Contacts of the helix formed by residues 211 - 228 (chain B) in PDB entry 4PIM
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 GLY 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ALA* 4.9 5.5 - - - +
234A LEU* 4.6 8.1 - - - -
208B ASP* 3.1 15.2 + - - -
209B ALA 3.3 1.4 - - - -
210B ALA* 1.3 77.6 - - - +
212B VAL* 1.3 64.2 + - - +
213B THR 3.4 2.5 - - - -
214B ALA* 3.4 15.6 + - - +
215B ALA* 3.1 20.3 + - - +
218B ARG* 5.4 0.3 + - - -
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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
----------------------------------------------------------
42A VAL* 4.0 17.5 - - + -
46A LEU* 4.5 9.2 - - + -
215A ALA* 5.6 2.0 - - + -
46B LEU* 4.1 21.7 - - + +
49B GLN* 4.1 24.5 - - + +
50B ILE* 3.7 20.0 - - + -
53B LEU* 3.9 9.9 - - + -
208B ASP* 3.0 12.7 + - - +
210B ALA* 4.0 16.6 - - + +
211B GLY* 1.3 75.8 - - - +
213B THR* 1.3 66.0 + - - +
215B ALA* 3.1 7.8 + - - +
216B PHE* 3.0 21.1 + - - +
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Residues in contact with THR 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 3.8 28.0 - - + +
53B LEU* 4.7 0.2 - - - +
205B ALA 4.3 8.3 + - - -
206B TYR* 3.3 36.1 - - + +
207B ASP* 4.5 0.7 - - - -
208B ASP* 2.7 29.9 + - - +
212B VAL* 1.3 73.5 - - - +
214B ALA* 1.3 57.6 - - - +
216B PHE* 3.2 4.3 + - + +
217B ASN* 2.9 28.8 + - - +
239B HIS* 3.7 10.5 - - + -
252B MSE 3.9 16.6 - - + -
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Residues in contact with ALA 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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207B ASP* 5.5 0.9 - - - +
211B GLY* 3.4 17.9 + - - +
212B VAL 3.2 0.4 - - - -
213B THR* 1.3 80.7 - - - +
215B ALA* 1.3 56.8 + - - +
217B ASN* 3.4 1.9 + - - +
218B ARG* 3.0 50.2 + - - +
239B HIS* 3.5 37.8 - - + +
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Residues in contact with ALA 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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210A ALA 4.7 4.1 - - - +
211A GLY 4.7 9.2 - - - +
212A VAL* 5.7 0.4 - - - -
215A ALA* 3.9 24.5 - - + -
46B LEU* 4.1 15.9 - - + +
211B GLY 3.1 12.0 + - - +
212B VAL* 3.1 10.8 + - - +
214B ALA* 1.3 73.1 - - - +
216B PHE* 1.3 60.8 + - - +
218B ARG* 3.4 10.3 + - - +
219B ASN* 2.9 30.7 + - - +
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Residues in contact with PHE 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 3.5 62.1 - + + +
39B TYR* 3.8 21.3 - + - -
43B GLY* 3.5 29.2 - - - -
46B LEU* 4.0 15.1 - - + +
47B PHE* 3.8 25.1 - + + -
50B ILE* 3.8 19.7 - - + -
212B VAL 3.0 12.2 + - - +
213B THR* 3.4 15.0 - - + +
215B ALA* 1.3 77.2 - - - +
217B ASN* 1.3 66.1 + - - +
219B ASN* 3.3 14.2 + - - +
252B MSE 4.9 5.8 - - + -
282B GLU* 4.7 5.8 - - - -
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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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38B PHE* 3.5 10.2 - - - -
213B THR 2.9 15.8 + - - +
214B ALA 3.7 2.7 - - - +
215B ALA 3.3 0.2 - - - -
216B PHE* 1.3 78.2 - - - +
218B ARG* 1.3 62.2 + - - +
219B ASN 3.1 1.2 + - - -
220B VAL* 3.2 22.2 + - - +
239B HIS* 3.0 28.6 + - - +
252B MSE 3.6 12.0 - - + +
253B TRP 3.0 23.6 + - - +
254B LEU* 3.5 12.6 - - + +
281B THR* 2.7 35.4 + - - +
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Residues in contact with ARG 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ALA 5.8 0.2 - - - +
218A ARG* 4.0 27.7 - - - +
235A ASP* 4.4 6.5 + - - -
211B GLY 5.4 0.6 + - - -
214B ALA* 3.0 38.2 + - - +
215B ALA* 4.0 8.2 - - - +
217B ASN* 1.3 76.4 - - - +
219B ASN* 1.3 56.5 + - - +
220B VAL 3.1 0.2 - - - -
221B LEU* 2.9 29.1 + - + +
222B ALA 3.6 2.1 + - - -
234B LEU* 3.1 49.0 - - + +
235B ASP* 5.8 0.6 - - - +
237B PHE* 2.9 23.1 + - + +
238B GLU* 4.0 1.8 - - - +
239B HIS* 3.6 19.8 - - - +
254B LEU* 3.9 22.4 - - + -
257B ARG* 4.2 9.3 - - - +
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Residues in contact with ASN 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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210A ALA* 3.5 31.5 + - - +
38B PHE 4.0 4.9 + - - -
40B ASP* 3.0 33.0 + - - +
42B VAL* 3.7 11.0 - - - +
43B GLY* 3.5 15.3 - - - +
46B LEU* 4.4 7.2 - - + -
215B ALA 2.9 17.2 + - - +
216B PHE* 3.5 8.9 + - - +
217B ASN 3.1 0.4 - - - -
218B ARG* 1.3 74.5 - - - +
220B VAL* 1.3 65.7 + - - +
222B ALA* 2.9 20.5 + - - +
223B VAL* 2.9 13.5 + - - +
226B ARG* 5.4 0.7 + - - -
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Residues in contact with VAL 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.9 32.5 - - + -
34B PRO 4.9 2.5 - - - +
37B TRP* 4.1 35.2 - - + +
38B PHE* 3.7 21.7 - - + +
216B PHE 3.9 2.4 + - - -
217B ASN 3.2 18.7 + - - +
218B ARG 3.1 1.6 - - - -
219B ASN* 1.3 77.9 - - - +
221B LEU* 1.3 71.9 + - + +
223B VAL* 3.3 7.8 + - + +
224B VAL* 3.1 26.1 + - + +
254B LEU* 4.1 7.9 - - + -
281B THR* 4.4 5.6 - - + -
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 4.3 4.7 - - + -
218B ARG* 2.9 16.3 + - + +
220B VAL* 1.3 83.9 - - + +
222B ALA* 1.3 56.6 + - - +
224B VAL* 3.4 3.1 + - - +
225B ASN* 2.8 35.0 + - - +
232B PHE* 3.9 33.8 - - + -
234B LEU* 3.8 18.8 - - + -
237B PHE* 3.7 38.6 - - + -
254B LEU* 3.8 19.3 - - + -
279B MSE 3.8 26.2 - - + -
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Residues in contact with ALA 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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209A ALA* 3.8 25.1 - - + +
210A ALA* 3.8 10.5 - - + -
218B ARG 3.6 1.4 + - - -
219B ASN* 2.9 27.2 + - - +
221B LEU* 1.3 76.1 - - - +
223B VAL* 1.3 58.9 + - - +
225B ASN* 3.5 10.8 - - - +
226B ARG* 2.9 38.2 + - - +
234B LEU* 4.0 4.6 - - + +
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Residues in contact with VAL 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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18B LEU* 4.7 11.9 - - + -
37B TRP* 3.7 33.0 - - + +
40B ASP* 3.5 38.1 - - + +
219B ASN* 2.9 20.4 + - - +
220B VAL* 3.4 10.1 - - + +
222B ALA* 1.3 76.1 - - - +
224B VAL* 1.3 59.2 + - + +
226B ARG* 3.3 11.4 + - - +
227B GLU* 2.9 43.6 + - + +
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Residues in contact with VAL 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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18B LEU* 4.9 7.0 - - + -
22B VAL* 4.0 38.8 - - + -
33B LEU* 4.3 17.3 - - + -
37B TRP* 6.3 0.4 - - + -
220B VAL* 3.1 17.9 + - + +
221B LEU* 3.8 6.5 - - - +
223B VAL* 1.3 76.9 - - + +
225B ASN* 1.3 64.3 + - - +
227B GLU* 5.1 0.4 - - - -
228B LEU* 2.9 37.2 + - + +
229B SER 3.7 0.9 + - - -
230B ALA* 3.7 16.9 + - + -
232B PHE* 4.0 16.8 - - + -
264B VAL* 4.5 3.4 - - + -
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Residues in contact with ASN 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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209A ALA* 5.7 1.3 + - + -
221B LEU 2.8 25.4 + - - +
222B ALA* 3.5 8.4 - - - +
224B VAL* 1.3 72.9 - - - +
226B ARG* 1.3 61.9 + - - +
229B SER* 3.2 19.1 + - - -
230B ALA* 3.1 30.2 + - - +
231B ASP* 4.4 0.8 - - - +
232B PHE* 2.9 50.2 + - - +
234B LEU* 3.7 13.9 - - - +
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Residues in contact with ARG 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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54A PRO* 6.6 0.2 - - - -
210A ALA* 6.1 2.2 - - - +
40B ASP* 2.8 39.3 + - - +
42B VAL* 5.7 3.8 - - - +
219B ASN* 5.4 1.0 + - - -
222B ALA* 2.9 30.6 + - - +
223B VAL* 4.0 17.3 - - - +
225B ASN* 1.3 78.4 - - - +
227B GLU* 1.3 88.4 + - - +
229B SER* 3.8 6.8 + - - -
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Residues in contact with GLU 227 (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 LEU* 3.6 26.7 - - + -
223B VAL* 2.9 27.0 + - + +
226B ARG* 1.3 110.9 + - - +
228B LEU* 1.3 67.3 + - - +
229B SER* 3.6 0.8 + - - -
266B ALA* 4.7 2.6 - - - +
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Residues in contact with LEU 228 (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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15B ALA 5.4 0.4 - - - +
18B LEU* 4.1 23.1 - - + +
19B ARG* 3.8 28.5 - - + +
22B VAL* 3.8 41.5 - - + -
224B VAL* 2.9 15.8 + - + +
227B GLU* 1.3 85.2 - - - +
229B SER* 1.3 69.5 + - - +
230B ALA 3.3 1.3 + - - -
264B VAL* 3.6 12.8 - - + +
265B ALA 3.5 3.6 + - - -
266B ALA* 3.0 39.0 + - + -
267B LEU* 4.1 12.6 - - + -
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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
------------------------------------------------------------
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