Contacts of the helix formed by residues 214 - 227 (chain B) in PDB entry 3H8Q
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 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B LEU* 6.5 0.2 - - + -
212B VAL 3.4 1.0 + - - -
213B ASP* 1.3 77.4 - - + +
215B GLY* 1.3 58.6 + - - +
216B ALA* 3.2 6.7 + - - +
217B ARG* 3.2 32.3 + - + +
218B VAL* 3.1 27.7 + - + +
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Residues in contact with GLY 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 LEU* 3.4 31.5 - - - +
212B VAL* 3.4 18.0 + - - -
214B ASP* 1.3 73.9 - - - +
216B ALA* 1.3 58.9 + - - +
218B VAL* 3.7 5.1 - - - +
219B GLN* 3.0 28.2 + - - +
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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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214B ASP* 3.2 4.2 - - - +
215B GLY* 1.3 75.1 - - - +
217B ARG* 1.3 58.3 - - - +
219B GLN* 3.3 6.8 + - - +
220B GLU* 3.0 28.3 + - - +
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Residues in contact with ARG 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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163B ARG* 5.7 4.7 - - + -
166B LEU* 4.4 13.7 - - + -
214B ASP* 3.2 34.9 + - - +
216B ALA* 1.3 78.8 - - - +
218B VAL* 1.3 57.3 + - - +
220B GLU* 3.6 24.2 + - - +
221B VAL* 3.1 36.7 + - + +
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Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 4.3 25.6 - - + -
170B LEU* 4.2 26.8 - - + +
207B LEU* 4.6 6.7 - - + -
209B LEU* 3.3 25.4 - - + -
212B VAL* 4.2 10.3 - - + -
213B ASP 4.6 3.6 - - - +
214B ASP* 3.1 19.6 + - + +
215B GLY* 3.7 9.6 - - - +
216B ALA 3.2 0.2 - - - -
217B ARG* 1.3 75.0 - - - +
219B GLN* 1.3 58.6 + - - +
221B VAL* 3.4 2.7 + - - +
222B LEU* 2.9 30.1 + - + +
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Residues in contact with GLN 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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184B LYS* 3.3 36.6 - - - -
209B LEU* 4.3 12.5 - - + +
215B GLY 3.0 17.8 + - - +
216B ALA* 3.7 6.5 - - - +
218B VAL* 1.3 73.8 - - - +
220B GLU* 1.3 59.5 + - - +
222B LEU* 3.6 8.2 - - + +
223B SER* 2.9 35.5 + - - +
229B LYS 4.1 21.5 - - - +
231B VAL* 4.3 11.9 - - + -
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Residues in contact with GLU 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 ALA 3.0 16.5 + - - +
217B ARG* 3.6 37.3 + - - +
219B GLN* 1.3 75.0 - - - +
221B VAL* 1.3 65.0 + - + +
223B SER* 3.2 16.8 + - - -
224B GLU* 3.2 26.8 + - + +
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Residues in contact with VAL 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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163B ARG* 5.0 16.8 - - + +
166B LEU* 4.0 15.3 - - + -
167B ARG* 3.8 39.9 - - + +
170B LEU* 3.4 23.3 - - + -
217B ARG* 3.1 21.0 + - + +
218B VAL 4.0 3.1 - - - +
219B GLN 3.4 0.2 - - - -
220B GLU* 1.3 80.5 - - + +
222B LEU* 1.3 61.4 + - - +
224B GLU* 3.2 11.1 + - + +
225B ILE* 3.1 23.7 + - + +
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Residues in contact with LEU 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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170B LEU* 4.3 9.8 - - + +
174B ILE* 5.1 1.6 - - + -
182B PHE* 3.6 62.6 - - + -
209B LEU* 4.3 17.0 - - + -
218B VAL* 2.9 19.5 + - + +
219B GLN* 3.6 8.3 - - + +
221B VAL* 1.3 78.9 - - - +
223B SER* 1.3 51.4 + - - +
225B ILE* 3.5 11.5 + - + +
226B THR* 2.7 51.0 + - + +
228B GLN 4.5 0.7 - - - +
231B VAL* 5.4 2.2 - - + -
233B ASN* 4.0 17.5 - - + +
235B PHE* 4.8 1.1 - - + -
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Residues in contact with SER 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 GLN* 2.9 19.4 + - - +
220B GLU* 3.2 11.5 + - - -
222B LEU* 1.3 72.6 - - - +
224B GLU* 1.3 61.9 + - - +
226B THR* 3.9 0.2 - - - -
227B ASN* 2.9 28.6 + - - +
228B GLN 3.1 25.7 + - - -
229B LYS* 3.5 22.8 + - - +
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Residues in contact with GLU 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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167B ARG* 3.5 30.3 - - - +
220B GLU* 3.2 24.2 + - + +
221B VAL* 3.2 12.7 + - + +
223B SER* 1.3 77.8 - - - +
225B ILE* 1.3 62.8 + - - +
227B ASN* 3.3 15.0 - - - +
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Residues in contact with ILE 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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167B ARG* 4.5 11.0 - - + +
170B LEU* 4.0 32.8 - - + -
171B VAL* 4.2 22.4 - - + +
174B ILE* 4.8 13.7 - - + -
221B VAL* 3.1 18.5 + - + +
222B LEU* 3.7 13.5 - - + +
224B GLU* 1.3 79.9 - - + +
226B THR* 1.3 70.2 + - + +
227B ASN* 4.2 2.8 - - - +
235B PHE* 4.9 3.6 - - + -
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Residues in contact with THR 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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222B LEU* 2.7 25.2 + - + +
225B ILE* 1.3 83.6 - - + +
227B ASN* 1.3 68.8 + - - +
228B GLN 3.1 14.8 + - - -
233B ASN* 3.2 28.5 + - - +
235B PHE* 3.4 34.5 - - + -
240B HIS* 3.9 24.4 + - - -
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Residues in contact with ASN 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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223B SER* 2.9 16.8 + - - +
224B GLU* 3.3 15.6 - - - +
225B ILE 4.2 2.8 - - - +
226B THR* 1.3 78.9 - - - +
228B GLN* 1.3 57.2 + - - +
229B LYS* 5.5 2.9 - - - +
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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