Contacts of the helix formed by residues 211 - 224 (chain B) in PDB entry 1PR9
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 211 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B VAL* 4.2 4.0 - - - -
208B LYS* 4.7 10.3 + - - +
209B PHE 4.3 8.0 - - - +
210B ALA* 1.3 75.1 - - - +
212B VAL* 1.3 64.6 - - - +
213B GLU* 3.9 11.4 - - + +
214B HIS* 3.0 40.9 + - + +
215B VAL* 3.4 11.8 + - - +
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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
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18B GLY* 4.4 4.9 - - - +
19B ILE* 4.2 17.9 - - + +
22B GLY* 4.2 18.6 - - - -
182B VAL* 4.0 21.5 - - + +
184B THR* 4.2 13.9 - - + +
211B GLU* 1.3 72.5 - - - +
213B GLU* 1.3 64.2 + - - +
215B VAL* 3.1 8.9 + - - +
216B VAL* 2.9 36.9 + - + +
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Residues in contact with GLU 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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211B GLU* 3.1 10.0 - - + +
212B VAL* 1.3 82.3 - - - +
214B HIS* 1.3 67.3 + - + +
216B VAL* 3.9 7.0 - - + +
217B ASN* 3.0 41.2 + - - +
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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
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208B LYS* 4.2 22.4 + - - +
209B PHE 5.2 0.2 - - - -
210B ALA* 4.0 7.6 - - + -
211B GLU* 3.0 54.6 + - + +
213B GLU* 1.3 82.7 - - + +
215B VAL* 1.3 64.3 + - - +
217B ASN* 3.4 11.1 + - - +
218B ALA* 3.2 20.6 + - - +
237B VAL* 3.8 21.9 - - + +
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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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19B ILE* 3.8 34.3 - - + -
134B VAL* 5.1 1.1 - - + -
177B VAL* 4.4 8.7 - - + -
179B PRO* 3.8 37.0 - - + -
182B VAL* 4.1 13.2 - - + -
210B ALA* 4.8 0.9 - - + -
211B GLU 3.4 11.0 + - - +
212B VAL* 3.1 7.9 + - - +
214B HIS* 1.3 78.0 - - - +
216B VAL* 1.3 63.4 + - - +
218B ALA* 3.0 7.3 + - - +
219B ILE* 3.0 30.3 + - + +
237B VAL* 4.4 11.7 - - + -
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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
----------------------------------------------------------
19B ILE* 4.3 3.6 - - + +
22B GLY 3.8 17.5 - - - +
23B THR* 3.7 24.5 - - + +
26B ALA* 3.5 30.1 - - + -
212B VAL* 2.9 30.6 + - + +
213B GLU* 3.9 6.5 - - + +
215B VAL* 1.3 74.7 - - - +
217B ASN* 1.3 66.8 + - - +
219B ILE* 3.0 9.9 + - - +
220B LEU* 2.8 35.3 + - + +
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Residues in contact with ASN 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 GLU* 3.0 40.6 + - - +
214B HIS* 3.7 10.2 + - - +
216B VAL* 1.3 80.1 - - - +
218B ALA* 1.3 64.4 + - - +
220B LEU* 3.4 12.2 + - - +
221B PHE* 3.1 22.9 + - - +
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Residues in contact with ALA 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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177B VAL* 4.1 14.4 - - + -
214B HIS 3.2 8.9 + - - +
215B VAL 3.0 9.4 + - - +
217B ASN* 1.3 79.1 - - - +
219B ILE* 1.3 63.3 + - - +
221B PHE* 3.2 7.2 + - - +
222B LEU* 3.0 26.9 + - - +
235B LEU* 4.4 15.0 - - + -
237B VAL* 3.9 22.7 - - + -
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Residues in contact with ILE 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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19B ILE* 4.2 3.6 - - + -
23B THR* 3.6 30.3 - - + +
81B VAL* 3.9 33.2 - - + -
132B VAL* 4.1 19.7 - - + +
134B VAL* 4.1 17.9 - - + -
177B VAL* 4.3 13.9 - - + -
215B VAL* 3.0 32.2 + - + +
216B VAL* 3.5 8.3 - - - +
218B ALA* 1.3 76.3 - - - +
220B LEU* 1.3 65.6 + - + +
222B LEU* 3.2 3.9 + - - +
223B LEU* 2.9 31.5 + - + +
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Residues in contact with LEU 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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3B LEU* 4.5 12.0 - - + +
5B LEU* 3.3 30.9 - - + +
23B THR* 6.0 1.6 - - + -
26B ALA* 4.1 12.1 - - + +
27B LEU* 3.6 30.1 - - + -
30B THR* 5.3 9.9 - - + -
216B VAL* 2.8 39.6 + - + +
217B ASN* 3.9 10.8 - - - +
219B ILE* 1.3 81.2 - - + +
221B PHE* 1.3 61.3 + - - +
223B LEU* 3.3 7.5 + - + +
224B SER* 3.0 24.4 + - - -
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Residues in contact with PHE 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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1B MET* 4.8 11.0 - - + -
3B LEU* 4.9 10.0 - - + +
217B ASN 3.1 13.6 + - - +
218B ALA* 3.2 9.2 + - - +
220B LEU* 1.3 77.6 - - - +
222B LEU* 1.3 73.0 + - + +
224B SER* 3.2 17.6 + - - -
226B ARG* 3.9 31.9 - - + -
227B SER* 2.9 36.8 + - - -
230B THR* 5.6 2.7 - - + -
235B LEU* 4.6 11.7 - - + -
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Residues in contact with LEU 222 (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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130B ALA* 4.2 4.5 - - - +
131B ILE 5.5 0.3 - - - +
132B VAL* 3.8 19.5 - - + +
173B ARG* 3.2 22.0 + - - -
175B ASN* 4.0 32.3 + - + +
176B ALA 4.0 11.2 - - - +
177B VAL* 3.3 34.5 - - + -
218B ALA 3.0 13.4 + - - +
219B ILE 3.2 0.4 + - - +
221B PHE* 1.3 84.9 - - + +
223B LEU* 1.3 61.4 + - - +
227B SER* 3.5 7.0 - - - +
230B THR* 4.2 15.5 - - + -
233B SER* 4.7 2.2 - - - +
235B LEU* 3.5 27.1 - - + -
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Residues in contact with LEU 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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5B LEU* 4.4 7.4 - - + +
8B ARG* 5.2 2.1 + - - -
10B VAL* 4.6 12.8 - - + -
27B LEU* 4.6 15.9 - - + -
79B LEU* 4.1 29.2 - - + +
80B LEU 4.1 11.4 - - - +
81B VAL* 3.8 21.1 - - + -
130B ALA* 3.8 33.4 - - + +
132B VAL* 3.7 20.6 - - + -
173B ARG* 3.7 6.2 + - - -
219B ILE* 2.9 25.8 + - + +
220B LEU* 3.8 8.3 - - + +
222B LEU* 1.3 77.6 - - - +
224B SER* 1.3 65.7 + - - +
225B ASP* 3.9 1.7 + - - +
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Residues in contact with SER 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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3B LEU* 3.1 54.4 - - - +
5B LEU* 3.9 6.1 - - - -
8B ARG* 5.8 0.7 - - - +
173B ARG* 3.0 8.4 + - - -
220B LEU 3.0 12.8 + - - -
221B PHE 3.2 6.5 + - - -
223B LEU* 1.3 80.7 - - - +
225B ASP* 1.3 59.4 + - - +
226B ARG* 3.1 15.9 + - - +
227B SER* 2.9 23.2 + - - -
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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