Contacts of the helix formed by residues 219 - 236 (chain B) in PDB entry 2PMW
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 GLN 219 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B ALA* 1.3 68.9 + - - +
221B SER* 2.6 29.2 + - - +
222B LYS* 3.2 23.5 + - + +
223B CYS* 2.9 35.5 + - - -
374B ASP* 5.3 0.3 - - - +
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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
----------------------------------------------------------
219B GLN* 1.3 72.5 - - - +
221B SER* 1.3 58.3 + - - +
223B CYS* 3.3 6.5 + - - +
224B ASP* 2.9 45.7 + - - +
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Residues in contact with SER 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B GLN* 5.5 0.7 - - - +
219B GLN* 2.6 32.0 + - - +
220B ALA* 1.3 78.7 - - - +
222B LYS* 1.3 67.9 + - - +
225B SER* 3.2 10.0 + - - -
373B SER* 2.5 46.3 + - - -
374B ASP* 3.8 23.1 + - - +
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Residues in contact with LYS 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B GLN* 3.2 30.6 + - + +
221B SER* 1.3 81.8 + - - +
223B CYS* 1.3 65.9 + - - +
224B ASP 3.4 0.2 + - - -
225B SER* 3.4 19.4 + - - -
226B HIS 5.0 0.2 + - - -
255B CYS* 4.4 20.8 - - + +
256B GLN* 5.5 9.7 - - - +
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Residues in contact with CYS 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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187B THR* 3.4 28.1 + - - +
188B SER* 3.9 12.3 + - - +
219B GLN 2.9 35.9 + - - +
220B ALA* 3.7 6.7 - - - +
222B LYS* 1.3 78.5 - - - +
224B ASP* 1.3 61.9 + - - +
225B SER 3.3 1.1 + - - -
226B HIS 4.7 0.3 + - - -
251B ARG* 5.0 0.6 + - - +
254B ASN 5.5 0.2 - - - -
255B CYS* 2.0 60.5 - - - +
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Residues in contact with ASP 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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188B SER* 2.6 41.2 + - - +
189B ILE 3.7 12.7 - - - +
190B GLN* 3.7 16.2 + - - +
220B ALA* 2.9 34.6 + - - +
223B CYS* 1.3 77.4 - - - +
225B SER* 1.3 63.4 + - - +
226B HIS 3.4 1.1 - - - -
227B GLY 3.6 0.5 + - - -
228B THR* 2.6 40.6 + - - +
373B SER* 3.7 12.6 - - - -
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Residues in contact with SER 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B SER 3.2 9.6 + - - -
222B LYS* 3.4 17.5 - - - -
223B CYS 3.3 2.0 - - - -
224B ASP* 1.3 77.2 - - - +
226B HIS* 1.3 63.2 + - - +
228B THR* 4.1 0.9 - - - -
229B HIS* 3.2 24.4 + - - +
371B ALA 4.8 1.0 - - - +
372B SER* 5.9 0.2 - - - -
373B SER* 3.4 13.5 + - - +
380B VAL* 5.6 1.7 - - - +
382B GLN* 3.5 15.1 + - - +
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Residues in contact with HIS 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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151A ALA* 3.6 25.3 - - + +
152A GLN 2.8 26.7 + - - -
186B ASP* 2.6 37.2 + - - +
187B THR* 4.0 12.7 + - + +
222B LYS 5.0 0.2 + - - -
223B CYS 4.7 0.8 + - - -
224B ASP 3.4 0.4 - - - -
225B SER* 1.3 80.4 - - - +
227B GLY* 1.3 63.8 + - - +
229B HIS* 3.4 2.8 + - - +
230B LEU* 3.1 46.5 + - + +
253B LEU* 4.5 0.2 - - - +
257B GLY* 6.3 0.2 - - - -
288B PRO 3.7 2.5 - - - -
382B GLN* 4.4 20.4 + - - +
386B SER* 3.4 16.2 + - - -
387B GLN* 4.9 1.5 + - - -
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Residues in contact with GLY 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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184B LEU* 3.7 3.9 - - - +
186B ASP* 2.9 23.5 + - - -
187B THR* 2.9 18.4 + - - -
189B ILE* 3.4 17.8 - - - +
226B HIS* 1.3 73.4 - - - +
228B THR* 1.3 59.6 + - - +
230B LEU* 3.3 2.4 + - - -
231B ALA* 2.9 30.5 + - - +
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Residues in contact with THR 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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189B ILE* 3.7 7.6 - - - +
190B GLN* 2.9 38.7 + - + +
193B HIS* 4.5 6.3 - - + -
196B ILE* 4.5 4.4 - - + +
224B ASP* 2.6 26.3 + - - +
225B SER 4.1 2.9 - - - -
227B GLY* 1.3 75.1 - - - +
229B HIS* 1.3 64.1 + - - +
231B ALA* 3.4 5.0 + - - +
232B GLY 3.1 16.6 + - - -
371B ALA* 3.8 28.1 - - + +
373B SER* 3.8 19.7 - - - +
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Residues in contact with HIS 229 (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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225B SER 3.2 17.4 + - - +
226B HIS 3.6 4.5 - - - +
228B THR* 1.3 78.6 - - - +
230B LEU* 1.3 58.0 + - - +
232B GLY* 3.1 3.1 + - - -
233B VAL* 2.9 45.6 + - + +
368B ILE* 2.9 29.4 + - + -
370B GLY* 3.5 19.8 + - - -
371B ALA 3.3 13.7 + - - +
380B VAL* 3.4 29.9 + - + -
382B GLN* 3.6 21.5 - - + +
387B GLN* 3.1 35.5 + - + -
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Residues in contact with LEU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 4.4 12.3 - - + -
186B ASP* 3.7 5.2 - - - +
226B HIS* 3.1 47.4 + - + +
227B GLY 3.8 4.5 - - - +
229B HIS* 1.3 74.0 - - - +
231B ALA* 1.3 66.6 + - - +
233B VAL* 3.1 4.9 + - + +
234B VAL* 3.1 29.0 + - - +
286B LEU* 5.0 1.1 - - + -
288B PRO* 3.5 24.9 - - + -
386B SER* 3.6 27.8 - - - +
387B GLN* 3.7 28.0 - - + +
390B ALA* 4.1 8.9 - - + +
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Residues in contact with ALA 231 (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 LEU* 4.2 8.6 - - + +
189B ILE* 4.8 6.5 - - + -
196B ILE* 3.8 23.9 - - + +
200B VAL* 4.4 5.8 - - + -
227B GLY 2.9 17.0 + - - +
228B THR* 3.7 5.8 - - - +
230B LEU* 1.3 76.0 - - - +
232B GLY* 1.3 61.9 + - - +
234B VAL 3.5 0.3 + - - -
235B SER* 3.1 30.5 + - - -
236B GLY 3.7 0.3 + - - -
247B MET* 3.7 22.9 - - + +
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Residues in contact with GLY 232 (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 GLU* 4.9 2.7 - - - -
196B ILE* 3.9 7.5 - - - +
228B THR 3.1 14.3 + - - -
229B HIS 3.1 4.5 + - - -
230B LEU 3.1 0.4 - - - -
231B ALA* 1.3 75.0 - - - +
233B VAL* 1.3 60.9 + - - +
236B GLY* 2.6 36.5 + - - -
239B ALA 4.1 2.3 - - - +
240B GLY* 3.2 7.6 + - - -
370B GLY* 5.4 2.5 - - - -
371B ALA* 4.5 15.9 - - - -
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Residues in contact with VAL 233 (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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157B ASN* 5.5 1.1 - - - +
229B HIS* 2.9 46.2 + - + +
230B LEU* 3.1 7.8 + - - +
232B GLY* 1.3 75.8 - - - +
234B VAL* 1.3 57.6 + - - +
239B ALA 4.3 7.3 - - - +
240B GLY* 3.4 0.5 - - - -
241B VAL* 2.9 29.8 + - + +
368B ILE* 4.0 11.4 - - + -
369B ILE 4.8 5.6 - - - +
370B GLY* 5.1 0.7 - - - -
387B GLN* 4.1 5.8 - - + +
390B ALA* 3.6 22.4 - - + -
391B HIS* 3.7 35.2 - - + +
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Residues in contact with VAL 234 (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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182B VAL* 4.3 22.4 - - + -
230B LEU 3.1 15.3 + - - +
233B VAL* 1.3 77.5 - - - +
235B SER* 1.3 57.1 + - - +
236B GLY 3.8 0.2 - - - -
241B VAL* 3.3 3.7 + - - +
242B ALA* 2.7 36.3 + - + +
245B ALA* 5.6 1.1 - - + -
247B MET* 3.9 26.0 - - + -
286B LEU* 3.9 17.3 - - + -
390B ALA* 3.7 28.3 - - + +
393B ALA* 4.6 2.2 - - + -
394B GLY* 4.1 18.6 - - - +
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Residues in contact with SER 235 (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 GLU 4.1 3.0 - - - +
196B ILE* 4.3 8.0 - - - +
199B ARG* 4.8 6.0 + - - +
200B VAL* 4.3 3.5 - - - +
231B ALA 3.1 6.1 + - - -
234B VAL* 1.3 79.6 - - - +
236B GLY* 1.3 69.8 + - - +
237B ARG 3.5 1.2 + - - -
240B GLY* 4.1 1.3 - - - -
242B ALA 3.4 14.6 - - - -
243B LYS* 4.2 0.2 - - - -
244B GLY* 3.3 15.6 + - - -
245B ALA* 3.6 24.7 + - - -
247B MET* 3.1 28.3 - - - +
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Residues in contact with GLY 236 (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 GLU* 3.4 20.0 - - - -
196B ILE* 4.4 0.4 - - - -
231B ALA 3.7 0.2 + - - -
232B GLY* 2.6 35.0 + - - -
235B SER* 1.3 73.5 + - - +
237B ARG* 1.3 66.8 + - - -
238B ASP 3.3 2.9 - - - -
240B GLY* 2.9 18.1 + - - -
243B LYS* 3.3 9.0 - - - +
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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