Contacts of the helix formed by residues 189 - 203 (chain B) in PDB entry 2PY5
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 THR 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B TYR* 4.0 10.1 - - + -
124B LYS* 3.4 25.8 - - + -
125B LYS* 4.3 2.9 - - - +
187B ARG 3.3 0.4 - - - -
188B MET* 1.3 85.2 - - + +
190B ALA* 1.3 63.9 + - - +
191B GLY 3.5 1.8 + - - -
192B SER* 2.9 15.7 + - - -
193B ASP* 3.0 28.9 + - - +
3E A 3.8 31.9 - - - +
4E C 2.6 27.4 + - - +
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Residues in contact with ALA 190 (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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124B LYS 3.0 16.8 + - - +
125B LYS* 4.0 11.5 - - - +
127B PRO* 4.7 4.9 - - + -
180B GLN* 5.4 0.2 - - - +
189B THR* 1.3 72.0 - - - +
191B GLY* 1.3 57.6 + - - +
193B ASP* 3.3 12.5 + - - +
194B SER* 3.0 29.1 + - - -
384B LEU* 3.9 26.3 - - + +
385B MET* 5.0 0.9 - - - +
388B SER* 3.7 19.0 - - - +
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Residues in contact with GLY 191 (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 THR* 3.3 5.1 + - - -
190B ALA* 1.3 78.0 - - - +
192B SER* 1.3 57.0 + - - +
194B SER* 3.3 1.2 + - - -
195B LEU 3.0 24.6 + - - -
388B SER* 3.5 22.5 - - - -
392B LYS* 3.5 26.3 - - - +
4E C 4.6 8.1 + - - -
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Residues in contact with SER 192 (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 ARG* 2.8 35.5 + - - +
189B THR* 2.9 24.4 + - - -
191B GLY* 1.3 76.1 - - - +
193B ASP* 1.3 57.1 + - - +
195B LEU* 3.5 2.6 + - - +
196B LYS* 3.0 31.2 + - - +
392B LYS* 4.0 9.6 - - - +
3E A 2.6 30.8 + - - -
4E C 3.8 4.6 + - - -
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Residues in contact with ASP 193 (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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125B LYS* 2.7 30.4 + - - -
180B GLN* 4.1 4.9 + - - -
184B GLY 4.9 0.2 - - - +
185B LEU* 3.6 21.8 - - + +
186B ASP 3.3 5.7 + - - -
187B ARG* 3.0 33.4 + - - +
189B THR 3.0 14.8 + - - +
190B ALA* 3.3 10.1 + - - +
192B SER* 1.3 77.2 - - - +
194B SER* 1.3 61.8 + - - +
196B LYS* 3.9 1.4 - - - +
197B GLY* 3.0 18.7 + - - -
385B MET* 3.5 23.2 - - - +
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Residues in contact with SER 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ALA 3.0 8.0 + - - -
191B GLY 3.7 4.3 - - - -
192B SER 3.3 0.2 - - - -
193B ASP* 1.3 76.4 - - - +
195B LEU* 1.3 64.5 + - - +
197B GLY 3.2 1.4 + - - -
198B PHE* 3.0 23.6 + - - +
363B PHE* 3.6 5.8 - - - -
385B MET* 2.8 42.0 + - - -
388B SER* 3.2 37.1 - - - -
389B LEU* 3.6 9.6 - - - +
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Residues in contact with LEU 195 (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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191B GLY 3.0 17.4 + - - +
192B SER* 4.0 3.1 - - - +
194B SER* 1.3 76.4 - - - +
196B LYS* 1.3 58.6 + - - +
198B PHE* 3.3 4.8 + - + +
199B LYS* 2.9 47.4 + - - +
207B PHE* 4.0 26.9 - - + -
389B LEU* 3.8 17.4 - - + +
392B LYS* 4.0 34.1 - - + +
393B PHE* 4.6 7.2 - - + -
425B VAL* 4.6 19.5 - - + -
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Residues in contact with LYS 196 (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 GLY 5.6 5.6 - - - +
186B ASP* 5.2 6.1 - - - +
187B ARG* 3.4 40.9 - - + +
192B SER 3.0 18.3 + - - +
193B ASP* 4.0 2.0 - - - +
195B LEU* 1.3 77.1 - - - +
197B GLY* 1.3 57.3 + - - +
199B LYS* 3.2 9.4 + - + +
200B ASP* 2.8 58.3 + - - +
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Residues in contact with GLY 197 (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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193B ASP 3.0 15.7 + - - -
194B SER 3.6 3.4 - - - -
196B LYS* 1.3 78.6 - - - +
198B PHE* 1.3 60.1 + - - +
200B ASP* 3.5 10.3 + - - +
201B ILE* 3.3 27.9 + - - +
363B PHE* 3.9 12.3 - - - -
367B TRP* 5.7 1.3 - - - -
385B MET* 4.4 5.8 - - - -
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Residues in contact with PHE 198 (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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194B SER 3.0 13.2 + - - +
195B LEU* 3.3 10.1 + - + +
197B GLY* 1.3 76.6 - - - +
199B LYS* 1.3 63.2 + - - +
201B ILE* 3.2 5.8 + - + +
202B ILE* 3.1 55.4 + - + +
207B PHE* 3.7 17.5 - + - -
211B PHE* 3.7 22.4 - + - -
359B LEU* 3.4 21.3 - - + -
360B PHE* 3.4 37.5 - + - -
363B PHE* 3.6 24.3 - - + -
389B LEU* 3.9 16.2 - - + -
393B PHE* 4.0 11.9 - + - -
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Residues in contact with LYS 199 (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 LEU* 2.9 38.8 + - + +
196B LYS* 3.6 8.5 - - + +
198B PHE* 1.3 74.0 - - - +
200B ASP* 1.3 59.4 + - - +
202B ILE* 4.2 7.0 - - - -
203B THR* 2.7 37.7 + - - -
204B THR* 3.7 23.2 + - + +
207B PHE* 3.6 54.2 - - + -
425B VAL* 6.2 0.2 - - - +
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Residues in contact with ASP 200 (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 LYS* 2.8 59.2 + - - +
197B GLY* 3.6 10.4 - - - +
198B PHE 3.3 0.4 - - - -
199B LYS* 1.3 76.4 - - - +
201B ILE* 1.3 63.4 + - + +
203B THR* 3.7 9.8 + - - +
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Residues in contact with ILE 201 (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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197B GLY 3.3 13.9 + - - +
198B PHE* 3.2 7.3 + - + +
199B LYS 3.2 0.4 - - - -
200B ASP* 1.3 81.2 - - + +
202B ILE* 1.3 70.0 + - + +
203B THR* 3.4 6.1 + - - +
362B ASP* 3.7 32.5 - - + +
363B PHE* 3.6 39.0 - - + +
366B LYS* 4.3 22.2 - - + +
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Residues in contact with ILE 202 (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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198B PHE* 3.1 46.1 + - + +
199B LYS* 4.0 5.2 - - - +
201B ILE* 1.3 81.9 - - + +
203B THR* 1.3 82.1 + - - +
206B LYS* 3.2 38.5 - - + +
207B PHE* 3.5 42.4 - - + +
210B VAL* 5.6 1.3 - - + -
211B PHE* 4.2 6.1 - - + -
359B LEU* 4.2 11.9 - - + +
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Residues in contact with THR 203 (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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199B LYS 2.7 20.8 + - - -
200B ASP* 4.1 7.4 - - - +
201B ILE 3.2 8.6 - - - +
202B ILE* 1.3 82.2 + - - +
204B THR* 1.3 60.2 + - - +
205B LYS* 3.8 7.6 + - - +
206B LYS* 3.3 15.9 + - - +
207B PHE* 2.8 28.5 + - - +
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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