Contacts of the helix formed by residues 211 - 225 (chain B) in PDB entry 3H90
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 PRO 211 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209B ALA 3.9 0.9 - - - +
210B LEU* 1.3 92.0 - - + +
212B ASP* 1.3 67.2 + - - +
213B GLU* 3.1 7.2 - - + +
214B GLU* 2.9 41.1 + - + +
215B ARG 3.1 9.0 + - - -
238B GLN* 5.3 4.5 - - - +
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Residues in contact with ASP 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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210B LEU 3.7 1.6 + - - -
211B PRO* 1.3 71.3 - - - +
213B GLU* 1.3 52.6 + - - +
215B ARG* 3.6 32.8 + - - +
216B GLN* 2.7 37.1 + - - +
69D ASP* 5.2 2.4 - - - +
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Residues in contact with GLU 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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211B PRO* 3.0 6.0 + - + +
212B ASP* 1.3 77.3 - - - +
214B GLU* 1.3 72.2 + - + +
216B GLN* 3.2 8.2 + - - +
217B GLU* 3.0 48.4 + - - +
274B ARG* 5.4 1.2 + - - +
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Residues in contact with GLU 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 LEU* 3.8 14.2 - - + +
211B PRO* 2.9 34.4 + - + +
213B GLU* 1.3 76.7 - - + +
215B ARG* 1.3 61.3 + - - +
217B GLU* 3.1 5.2 + - - +
218B ILE* 3.0 35.2 + - - +
243B ARG* 3.0 47.1 + - - -
274B ARG* 5.9 0.7 - - - +
275B PHE* 3.7 25.8 - - + -
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Residues in contact with ARG 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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209B ALA* 3.4 29.7 - - - +
210B LEU* 3.5 17.1 + - + +
211B PRO 3.1 9.4 + - - +
212B ASP* 3.6 32.3 + - - +
214B GLU* 1.3 75.9 - - - +
216B GLN* 1.3 62.5 + - - +
218B ILE* 3.7 9.9 + - - +
219B ILE* 3.2 26.2 + - + +
234B LEU* 3.7 28.0 - - + +
236B THR* 4.3 12.0 + - + +
69D ASP* 3.3 30.1 + - - -
70D ASN* 3.9 18.0 - - - +
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Residues in contact with GLN 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 ASP 2.7 18.8 + - - +
213B GLU* 3.4 9.9 - - - +
215B ARG* 1.3 75.5 - - - +
217B GLU* 1.3 65.8 + - + +
219B ILE* 3.2 16.3 + - - +
220B ASP* 3.0 59.8 + - - +
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Residues in contact with GLU 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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213B GLU* 3.0 49.0 + - - +
214B GLU* 3.1 7.7 + - - +
216B GLN* 1.3 74.6 - - + +
218B ILE* 1.3 67.0 + - - +
220B ASP* 3.1 9.6 + - - +
221B ILE* 3.0 32.0 + - + +
274B ARG* 2.6 43.7 + - - +
275B PHE* 3.4 15.5 - - + -
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Residues in contact with ILE 218 (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 LEU* 4.0 20.4 - - + -
214B GLU 3.0 23.6 + - - +
215B ARG* 3.9 6.7 - - - +
217B GLU* 1.3 75.8 - - - +
219B ILE* 1.3 63.7 + - - +
221B ILE* 3.3 9.4 + - - +
222B VAL* 3.0 41.1 + - + +
234B LEU* 4.4 21.5 - - + -
236B THR* 4.2 9.6 - - + -
245B ILE* 3.6 33.9 - - + -
247B ILE* 4.8 0.9 - - + -
271B ILE* 4.1 14.1 - - + -
275B PHE* 3.7 20.4 - - + -
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Residues in contact with ILE 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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215B ARG* 3.2 9.6 + - + +
216B GLN* 3.2 32.0 + - - +
218B ILE* 1.3 78.5 - - - +
220B ASP* 1.3 64.3 + - - +
222B VAL* 3.5 4.3 + - - +
223B THR* 2.9 44.9 + - + +
231B ALA* 5.7 5.2 - - + +
232B HIS 5.4 2.7 - - - +
234B LEU* 3.7 41.5 - - + -
247B ILE* 4.7 6.5 - - + -
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Residues in contact with ASP 220 (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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216B GLN* 3.0 44.2 + - - +
217B GLU* 3.1 10.0 + - - +
219B ILE* 1.3 79.9 - - - +
221B ILE* 1.3 56.8 + - + +
223B THR* 3.7 5.4 + - - -
224B SER* 2.7 36.7 + - - -
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Residues in contact with ILE 221 (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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217B GLU* 3.0 26.0 + - + +
218B ILE* 3.6 8.5 - - - +
220B ASP* 1.3 76.5 - - - +
222B VAL* 1.3 66.1 + - - +
224B SER* 3.4 11.1 + - - -
225B TRP* 3.6 14.9 + - + +
267B VAL* 5.4 0.6 - - + +
270B ALA* 3.6 39.3 - - + +
271B ILE* 4.1 12.8 - - + +
274B ARG* 3.6 41.1 - - + -
275B PHE* 4.5 3.4 - - + -
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Residues in contact with VAL 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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218B ILE* 3.0 21.0 + - + +
219B ILE 3.8 4.7 - - - +
221B ILE* 1.3 78.3 - - - +
223B THR* 1.3 60.0 + - - +
224B SER 3.5 0.5 + - - -
225B TRP* 3.5 5.2 + - - +
228B VAL* 3.2 26.0 - - + +
231B ALA* 3.7 18.8 - - + -
247B ILE* 3.9 20.6 - - + -
249B LEU* 3.5 32.3 - - + -
267B VAL* 3.9 11.0 - - + -
271B ILE* 3.9 26.5 - - + -
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Residues in contact with THR 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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219B ILE* 2.9 29.3 + - + +
220B ASP* 3.7 9.2 + - - -
221B ILE 3.5 0.2 - - - -
222B VAL* 1.3 77.8 - - + +
224B SER* 1.3 65.0 + - - +
225B TRP 3.4 1.3 - - - +
228B VAL* 3.5 19.9 - - + +
229B SER 5.9 0.2 - - - -
230B GLY* 5.1 2.9 - - - -
231B ALA* 4.2 28.9 - - + +
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Residues in contact with SER 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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220B ASP 2.7 21.6 + - - -
221B ILE* 3.4 6.1 + - - -
223B THR* 1.3 82.4 + - - +
225B TRP* 1.3 66.4 + - - +
226B PRO* 3.4 5.8 - - - +
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Residues in contact with TRP 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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225A TRP* 4.4 6.5 - + - -
226A PRO* 3.7 24.3 - - + +
266A GLN* 4.1 28.3 - - - -
221B ILE* 3.6 10.0 + - + +
222B VAL 3.5 13.6 + - - +
223B THR 3.4 0.7 - - - +
224B SER* 1.3 82.0 + - - +
226B PRO* 1.3 78.6 - - + +
227B GLY 4.0 9.0 - - - -
228B VAL* 3.3 23.0 + - + +
263B VAL* 4.6 2.2 - - + -
266B GLN* 2.9 51.5 + - + +
267B VAL* 3.9 22.0 - - + -
270B ALA* 3.8 27.6 - - + -
273B ARG* 5.0 3.1 - - - -
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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