Contacts of the helix formed by residues 203 - 218 (chain B) in PDB entry 4HH3
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 ARG 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196B ALA* 3.5 6.5 - - - -
197B GLN* 6.4 0.7 - - - -
201B GLY 4.9 4.7 - - - +
202B ARG* 1.3 79.0 - - - +
204B ARG* 1.3 67.5 + - - +
205B GLY 3.3 2.2 + - - +
206B GLU* 2.9 19.6 + - + +
207B PHE* 2.9 22.7 + - - +
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Residues in contact with ARG 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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167B MET 4.9 2.0 + - - -
168B SER 2.9 28.7 + - - -
169B THR* 3.1 30.7 + - - +
170B GLY* 3.9 8.4 - - - +
194B ALA* 6.1 6.3 - - + -
195B ILE* 6.4 0.9 - - + -
196B ALA* 3.5 16.6 - - + +
197B GLN* 6.2 2.0 - - - +
203B ARG* 1.3 72.0 - - - +
205B GLY* 1.3 64.8 + - - +
207B PHE* 4.0 0.2 - - - +
208B MET* 2.9 41.5 + - + +
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Residues in contact with GLY 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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203B ARG* 3.4 2.2 - - - +
204B ARG* 1.3 80.8 - - - +
206B GLU* 1.3 61.8 + - - +
208B MET* 3.4 2.9 + - - +
209B GLU* 3.1 23.7 + - - +
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Residues in contact with GLU 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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201B GLY 4.3 1.6 - - - +
202B ARG* 2.8 46.9 + - - +
203B ARG* 2.9 39.1 + - + +
205B GLY* 1.3 74.7 - - - +
207B PHE* 1.3 65.0 + - - +
209B GLU* 3.5 12.6 + - - +
210B THR* 2.8 34.1 + - - -
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Residues in contact with PHE 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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195B ILE* 4.1 28.9 - - + -
196B ALA* 4.0 20.6 - - + -
199B PHE* 3.7 31.2 - + - -
202B ARG* 3.8 31.2 - - + +
203B ARG 2.9 20.1 + - - +
204B ARG 4.0 1.3 - - - +
206B GLU* 1.3 84.2 - - - +
208B MET* 1.3 70.7 + - - +
210B THR* 3.3 3.1 + - - -
211B MET* 3.0 63.6 + - + +
223B VAL* 4.8 1.1 - - + -
225B VAL* 4.1 17.3 - - + -
236B VAL* 5.4 3.8 - - + -
249B LEU* 5.4 1.3 - - + -
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Residues in contact with MET 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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165B VAL* 4.5 6.1 - - + -
166B SER 4.6 0.9 - - - +
167B MET* 4.1 37.9 - - + +
170B GLY* 4.6 6.7 - - - -
195B ILE* 4.0 26.5 - - + -
204B ARG* 2.9 35.3 + - + +
205B GLY* 4.0 3.1 - - - +
207B PHE* 1.3 80.6 - - + +
209B GLU* 1.3 57.3 + - - +
211B MET* 3.4 2.4 + - + +
212B THR* 2.8 41.6 + - - +
249B LEU* 3.9 26.5 - - + -
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Residues in contact with GLU 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 GLY 3.1 18.5 + - - +
206B GLU* 3.7 12.4 - - - +
208B MET* 1.3 76.3 - - - +
210B THR* 1.3 57.9 + - - +
212B THR* 3.8 4.7 - - - -
213B ASN* 2.9 56.8 + - - +
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Residues in contact with THR 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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202B ARG* 3.4 22.3 + - - +
206B GLU* 2.8 20.4 + - - -
207B PHE* 3.4 9.0 - - + -
209B GLU* 1.3 77.9 + - - +
211B MET* 1.3 64.1 + - + +
213B ASN* 3.9 5.8 - - - +
214B LEU* 3.1 27.7 + - + +
223B VAL* 3.7 28.7 - - + -
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Residues in contact with MET 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 PHE* 3.0 55.8 + - + +
208B MET* 3.7 5.4 - - - +
210B THR* 1.3 78.8 - - + +
212B THR* 1.3 56.8 + - - +
214B LEU* 3.4 1.1 + - + -
215B ALA* 2.9 30.2 + - - +
223B VAL* 3.6 36.6 - - + -
236B VAL* 4.0 17.0 - - + -
238B PRO* 3.6 32.9 - - + +
249B LEU* 4.0 24.7 - - + -
251B CYS* 4.3 8.5 - - - -
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Residues in contact with THR 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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167B MET* 3.8 26.7 - - + +
208B MET* 2.8 31.4 + - - +
209B GLU* 3.8 6.1 - - - -
211B MET* 1.3 73.8 - - - +
213B ASN* 1.3 68.3 + - - +
215B ALA* 3.4 7.3 + - - +
216B ALA* 3.1 23.4 + - + +
240B VAL* 4.5 9.6 - - + +
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Residues in contact with ASN 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 GLU* 2.9 45.9 + - - +
210B THR* 3.9 5.7 - - - +
212B THR* 1.3 82.2 - - - +
214B LEU* 1.3 61.8 + - + +
216B ALA* 3.3 7.6 + - - +
217B THR* 2.9 27.3 + - - -
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Residues in contact with LEU 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 THR* 3.1 21.8 + - + +
211B MET 3.8 3.4 - - - +
213B ASN* 1.3 77.6 - - + +
215B ALA* 1.3 62.7 + - - +
217B THR* 3.2 11.4 + - - +
218B GLU* 3.2 16.1 + - - -
219B SER* 3.9 15.7 + - - -
220B ALA 4.7 4.9 + - - +
221B ALA* 3.3 28.5 - - + +
222B PRO 4.6 0.2 - - - -
223B VAL* 3.4 30.7 - - + +
238B PRO* 3.8 21.1 - - + -
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Residues in contact with ALA 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 MET 2.9 17.5 + - - +
212B THR 3.6 5.2 - - - +
213B ASN 3.3 0.2 - - - -
214B LEU* 1.3 77.0 - - - +
216B ALA* 1.3 61.5 + - - +
218B GLU* 3.3 18.9 + - - +
238B PRO* 3.8 24.6 - - + +
239B ARG* 4.1 1.4 - - - +
240B VAL* 3.7 34.8 - - + +
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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 THR* 3.1 18.4 + - + +
213B ASN* 3.8 6.7 - - - +
214B LEU 3.2 0.2 - - - -
215B ALA* 1.3 72.3 - - - +
217B THR* 1.3 63.9 + - - +
218B GLU* 3.1 13.7 + - - +
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Residues in contact with THR 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 ASN 2.9 16.7 + - - -
214B LEU* 3.2 15.0 + - + +
216B ALA* 1.3 75.4 - - - +
218B GLU* 1.3 67.8 + - - +
219B SER* 3.0 23.3 + - - -
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Residues in contact with GLU 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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214B LEU 3.2 6.9 + - - -
215B ALA* 3.3 14.1 + - - +
216B ALA* 3.1 12.1 - - - +
217B THR* 1.3 79.5 - - - +
219B SER* 1.3 62.2 + - - +
220B ALA* 3.3 7.2 - - - +
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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