Contacts of the helix formed by residues 220 - 233 (chain B) in PDB entry 3DXF
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 THR 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B THR* 3.7 5.8 - - - -
181B GLY 4.0 9.6 - - - -
182B ASP* 3.4 31.0 - - - +
183B VAL 4.1 1.1 - - - -
184B PRO* 3.6 20.4 - - + +
219B HIS* 1.3 76.9 - - - +
221B ALA* 1.3 59.8 + - - +
222B GLU* 3.6 13.8 + - - +
223B GLU* 3.0 34.0 + - - +
224B TYR* 2.9 25.9 + - - -
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Residues in contact with ALA 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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176B LEU* 3.4 7.8 - - + +
178B LEU* 3.3 41.3 - - + +
180B THR* 2.9 16.9 - - + +
181B GLY 4.6 1.8 + - - +
220B THR* 1.3 72.2 - - - +
222B GLU* 1.3 56.9 + - - +
224B TYR* 3.4 10.1 - - - +
225B ALA* 2.8 28.1 + - - +
238B ASP* 3.7 21.9 - - - +
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Residues in contact with GLU 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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181B GLY 5.6 0.2 + - - -
220B THR* 3.6 11.4 + - - +
221B ALA* 1.3 80.4 - - - +
223B GLU* 1.3 58.4 + - + +
225B ALA* 3.4 2.4 + - - +
226B ALA* 3.0 28.2 + - + +
238B ASP* 3.3 23.4 + - + +
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Residues in contact with GLU 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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184B PRO* 5.4 2.7 - - - +
218B ARG 3.7 3.8 - - - +
219B HIS* 2.9 41.2 + - + +
220B THR* 3.0 26.5 + - - +
222B GLU* 1.3 78.1 - - + +
224B TYR* 1.3 60.4 + - - +
226B ALA* 3.3 7.2 + - - +
227B LEU* 2.9 36.9 + - + +
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Residues in contact with TYR 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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154B CYS* 5.1 0.9 + - - -
156B PHE* 3.8 22.0 - + - -
159B LEU* 3.9 28.7 - - + -
176B LEU* 3.7 11.9 - - + -
178B LEU* 3.7 16.2 - - + -
185B MET* 3.5 32.2 + - + +
186B ASP 4.3 0.2 + - - -
187B GLY* 4.1 8.5 - - - -
217B CYS* 5.2 0.5 - - - -
219B HIS* 3.6 33.6 - + + -
220B THR 2.9 22.8 + - - -
221B ALA* 3.4 10.1 - - - +
223B GLU* 1.3 73.4 - - - +
225B ALA* 1.3 59.1 + - - +
227B LEU* 3.3 1.7 + - - +
228B LEU* 2.9 36.3 + - + +
285B LEU* 3.6 35.2 - - + -
289B LEU* 4.9 0.5 - - - +
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Residues in contact with ALA 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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176B LEU* 3.8 8.9 - - + +
221B ALA 2.8 18.6 + - - +
222B GLU 3.8 4.0 - - - +
224B TYR* 1.3 72.6 - - - +
226B ALA* 1.3 53.7 + - - +
228B LEU* 3.7 2.0 - - - +
229B THR* 2.6 38.9 + - - -
236B VAL* 3.3 27.3 - - + +
237B HIS 3.7 3.4 - - - +
238B ASP* 3.5 25.1 - - + +
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Residues in contact with ALA 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 GLU* 3.0 17.5 + - + +
223B GLU* 3.5 9.4 - - - +
225B ALA* 1.3 77.1 - - - +
227B LEU* 1.3 59.4 + - + +
229B THR* 3.3 9.4 + - - -
230B LYS* 3.1 25.3 + - - +
236B VAL 5.2 0.2 - - - -
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Residues in contact with LEU 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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219B HIS* 4.0 24.0 - - + +
223B GLU* 2.9 22.4 + - + +
224B TYR 3.3 2.2 + - - +
226B ALA* 1.3 71.8 - - + +
228B LEU* 1.3 66.7 + - - +
230B LYS* 3.2 11.0 + - + -
231B HIS* 3.0 34.6 + - - +
285B LEU* 3.7 25.1 - - + -
286B ASP* 3.4 39.0 - - + +
289B LEU* 3.6 16.6 - - + -
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Residues in contact with LEU 228 (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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159B LEU* 4.3 15.0 - - + -
165B PRO* 4.2 9.6 - - + -
176B LEU* 3.8 28.5 - - + -
224B TYR* 2.9 23.5 + - + +
225B ALA* 3.7 4.3 - - - +
227B LEU* 1.3 74.9 - - - +
229B THR* 1.3 55.6 + - - +
231B HIS* 5.2 0.2 - - - -
232B THR* 2.6 51.0 + - + +
236B VAL* 4.1 23.8 - - + -
289B LEU* 3.7 19.9 - - + +
296B PHE* 3.7 35.9 - - + -
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Residues in contact with THR 229 (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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225B ALA 2.6 25.5 + - - -
226B ALA* 3.4 9.0 - - - -
227B LEU 3.3 0.4 - - - -
228B LEU* 1.3 74.9 - - - +
230B LYS* 1.3 62.3 + - - +
233B ARG* 3.3 21.9 + - - -
234B LYS 3.3 18.9 - - - +
235B VAL* 4.3 11.9 - - + -
236B VAL* 3.0 23.5 + - - +
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Residues in contact with LYS 230 (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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226B ALA 3.1 12.1 + - - +
227B LEU* 3.4 17.7 - - + +
228B LEU 3.2 0.4 - - - -
229B THR* 1.3 80.9 - - - +
231B HIS* 1.3 96.3 + - + +
233B ARG* 4.1 13.0 + - - +
286B ASP* 3.9 9.0 - - - +
290B GLU* 4.0 10.5 + - - +
293B LYS* 5.2 3.0 + - - +
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Residues in contact with HIS 231 (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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227B LEU* 3.0 28.8 + - + +
228B LEU 4.6 0.4 - - - +
230B LYS* 1.3 108.9 + - + +
232B THR* 1.3 65.8 + - + +
233B ARG* 3.2 7.4 + - - +
286B ASP* 2.5 40.5 + - - -
289B LEU* 3.5 40.8 - - + +
290B GLU* 3.5 28.1 - - + +
293B LYS* 3.1 37.0 + - + +
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Residues in contact with THR 232 (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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228B LEU* 2.6 38.7 + - + +
231B HIS* 1.3 76.9 - - + +
233B ARG* 1.3 69.2 + - - +
234B LYS* 3.1 36.2 + - - +
236B VAL* 4.0 5.5 - - + +
289B LEU* 5.5 0.9 - - + -
293B LYS* 4.8 6.3 - - + -
296B PHE* 4.1 38.1 - - + -
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Residues in contact with ARG 233 (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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229B THR 3.3 16.0 + - - -
230B LYS 4.1 13.1 + - - +
231B HIS 3.2 3.9 + - - +
232B THR* 1.3 81.0 + - - +
234B LYS* 1.3 68.5 + - - +
235B VAL* 5.8 0.7 - - - +
293B LYS* 4.0 35.6 - - - +
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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