Contacts of the helix formed by residues 220 - 233 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218G ARG* 3.7 22.3 - - + +
219G SER* 1.3 79.8 - - - +
221G ALA* 1.3 56.4 + - - +
222G GLU* 3.9 22.9 + - - +
223G ASN* 2.5 57.2 + - - +
224G ILE 3.1 8.5 + - - -
252G ASN* 3.6 5.6 - - - +
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Residues in contact with ALA 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220G THR* 1.3 72.4 - - - +
222G GLU* 1.3 70.9 + - - +
224G ILE* 4.1 4.7 - - - -
225G TYR* 2.9 28.7 + - - +
252G ASN* 3.1 33.2 + - - +
255G LYS* 3.9 17.9 - - + +
256G SER* 3.5 24.6 - - - +
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Residues in contact with GLU 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220G THR* 2.9 21.2 + - - +
221G ALA* 1.3 87.2 + - - +
223G ASN* 1.3 61.5 + - - +
225G TYR* 4.1 4.9 - - - +
226G LYS* 3.2 25.6 + - - +
255G LYS* 5.0 7.1 - - - +
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Residues in contact with ASN 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214G LEU* 4.4 14.1 - - + +
217G GLU* 3.7 40.1 + - - +
218G ARG* 4.5 1.4 - - - +
219G SER* 5.0 1.6 - - - -
220G THR* 2.5 43.3 + - - +
222G GLU* 1.3 75.0 + - - +
224G ILE* 1.3 65.9 + - - +
225G TYR 3.1 1.3 - - - -
226G LYS* 3.0 15.7 + - - +
227G LYS* 2.8 26.7 + - - +
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Residues in contact with ILE 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179G ILE* 5.2 6.3 - - + -
181G LEU* 3.5 31.6 - - + -
192G LEU* 3.5 31.0 - - + +
214G LEU* 4.4 12.3 - - + +
219G SER* 3.8 11.7 - - - +
220G THR 3.1 11.0 + - - +
221G ALA* 3.6 4.7 - - - +
223G ASN* 1.3 75.4 - - - +
225G TYR* 1.3 65.8 + - - +
227G LYS 3.2 0.5 + - - -
228G LEU* 2.9 20.1 + - + +
252G ASN* 3.6 39.5 - - + +
253G VAL* 3.8 10.3 - - + +
256G SER* 4.0 11.2 - - - +
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Residues in contact with TYR 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221G ALA 2.9 17.3 + - - +
222G GLU* 4.1 5.2 - - - +
224G ILE* 1.3 75.2 - - - +
226G LYS* 1.3 58.4 + - - +
228G LEU* 2.6 37.2 + - + +
229G LYS* 3.0 54.8 + - + -
240G LEU* 4.4 5.7 - - + +
256G SER* 2.7 37.4 - - - -
257G LEU* 4.6 8.7 - - + -
259G ASN* 5.2 6.4 - - + +
260G ASN* 3.5 31.9 + - - -
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Residues in contact with LYS 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222G GLU 3.2 18.1 + - - +
223G ASN* 3.0 17.4 + - - +
225G TYR* 1.3 82.6 - - - +
227G LYS* 1.3 69.2 + - - +
229G LYS* 3.7 8.0 + - + +
230G ALA* 3.1 25.4 + - + +
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Residues in contact with LYS 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192G LEU* 3.7 14.8 - - + -
212G LYS* 4.1 37.5 - - + +
213G SER 3.3 23.9 + - - +
214G LEU* 4.0 25.3 - - + +
215G ASP* 5.5 6.8 + - - +
223G ASN 2.8 18.1 + - - +
224G ILE 3.6 3.8 - - - +
226G LYS* 1.3 83.8 - - + +
228G LEU* 1.3 56.2 + - - +
230G ALA* 3.1 15.3 + - + +
231G ILE* 2.8 38.0 + - + +
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Residues in contact with LEU 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179G ILE* 3.3 34.5 - - + -
192G LEU* 3.6 7.8 - - + +
194G VAL* 3.8 14.8 - - + -
224G ILE* 2.9 13.1 + - + +
225G TYR* 2.6 27.7 + - + +
227G LYS* 1.3 70.5 - - - +
229G LYS* 1.3 63.2 + - + +
231G ILE* 3.2 4.3 + - - +
232G PHE* 3.1 57.0 + - + -
240G LEU* 4.4 6.7 - - + -
245G PHE* 4.2 11.7 - - + -
256G SER* 6.1 0.2 - - - +
257G LEU* 3.9 23.6 - - + -
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Residues in contact with LYS 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G TYR* 3.0 55.6 + - + +
226G LYS* 3.7 10.5 - - - +
228G LEU* 1.3 75.9 - - + +
230G ALA* 1.3 53.7 + - - +
232G PHE* 3.2 7.6 + - - +
233G SER* 2.8 41.4 + - - +
237G VAL 4.8 0.7 - - - +
238G GLU 3.7 23.4 + - - +
239G ASP* 5.4 0.6 - - - +
240G LEU* 4.6 20.6 - - + +
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Residues in contact with ALA 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212G LYS* 4.9 9.0 + - - +
226G LYS* 3.1 15.4 + - + +
227G LYS* 3.1 30.0 + - + +
229G LYS* 1.3 77.2 - - - +
231G ILE* 1.3 64.0 + - - +
233G SER* 3.5 16.9 + - - -
234G GLN* 3.6 11.8 - - - +
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Residues in contact with ILE 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192G LEU* 4.1 24.7 - - + +
194G VAL* 3.3 35.7 - - + -
209G LEU* 3.8 37.7 - - + +
210G GLY* 4.2 11.2 - - - +
212G LYS* 4.5 23.8 - - + -
227G LYS 2.8 18.9 + - - +
228G LEU* 3.2 6.5 + - - +
230G ALA* 1.3 72.0 - - - +
232G PHE* 1.3 65.3 - - + +
234G GLN* 3.0 33.1 - - - +
235G PHE* 3.8 5.3 - - + -
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Residues in contact with PHE 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166G ILE* 5.4 0.9 - - + -
170G VAL* 5.3 2.0 - - + -
177G ALA* 4.5 13.0 - - + -
194G VAL* 4.3 9.0 - - + -
196G LEU* 4.5 12.1 - - + -
209G LEU* 3.4 31.4 - - + -
228G LEU* 3.1 41.4 + - + +
229G LYS 3.6 6.1 - - - +
231G ILE* 1.3 77.2 - - + +
233G SER* 1.3 52.3 + - - +
234G GLN 2.7 4.8 + - - -
235G PHE* 2.7 38.3 + + - +
236G ASN 3.2 5.9 + - - -
237G VAL* 3.6 41.0 + - + +
240G LEU* 3.7 25.1 - - + -
243G ILE* 4.1 19.1 - - + -
245G PHE* 4.4 3.4 - + - -
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Residues in contact with SER 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229G LYS* 2.8 26.9 + - - +
230G ALA* 3.7 10.9 - - - -
231G ILE 3.4 0.4 - - - -
232G PHE* 1.3 69.8 - - - +
234G GLN* 1.3 60.8 + - - +
236G ASN* 3.3 18.4 + - - +
237G VAL 3.9 8.4 + - - -
238G GLU* 4.2 19.7 + - - +
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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