with ILE 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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18B ILE* 3.5 42.0 - - + -
22B ILE* 4.2 9.2 - - + -
141B ILE* 4.2 21.3 - - + -
184B VAL* 4.1 21.8 - - + -
185B ALA 6.3 1.3 - - - -
207B ILE* 3.8 29.8 - - + +
208B GLU 3.5 1.3 + - - +
209B PRO* 3.1 8.6 + - + +
211B ASP* 1.3 73.2 - - - +
213B ALA* 1.3 64.9 + - - +
215B VAL* 2.9 6.7 + - - +
216B VAL* 2.9 22.4 + - + +
233B VAL* 4.6 13.2 - - + -
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Residues in contact with ALA 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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21B ALA* 3.5 37.2 - - + +
22B ILE* 3.8 15.4 - - - +
25B LYS* 3.7 16.3 - - + +
26B LEU* 5.5 0.3 - - - +
209B PRO 2.9 17.4 + - - +
210B ASP* 4.0 7.9 - - - +
212B ILE* 1.3 72.6 - - - +
214B ASP* 1.3 58.3 + - - +
216B VAL* 3.3 2.6 + - - +
217B ALA* 2.9 30.0 + - - +
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Residues in contact with ASP 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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25B LYS* 3.3 30.8 + - - +
210B ASP 3.1 19.8 + - - +
211B ASP* 3.4 9.7 - - - +
213B ALA* 1.3 74.0 - - - +
215B VAL* 1.3 60.6 + - + +
217B ALA* 3.3 4.8 + - - +
218B LEU* 2.8 39.9 + - + +
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Residues in contact with VAL 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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184B VAL* 4.1 25.8 - - + -
211B ASP* 3.1 17.0 + - - +
212B ILE* 2.9 9.9 + - - +
214B ASP* 1.3 76.3 - - + +
216B VAL* 1.3 63.8 + - - +
218B LEU* 3.0 19.0 + - + +
219B LEU* 2.9 24.1 + - + +
231B VAL* 3.9 30.3 - - + -
233B VAL* 3.8 24.9 - - + -
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Residues in contact with VAL 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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22B ILE* 4.0 33.2 - - + -
26B LEU* 4.3 10.8 - - + -
88B VAL* 4.3 11.2 - - + -
139B ILE* 3.9 23.9 - - + +
141B ILE* 3.8 28.9 - - + -
184B VAL* 4.6 4.0 - - + -
212B ILE* 2.9 18.0 + - + +
213B ALA 3.6 7.4 - - - +
215B VAL* 1.3 75.3 - - - +
217B ALA* 1.3 57.0 + - - +
219B LEU* 3.3 10.0 + - - +
220B ALA* 2.8 27.9 + - + +
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Residues in contact with ALA 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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25B LYS* 3.8 27.6 - - + -
26B LEU* 4.2 13.0 - - + +
29B LEU* 3.8 20.0 - - + -
213B ALA 2.9 17.4 + - - +
214B ASP 3.6 4.5 - - - +
216B VAL* 1.3 74.3 - - - +
218B LEU* 1.3 62.2 + - + +
220B ALA 3.2 0.7 + - - -
221B THR* 2.8 32.5 + - + +
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Residues in contact with LEU 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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214B ASP* 2.8 25.0 + - + +
215B VAL* 3.0 20.6 + - + +
217B ALA* 1.3 78.3 - - + +
219B LEU* 1.3 63.2 + - + +
221B THR* 3.5 7.9 + - - +
222B GLN* 3.3 22.1 + - - +
228B ILE* 6.5 0.2 - - - -
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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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137B HIS* 3.1 12.3 - - - +
139B ILE* 3.9 16.8 - - + -
182B SER* 3.5 22.9 - - - +
183B LEU 5.2 0.2 - - - +
184B VAL* 3.8 28.5 - - + -
215B VAL* 2.9 21.0 + - + +
216B VAL* 3.7 4.9 - - - +
218B LEU* 1.3 73.6 - - + +
220B ALA* 1.3 64.1 + - - +
221B THR 3.3 0.7 + - - -
222B GLN* 3.1 32.8 + - - +
228B ILE* 3.7 46.4 - - + +
231B VAL* 4.0 13.9 - - + -
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Residues in contact with ALA 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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4B LEU* 3.9 17.5 - - + +
7B GLN* 5.0 1.9 + - - +
26B LEU* 4.3 17.3 - - + -
86B VAL* 4.0 23.1 - - + +
137B HIS* 3.7 23.1 + - - -
139B ILE* 4.2 6.7 - - + +
216B VAL 2.8 20.5 + - - +
217B ALA 3.2 3.8 + - - +
219B LEU* 1.3 74.4 - - - +
221B THR* 1.3 59.9 + - - +
222B GLN 4.9 0.5 - - - +
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Residues in contact with THR 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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3B SER* 3.9 22.9 - - - +
4B LEU* 3.7 28.0 - - + -
29B LEU* 4.2 11.7 - - + -
217B ALA 2.8 20.8 + - - +
218B LEU* 3.5 10.6 + - - +
219B LEU 3.2 0.2 - - - -
220B ALA* 1.3 76.0 - - - +
222B GLN* 1.3 66.4 + - - +
223B ALA* 3.6 0.7 + - - -
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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