Contacts of the helix formed by residues 217 - 229 (chain B) in PDB entry 5DX1
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 217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B PHE 5.0 0.6 + - - -
154B GLY* 4.0 15.8 + - - -
216B SER* 1.3 69.7 - - - +
218B MET* 1.3 62.1 + - - +
219B ALA* 3.0 7.1 + - - -
220B GLN* 3.2 37.6 + - - +
221B HIS* 4.1 8.4 + - - -
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Residues in contact with MET 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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153B TYR 3.6 12.8 - - - +
154B GLY* 3.2 28.8 - - - +
156B LEU* 3.6 38.4 - - + +
159B GLN* 3.6 20.2 - - + +
194B GLY* 3.4 28.5 - - - +
195B SER* 3.8 8.5 - - - +
214B GLU* 4.2 5.6 - - + +
216B SER* 3.0 18.3 + - - +
217B THR* 1.3 79.6 + - - +
219B ALA* 1.3 62.0 + - - +
220B GLN 3.2 0.2 - - - -
221B HIS* 3.0 19.0 + - + +
222B ALA* 3.0 20.6 + - - +
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Residues in contact with ALA 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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214B GLU* 3.7 29.1 - - + +
216B SER 3.1 17.0 + - - +
217B THR* 3.0 1.5 - - - -
218B MET* 1.3 76.5 - - - +
220B GLN* 1.3 63.2 + - + +
222B ALA* 3.3 6.1 + - - +
223B GLU* 3.0 22.4 + - - +
237B VAL* 3.8 13.0 - - + +
239B PRO* 4.0 23.1 - - + -
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Residues in contact with GLN 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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217B THR* 3.2 31.2 + - - +
219B ALA* 1.3 78.1 - - + +
221B HIS* 1.3 73.2 + - + +
223B GLU* 3.2 8.7 + - - +
224B VAL* 3.2 26.1 + - + +
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Residues in contact with HIS 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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326A LEU* 3.7 32.0 - - + +
329A ALA* 4.0 21.5 - - + -
333A GLU* 5.4 1.4 + - - -
154B GLY 4.8 5.1 + - - -
156B LEU* 3.9 16.4 - - + +
195B SER* 4.9 0.7 - - - -
217B THR 4.4 5.0 + - - -
218B MET* 3.0 46.0 + - + +
220B GLN* 1.3 82.1 - - + +
222B ALA* 1.3 66.5 + - - +
224B VAL* 3.3 7.5 + - - +
225B LEU* 3.1 25.5 + - - +
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Residues in contact with ALA 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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193B CYS* 4.3 10.3 - - - -
194B GLY 3.5 17.9 + - - +
195B SER* 3.5 26.7 + - - +
196B GLY* 4.3 2.5 - - - +
200B PHE* 4.9 0.3 - - - -
218B MET 3.0 7.3 + - - +
219B ALA* 3.6 9.2 - - - +
221B HIS* 1.3 77.7 - - - +
223B GLU* 1.3 61.7 + - - +
225B LEU* 3.2 4.1 + - - +
226B VAL* 3.0 26.5 + - + +
237B VAL* 4.2 14.1 - - + -
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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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219B ALA 3.0 14.2 + - - +
220B GLN* 3.5 11.9 - - - +
221B HIS 3.2 0.4 - - - -
222B ALA* 1.3 75.5 - - - +
224B VAL* 1.3 64.4 + - + +
226B VAL* 3.3 8.9 + - - +
227B LYS* 3.2 60.3 + - - +
232B THR* 5.1 2.3 + - - -
237B VAL* 3.9 32.1 + - + +
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Residues in contact with VAL 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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325A ALA* 3.8 27.8 - - + +
326A LEU* 4.0 18.8 - - + -
220B GLN 3.2 14.3 + - - +
221B HIS* 3.5 11.0 - - - +
222B ALA 3.2 0.2 - - - -
223B GLU* 1.3 79.4 - - + +
225B LEU* 1.3 57.4 + - - +
227B LYS* 3.3 9.7 + - + +
228B SER* 2.9 28.3 + - - -
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Residues in contact with LEU 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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313A TRP* 4.6 3.8 - - + -
321A VAL* 5.4 0.2 - - + -
322A ASP 3.4 21.3 - - - +
323A LEU* 3.9 30.5 - - + +
325A ALA* 4.7 3.8 - - + -
326A LEU* 3.6 33.0 - - + -
195B SER* 3.6 23.1 - - - +
200B PHE* 3.7 19.5 - - + -
221B HIS 3.1 10.5 + - - +
222B ALA 3.2 6.5 + - - +
224B VAL* 1.3 72.8 - - - +
226B VAL* 1.3 61.8 + - - +
228B SER* 3.3 7.0 - - - +
229B ASN* 2.9 37.2 + - - +
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Residues in contact with VAL 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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196B GLY* 6.3 1.1 - - - -
200B PHE* 4.1 17.7 - - + -
222B ALA* 3.0 19.3 + - + +
223B GLU* 3.3 15.2 + - - +
225B LEU* 1.3 75.8 - - - +
227B LYS* 1.3 59.2 + - - +
229B ASN 3.8 0.5 - - - -
230B ASN 3.3 3.1 + - - -
231B LEU* 2.9 48.0 + - + +
232B THR* 3.7 8.2 + - - +
235B ILE* 3.5 48.9 - - + +
237B VAL* 4.0 12.6 - - + -
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Residues in contact with LYS 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 GLU* 3.2 43.5 + - + +
224B VAL* 3.7 10.8 - - + +
226B VAL* 1.3 75.7 - - - +
228B SER* 1.3 59.5 + - - +
230B ASN* 3.0 26.9 + - - +
232B THR* 3.8 19.5 - - - +
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Residues in contact with SER 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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322A ASP* 4.2 15.6 + - - +
325A ALA* 3.6 27.3 - - - +
224B VAL* 2.9 18.3 + - - -
225B LEU* 3.2 15.9 + - - +
227B LYS* 1.3 76.9 - - - +
229B ASN* 1.3 64.6 + - - +
230B ASN* 3.2 9.7 + - - -
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Residues in contact with ASN 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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320A GLY 4.8 1.2 - - - +
321A VAL* 3.8 15.7 - - - +
322A ASP* 2.8 53.6 + - - +
200B PHE* 4.1 14.7 - - + -
225B LEU* 2.9 31.8 + - - +
226B VAL 4.3 0.4 - - - +
228B SER* 1.3 81.2 + - - +
230B ASN* 1.3 71.4 + - - +
231B LEU* 3.4 15.9 + - + +
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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