Contacts of the helix formed by residues 201 - 216 (chain B) in PDB entry 2IHU
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 201 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199B ALA 3.4 0.2 + - - -
200B ASP* 1.3 83.1 + - - +
202B TRP* 1.3 65.4 + - - +
203B GLN* 3.2 11.1 + - - -
204B LYS* 3.1 14.7 + - - +
205B ALA* 3.1 19.4 + - - +
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Residues in contact with TRP 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 VAL* 3.3 29.0 - - + +
199B ALA* 3.2 18.9 + - + +
200B ASP 3.3 0.8 + - - -
201B GLY* 1.3 77.5 - - - +
203B GLN* 1.3 92.3 + - + +
205B ALA* 3.2 8.9 + - - +
206B ALA* 2.8 28.9 + - + +
335B VAL* 3.7 11.3 - - + +
336B VAL 3.6 17.0 - - - +
337B THR* 3.4 28.5 + - + -
341B ALA* 3.6 28.3 - - + -
342B PHE* 3.9 14.4 - - - -
345B HIS* 3.7 30.1 - + + -
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Residues in contact with GLN 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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201B GLY* 4.1 7.3 + - - -
202B TRP* 1.3 129.6 + - + +
204B LYS* 1.3 57.1 + - - +
206B ALA* 3.2 1.3 + - - -
207B ASP* 2.8 34.7 + - - +
345B HIS* 3.4 31.6 + - + +
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Residues in contact with LYS 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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201B GLY* 3.1 15.2 + - - +
203B GLN* 1.3 75.9 - - - +
205B ALA* 1.3 59.8 + - - +
207B ASP* 3.3 12.7 + - + +
208B GLN* 2.9 44.5 + - + +
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Residues in contact with ALA 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 GLY 3.1 12.2 + - - +
202B TRP* 3.5 11.9 - - - +
204B LYS* 1.3 76.2 - - - +
206B ALA* 1.3 56.3 + - - +
208B GLN* 3.1 15.4 + - - +
209B ALA* 2.9 23.0 + - - +
333B VAL* 3.2 18.0 - - + +
334B ASP 3.8 22.4 - - - +
335B VAL* 4.0 8.3 - - + -
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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 TRP* 2.8 21.9 + - + +
203B GLN* 3.5 8.7 - - - +
205B ALA* 1.3 71.0 - - - +
207B ASP* 1.3 58.2 + - - +
209B ALA* 3.2 10.4 + - - +
210B ALA* 2.9 26.3 + - - +
335B VAL* 4.0 6.3 - - + +
342B PHE* 3.9 24.5 - - + -
345B HIS* 3.5 22.7 - - + -
346B PHE* 3.9 5.4 - - + -
349B ALA* 5.8 0.2 - - - -
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Residues in contact with ASP 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 GLN* 2.8 19.1 + - - +
204B LYS* 3.4 13.9 - - + +
206B ALA* 1.3 72.7 - - - +
208B GLN* 1.3 59.8 + - - +
210B ALA* 3.2 9.0 + - - +
211B ALA* 3.0 27.0 + - - +
345B HIS* 2.8 27.6 + - - -
349B ALA* 4.0 11.8 - - - +
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Residues in contact with GLN 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 LYS* 2.9 33.9 + - + +
205B ALA* 3.1 20.5 + - - +
207B ASP* 1.3 74.8 - - + +
209B ALA* 1.3 57.2 + - - +
211B ALA* 3.2 8.7 + - - +
212B LEU* 3.0 32.8 + - - +
333B VAL* 4.2 21.6 - - + +
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Residues in contact with ALA 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 ALA 2.9 13.1 + - - +
206B ALA* 3.3 13.2 - - - +
208B GLN* 1.3 76.1 - - - +
210B ALA* 1.3 56.4 + - - +
212B LEU* 3.3 5.7 + - - +
213B LEU* 2.9 28.4 + - - +
290B LEU* 4.6 2.1 - - - +
292B LEU* 4.7 2.8 - - + +
316B VAL* 3.8 39.9 - - + +
333B VAL* 4.3 2.4 - - + +
335B VAL* 4.9 0.2 - - + -
342B PHE* 4.7 3.1 - - + -
346B PHE* 3.8 14.8 - - + -
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Residues in contact with ALA 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 2.9 13.3 + - - +
207B ASP* 3.4 9.4 - - - +
209B ALA* 1.3 76.6 - - - +
211B ALA* 1.3 56.0 + - - +
213B LEU* 3.3 1.5 + - - +
214B ALA 2.9 23.9 + - - -
346B PHE* 3.5 18.5 - - + -
349B ALA* 4.0 18.4 - - + +
350B THR* 4.0 16.2 - - + -
353B PHE* 3.4 16.6 - - + -
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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
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207B ASP 3.0 13.1 + - - +
208B GLN* 3.2 11.6 + - - +
210B ALA* 1.3 73.2 - - - +
212B LEU* 1.3 65.0 + - + +
214B ALA* 3.3 8.9 + - - +
215B GLU* 3.1 28.5 + - - +
353B PHE* 5.5 0.2 - - - -
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Residues in contact with LEU 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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208B GLN 3.0 15.1 + - - +
209B ALA 3.3 6.7 + - - +
211B ALA* 1.3 75.4 - - + +
213B LEU* 1.3 63.2 + - - +
215B GLU* 3.2 10.6 + - + +
216B ALA* 3.1 21.5 + - - +
290B LEU* 3.8 29.1 - - + +
314B LYS* 3.9 39.5 - - + -
315B THR 4.9 0.2 - - - +
316B VAL* 4.1 8.7 - - + -
332B ASP* 4.9 3.4 - - + -
333B VAL* 3.8 27.6 - - + -
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Residues in contact with LEU 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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209B ALA 2.9 14.8 + - - +
210B ALA 3.5 7.4 - - - +
212B LEU* 1.3 75.0 - - - +
214B ALA* 1.3 52.7 + - - +
216B ALA* 3.1 7.0 + - - +
219B PRO* 3.6 37.5 - - + -
243B LEU* 3.8 24.2 - - + -
245B ILE* 4.1 12.3 - - + -
290B LEU* 3.5 11.1 - - + +
292B LEU* 5.1 3.4 - - + -
346B PHE* 3.6 31.9 - - + -
350B THR* 4.0 9.4 - - + -
353B PHE* 4.1 7.9 - - + -
356B LYS* 2.8 41.0 + - + -
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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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210B ALA 2.9 13.8 + - - +
211B ALA* 3.4 14.6 - - - +
212B LEU 3.3 0.2 - - - -
213B LEU* 1.3 75.6 - - - +
215B GLU* 1.3 60.2 + - + +
353B PHE* 3.7 24.1 - - + -
356B LYS* 3.1 17.4 + - - +
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Residues in contact with GLU 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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211B ALA* 3.1 19.5 - - + +
212B LEU* 3.2 11.3 + - + +
214B ALA* 1.3 77.5 - - + +
216B ALA* 1.3 64.3 + - - +
217B LYS 3.7 1.4 + - - -
289B ASP* 4.6 1.2 - - - +
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Residues in contact with ALA 216 (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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212B LEU 3.1 15.5 + - - +
213B LEU* 3.1 9.5 + - - +
215B GLU* 1.3 78.2 - - - +
217B LYS* 1.3 60.1 + - - +
219B PRO* 4.4 11.0 - - + -
289B ASP* 3.6 17.9 - - - +
290B LEU* 4.0 23.1 - - + -
356B LYS* 2.7 32.1 + - - +
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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