Contacts of the helix formed by residues 193 - 211 (chain B) in PDB entry 2W93
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 ASP 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191B PRO 3.9 0.2 + - - -
192B ASN* 1.3 73.1 - - - +
194B ALA* 1.3 64.2 + - - +
195B GLU* 3.5 11.7 + - - +
196B SER* 3.0 40.9 + - - +
197B GLU* 3.0 23.6 + - - +
323B GLY 5.4 2.2 + - - -
324B VAL* 5.7 2.8 - - + +
318C ASN* 4.3 2.1 - - - +
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Residues in contact with ALA 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ASN 3.2 7.2 + - - +
193B ASP* 1.3 75.0 + - - +
195B GLU* 1.3 63.0 + - + +
197B GLU* 3.9 6.2 - - - +
198B LYS* 3.0 29.8 + - - +
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Residues in contact with GLU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ASP* 3.4 9.5 + - - +
194B ALA* 1.3 76.6 - - + +
196B SER* 1.3 61.9 + - - +
198B LYS* 3.3 13.2 + - - +
199B GLU* 3.0 24.8 + - - +
304C LYS* 2.8 45.1 + - + +
318C ASN* 3.5 22.1 + - - +
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Residues in contact with SER 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ASP* 3.0 29.4 + - - +
195B GLU* 1.3 74.5 - - - +
197B GLU* 1.3 60.0 + - - +
199B GLU* 3.3 3.5 + - - +
200B VAL* 2.9 32.2 + - - +
321B PHE* 4.5 3.2 - - - -
322B PRO 5.6 1.1 + - - -
324B VAL* 3.6 23.3 - - - -
318C ASN* 3.3 30.3 + - - +
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Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ASN* 2.9 40.8 + - + +
193B ASP 3.0 18.6 + - - +
194B ALA* 3.9 5.6 - - - +
196B SER* 1.3 76.6 - - - +
198B LYS* 1.3 58.8 + - - +
200B VAL* 3.3 2.0 + - - +
201B ILE* 2.9 46.5 + - + +
324B VAL* 4.3 9.1 - - - +
328B PHE* 3.2 17.7 - - - +
329B VAL* 4.0 9.6 - - + -
332B LYS* 2.7 41.8 + - - +
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Residues in contact with LYS 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 ALA 3.0 18.6 + - - +
195B GLU* 3.6 14.8 - - - +
197B GLU* 1.3 77.1 + - - +
199B GLU* 1.3 64.0 + - - +
201B ILE* 3.4 6.8 + - - +
202B ASP* 2.9 59.7 + - - +
304C LYS* 6.1 1.1 - - - +
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Residues in contact with GLU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLU 3.0 17.1 + - - +
196B SER* 3.3 4.9 + - - +
198B LYS* 1.3 77.1 - - - +
200B VAL* 1.3 57.0 + - - +
202B ASP* 3.8 6.0 - - + +
203B THR* 2.6 47.6 + - + +
321B PHE* 3.7 22.5 - - + -
316C ILE 4.3 1.6 - - - +
317C ARG* 3.4 36.2 + - - +
318C ASN* 2.8 39.7 + - - +
319C ALA* 4.2 4.7 + - - +
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Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B SER 2.9 20.4 + - - +
197B GLU* 3.7 7.0 - - - +
199B GLU* 1.3 77.5 - - - +
201B ILE* 1.3 62.5 + - - +
203B THR* 3.4 0.4 + - - -
204B ILE* 3.0 48.3 + - + +
314B MET* 3.9 23.3 - - + -
316B ILE* 3.8 11.4 - - + +
321B PHE* 3.4 42.8 - - + -
324B VAL* 4.2 9.6 - - + -
329B VAL* 4.0 9.9 - - + -
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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 GLU* 2.9 44.3 + - + +
198B LYS* 3.9 5.8 - - - +
200B VAL* 1.3 75.7 - - - +
202B ASP* 1.3 62.8 + - - +
204B ILE* 3.3 3.2 + - - +
205B LEU* 2.9 43.5 + - + +
329B VAL* 4.2 24.5 - - + +
332B LYS* 3.6 31.2 - - + -
333B LEU* 3.9 24.6 - - + +
336B ASN* 6.1 1.6 - - - +
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Residues in contact with ASP 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 LYS* 2.9 52.2 + - - +
199B GLU* 3.8 6.1 + - - +
201B ILE* 1.3 80.8 - - - +
203B THR* 1.3 59.4 + - + +
205B LEU* 3.4 10.8 + - - +
206B ALA* 3.1 28.1 + - - +
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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
----------------------------------------------------------
199B GLU* 2.6 44.1 + - + +
200B VAL* 4.0 5.6 - - - +
202B ASP* 1.3 74.3 - - + +
204B ILE* 1.3 65.9 + - - +
206B ALA* 3.3 7.1 + - - +
207B LEU* 3.0 28.3 + - - +
316B ILE* 3.8 26.6 - - + +
321B PHE* 5.2 3.4 - - + -
317C ARG* 6.2 1.3 - - - +
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Residues in contact with ILE 204 (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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200B VAL* 3.0 42.2 + - + +
201B ILE* 3.8 3.8 - - - +
203B THR* 1.3 75.3 - - - +
205B LEU* 1.3 62.1 + - - +
207B LEU* 3.2 8.7 + - + +
208B VAL* 2.9 33.8 + - + +
283B LEU* 4.5 15.9 - - + -
307B VAL* 3.7 27.4 - - + -
309B PHE* 4.1 8.1 - - + -
314B MET* 3.9 7.6 - - + -
316B ILE* 3.8 13.7 - - + -
329B VAL* 4.1 8.1 - - + -
333B LEU* 3.9 23.6 - - + -
337B ILE* 4.9 1.8 - - + -
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Residues in contact with LEU 205 (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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201B ILE* 2.9 36.2 + - + +
202B ASP* 3.8 11.2 - - - +
204B ILE* 1.3 74.6 - - - +
206B ALA* 1.3 57.9 + - - +
208B VAL* 3.3 6.0 + - - +
209B LYS* 3.0 28.8 + - - +
333B LEU* 3.8 21.1 - - + +
336B ASN* 4.0 37.5 - - + +
337B ILE* 4.1 7.9 - - + +
340B ALA* 3.9 25.9 - - + +
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Residues in contact with ALA 206 (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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202B ASP 3.1 17.5 + - - +
203B THR* 3.7 7.2 - - - +
204B ILE 3.2 0.2 - - - -
205B LEU* 1.3 74.5 - - - +
207B LEU* 1.3 64.1 + - + +
209B LYS* 3.4 7.9 + - - +
210B ASP* 3.3 29.4 + - - +
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Residues in contact with LEU 207 (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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203B THR* 3.0 22.7 + - - +
204B ILE* 3.6 6.5 - - - +
206B ALA* 1.3 72.4 - - + +
208B VAL* 1.3 66.8 + - - +
210B ASP* 3.2 8.6 + - + +
211B ALA* 3.1 23.7 + - - +
281B LEU* 3.9 18.4 - - + +
305B ASN* 4.1 27.1 - - + +
307B VAL* 3.9 18.6 - - + -
316B ILE* 3.7 30.3 - - + -
317B ARG* 5.2 12.6 - - + +
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Residues in contact with VAL 208 (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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204B ILE* 2.9 26.1 + - + +
205B LEU 3.3 8.3 + - - +
207B LEU* 1.3 73.7 - - - +
209B LYS* 1.3 65.3 + - - +
210B ASP 3.2 0.7 + - - -
211B ALA* 3.3 16.7 + - - +
240B PHE* 3.9 28.8 - - + -
281B LEU* 3.8 21.1 - - + -
283B LEU* 4.7 5.4 - - + -
337B ILE* 3.8 24.2 - - + -
340B ALA* 3.8 29.8 - - + +
341B ALA* 3.9 7.0 - - + +
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Residues in contact with LYS 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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205B LEU 3.0 16.5 + - - +
206B ALA* 3.7 9.6 - - - +
207B LEU 3.3 0.2 - - - -
208B VAL* 1.3 77.2 - - - +
210B ASP* 1.3 65.1 - - - +
211B ALA 4.5 2.6 - - - +
212B LYS* 4.8 5.7 + - - -
339B ASP* 4.7 14.5 + - - -
340B ALA* 3.4 26.2 + - - +
342B LYS* 5.4 6.3 - - - +
343B GLY* 6.1 0.5 - - - -
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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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206B ALA 3.3 13.6 + - - +
207B LEU* 3.2 12.5 + - + +
208B VAL 3.2 0.6 - - - -
209B LYS* 1.3 87.1 - - - +
211B ALA* 1.3 62.2 + - - +
212B LYS* 3.6 22.3 + - - +
280B ASP* 4.6 0.9 - - - +
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Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU 3.1 16.1 + - - +
208B VAL 3.3 13.1 + - - +
209B LYS 4.5 2.1 - - - +
210B ASP* 1.3 80.1 - - - +
212B LYS* 1.3 63.7 + - - +
214B PRO* 3.9 14.4 - - + +
280B ASP* 3.6 19.5 - - - +
281B LEU* 3.7 24.9 - - + -
344B TYR* 5.0 7.3 - - - +
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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