Contacts of the helix formed by residues 220 - 234 (chain B) in PDB entry 4D1Q
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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218B ARG* 3.8 30.3 - - + +
219B SER* 1.3 77.2 - - - +
221B ALA* 1.3 60.2 + - - +
222B GLU* 3.5 14.2 + - - +
223B ASN* 2.9 27.4 + - - +
224B ILE* 2.8 33.6 + - - +
252B ASN* 4.6 4.5 - - - +
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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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220B THR* 1.3 72.2 - - - +
222B GLU* 1.3 72.2 + - - +
224B ILE* 2.9 5.2 + - - +
225B TYR* 2.8 27.0 + - - +
252B ASN* 4.0 11.8 + - - +
255B LYS* 3.6 34.3 - - + +
256B SER* 3.7 29.3 - - - +
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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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220B THR* 3.8 11.9 + - - +
221B ALA* 1.3 85.4 + - - +
223B ASN* 1.3 61.7 + - - +
225B TYR* 3.5 6.8 + - - +
226B LYS* 2.9 30.6 + - - +
255B LYS* 5.0 7.1 + - - +
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Residues in contact with ASN 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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214B LEU* 4.8 14.4 - - + -
217B GLU* 3.1 42.3 + - + +
218B ARG* 4.6 2.8 + - - +
219B SER 4.2 5.0 + - - +
220B THR* 2.9 32.9 + - - +
221B ALA 3.1 0.6 - - - -
222B GLU* 1.3 78.5 - - - +
224B ILE* 1.3 60.9 + - - +
226B LYS* 3.2 16.7 + - - +
227B LYS* 2.8 33.9 + - + +
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Residues in contact with ILE 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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179B ILE* 5.1 6.3 - - + -
181B LEU* 3.6 31.0 - - + -
192B LEU* 3.6 27.4 - - + +
214B LEU* 4.5 19.5 - - + -
219B SER 4.5 1.1 - - - +
220B THR 2.8 23.6 + - - +
221B ALA* 3.5 4.9 - - - +
223B ASN* 1.3 74.4 - - - +
225B TYR* 1.3 53.4 + - - +
227B LYS 3.3 0.2 + - - -
228B LEU* 2.8 38.3 + - + +
252B ASN* 3.9 25.1 - - + +
253B VAL* 4.1 14.4 - - + +
256B SER* 4.0 15.0 - - - +
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Residues in contact with TYR 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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221B ALA 2.8 16.2 + - - +
222B GLU* 3.6 6.7 - - - +
224B ILE* 1.3 75.2 - - - +
226B LYS* 1.3 51.8 + - - +
228B LEU* 2.8 30.0 + - + +
229B LYS* 2.6 70.9 + - + +
240B LEU* 4.6 6.7 - - + +
256B SER* 3.6 30.2 - - - +
257B LEU* 5.2 0.2 - - + -
259B ASN* 6.6 0.2 - - + -
260B ASN* 4.4 21.1 + - - -
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Residues in contact with LYS 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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217B GLU* 5.7 1.6 - - - +
222B GLU 2.9 18.2 + - - +
223B ASN* 3.4 20.2 - - - +
225B TYR* 1.3 77.9 - - - +
227B LYS* 1.3 56.8 + - - +
229B LYS* 3.2 9.2 + - - +
230B ALA* 2.8 34.2 + - - +
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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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192B LEU* 4.1 8.3 - - + -
212B LYS* 3.6 33.9 - - + +
213B SER* 3.0 27.8 + - - +
214B LEU* 3.7 24.7 - - + +
215B ASP* 3.8 16.9 + - - -
223B ASN 2.8 18.4 + - - +
224B ILE 3.8 3.4 - - - +
226B LYS* 1.3 70.9 - - - +
228B LEU* 1.3 59.4 + - - +
230B ALA* 3.4 11.2 - - + +
231B ILE* 2.8 36.2 + - + +
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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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179B ILE* 3.4 33.2 - - + -
192B LEU* 3.8 10.7 - - + +
194B VAL* 3.8 14.1 - - + -
224B ILE* 2.8 14.6 + - + +
225B TYR* 3.1 27.4 - - + +
227B LYS* 1.3 73.3 - - - +
229B LYS* 1.3 63.8 - - - +
231B ILE* 3.2 4.4 + - + +
232B PHE* 3.1 45.4 + - + -
240B LEU* 3.7 20.2 - - + -
245B PHE* 4.2 11.2 - - + -
256B SER* 6.5 0.2 - - - -
257B LEU* 4.3 6.5 - - + -
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Residues in contact with LYS 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 TYR* 2.6 49.8 + - + +
226B LYS* 3.3 13.5 - - + +
228B LEU* 1.3 71.7 - - - +
230B ALA* 1.3 57.8 - - - +
232B PHE* 3.3 7.8 + - - +
233B SER* 3.2 26.4 + - - +
237B VAL 4.6 1.5 - - - +
238B GLU* 2.9 41.0 + - - +
239B ASP* 4.4 1.4 + - - +
240B LEU* 3.9 29.4 - - + +
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Residues in contact with ALA 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 LYS* 2.8 21.8 + - - +
227B LYS* 3.4 17.9 - - + +
229B LYS* 1.3 73.7 - - - +
231B ILE* 1.3 65.5 + - - +
232B PHE 3.1 1.7 + - - -
233B SER* 3.4 20.1 + - - -
234B GLN* 3.5 12.1 + - - +
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Residues in contact with ILE 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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192B LEU* 3.7 28.3 - - + +
194B VAL* 4.0 23.3 - - + -
209B LEU* 3.9 37.0 - - + +
210B GLY* 4.2 8.5 - - - +
212B LYS* 4.0 31.0 - - + +
227B LYS 2.8 30.3 + - - +
228B LEU* 3.2 5.6 + - - +
230B ALA* 1.3 73.4 - - - +
232B PHE* 1.3 63.1 + - - +
234B GLN* 3.1 30.1 - - - +
235B PHE* 3.6 5.9 - - - -
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Residues in contact with PHE 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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166B ILE* 5.4 1.3 - - + -
170B VAL* 5.1 2.7 - - + -
177B ALA* 4.5 4.5 - - + -
194B VAL* 4.1 12.1 - - + -
196B LEU* 3.7 21.3 - - + -
209B LEU* 3.4 29.6 - - + -
228B LEU* 3.1 42.4 + - + +
229B LYS 3.5 9.6 - - - +
230B ALA 3.1 0.6 - - - -
231B ILE* 1.3 74.4 - - - +
233B SER* 1.3 64.7 + - - +
234B GLN 3.1 2.2 - - - -
235B PHE* 2.9 20.5 + + - +
237B VAL* 3.4 41.4 + - + +
240B LEU* 3.4 26.9 - - + -
243B ILE* 3.7 22.0 - - + -
245B PHE* 4.2 7.4 - + - -
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Residues in contact with SER 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 LYS* 3.2 17.4 + - - +
230B ALA* 3.4 15.2 + - - -
232B PHE* 1.3 75.5 - - - +
234B GLN* 1.3 56.2 + - - +
236B ASN* 2.7 31.7 + - - +
237B VAL 3.8 4.6 + - - -
238B GLU* 3.7 25.1 + - - -
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Residues in contact with GLN 234 (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 LYS* 3.1 52.7 - - - +
160B ALA* 4.6 5.9 + - - +
209B LEU 4.1 9.0 - - - +
212B LYS* 3.3 37.0 - - - +
230B ALA 3.5 10.3 - - - +
231B ILE* 3.1 21.3 - - - +
232B PHE 3.0 0.6 + - - -
233B SER* 1.3 77.6 - - - +
235B PHE* 1.3 65.9 + - + +
236B ASN* 3.4 4.5 + - - -
595B ASP* 4.4 0.5 - - - +
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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