Contacts of the helix formed by residues 220 - 234 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218H ARG* 4.1 29.2 - - + +
219H SER* 1.3 78.9 - - - +
221H ALA* 1.3 66.5 + - - +
222H GLU* 2.8 21.2 + - - +
223H ASN* 2.6 35.4 + - - +
224H ILE* 3.2 13.0 + - - +
252H ASN* 5.1 2.2 - - - -
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Residues in contact with ALA 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220H THR* 1.3 72.9 - - - +
222H GLU* 1.3 71.8 + - - +
224H ILE* 3.1 7.9 + - - +
225H TYR* 3.0 22.0 + - - +
252H ASN* 4.5 10.2 + - - +
255H LYS* 3.8 41.5 - - + +
256H SER* 3.6 20.3 - - - +
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Residues in contact with GLU 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220H THR* 2.8 23.4 + - - +
221H ALA* 1.3 82.2 + - - +
223H ASN* 1.3 55.5 + - - +
225H TYR* 3.3 7.3 + - - +
226H LYS* 2.8 36.8 + - + +
255H LYS* 5.1 4.7 - - - +
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Residues in contact with ASN 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214H LEU* 3.8 19.8 - - + +
217H GLU* 3.9 37.1 + - + +
218H ARG* 5.8 0.2 - - - +
220H THR* 2.6 44.5 + - - +
222H GLU* 1.3 73.5 - - - +
224H ILE* 1.3 62.1 + - - +
226H LYS* 3.6 19.0 - - + +
227H LYS* 2.8 32.7 + - - +
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Residues in contact with ILE 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179H ILE* 5.3 7.9 - - + -
181H LEU* 4.0 26.0 - - + -
192H LEU* 3.9 24.5 - - + +
214H LEU* 4.9 6.5 - - + -
219H SER* 4.2 11.4 - - - +
220H THR 3.3 18.6 - - - +
221H ALA 3.1 6.7 + - - +
223H ASN* 1.3 76.6 - - - +
225H TYR* 1.3 64.4 + - - +
227H LYS* 3.8 2.6 - - - -
228H LEU* 2.9 27.4 + - + +
252H ASN* 3.8 31.0 - - + -
253H VAL* 4.5 7.4 - - - +
256H SER* 3.8 17.0 - - - +
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Residues in contact with TYR 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221H ALA 3.0 12.3 + - - +
222H GLU* 3.7 9.2 - - - +
224H ILE* 1.3 75.6 - - - +
226H LYS* 1.3 53.2 + - - +
228H LEU* 2.9 19.3 + - + +
229H LYS* 2.7 69.4 + - + +
240H LEU* 3.9 30.4 - - + +
256H SER* 3.5 26.4 - - - +
257H LEU* 4.6 2.0 - - + -
259H ASN* 6.1 4.7 - - + -
260H ASN* 3.7 23.5 + - - -
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Residues in contact with LYS 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217H GLU* 5.6 3.8 - - - +
222H GLU* 2.8 20.2 + - + +
223H ASN* 3.6 22.2 - - + +
225H TYR* 1.3 77.3 - - - +
227H LYS* 1.3 68.1 + - - +
229H LYS* 3.2 8.1 + - - +
230H ALA* 3.0 22.2 + - - +
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Residues in contact with LYS 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192H LEU* 3.8 28.3 - - + -
212H LYS* 3.5 29.4 - - + +
213H SER 3.0 28.4 + - - +
214H LEU* 4.4 14.1 + - + +
215H ASP* 5.8 3.8 + - - +
223H ASN 2.8 23.8 + - - +
224H ILE* 4.5 0.4 - - - -
226H LYS* 1.3 77.9 - - - +
228H LEU* 1.3 60.9 + - - +
230H ALA* 3.1 15.2 - - + +
231H ILE* 2.9 29.3 + - + +
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Residues in contact with LEU 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179H ILE* 3.5 33.4 - - + -
192H LEU* 3.6 11.1 - - + +
194H VAL* 3.8 15.3 - - + -
224H ILE* 2.9 14.9 + - + +
225H TYR* 2.9 16.7 + - + +
227H LYS* 1.3 77.6 - - - +
229H LYS* 1.3 62.6 + - - +
231H ILE* 3.0 15.9 + - - +
232H PHE* 3.2 42.9 + - + -
240H LEU* 4.2 18.4 - - + -
245H PHE* 4.2 4.9 - - + -
256H SER* 6.5 0.7 - - - -
257H LEU* 3.9 23.6 - - + -
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Residues in contact with LYS 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225H TYR* 2.7 49.1 + - + +
226H LYS* 3.5 10.3 - - - +
228H LEU* 1.3 71.7 - - - +
230H ALA* 1.3 52.0 + - - +
232H PHE* 3.1 6.1 + - - +
233H SER* 2.9 37.0 + - - +
237H VAL 4.6 3.2 - - - +
238H GLU* 2.8 35.9 + - - +
240H LEU* 4.0 21.1 - - + +
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Residues in contact with ALA 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212H LYS* 6.2 0.7 - - + -
226H LYS 3.0 12.1 + - - +
227H LYS* 3.1 27.8 - - + +
229H LYS* 1.3 74.5 - - - +
231H ILE* 1.3 65.3 + - - +
233H SER* 3.2 23.4 + - - -
234H GLN* 3.4 12.1 + - - +
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Residues in contact with ILE 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192H LEU* 3.6 31.2 - - + +
194H VAL* 3.4 38.4 - - + -
209H LEU* 4.3 11.7 - - + +
210H GLY* 4.3 25.4 - - - +
212H LYS* 4.2 24.7 - - + +
227H LYS* 2.9 11.9 - - + +
228H LEU* 3.0 6.0 + - - +
230H ALA* 1.3 76.7 - - - +
232H PHE* 1.3 58.9 + - + +
234H GLN* 3.4 20.9 - - - +
235H PHE* 3.1 27.2 - - - -
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Residues in contact with PHE 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166H ILE* 5.5 2.5 - - + -
170H VAL* 5.1 2.7 - - + -
177H ALA* 4.4 7.9 - - + -
194H VAL* 4.3 10.8 - - + -
196H LEU* 3.6 32.3 - - + -
209H LEU* 3.6 18.6 - - + -
228H LEU* 3.2 43.5 + - + -
229H LYS* 3.1 8.2 + - - +
231H ILE* 1.3 73.8 - - + +
233H SER* 1.3 55.3 + - - +
234H GLN 3.1 2.5 - - - -
235H PHE* 2.6 32.1 + + - +
236H ASN 3.1 7.8 + - - -
237H VAL* 3.4 39.9 + - + +
240H LEU* 3.4 24.0 - - + -
243H ILE* 3.9 16.6 - - + -
245H PHE* 4.3 6.3 - + - -
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Residues in contact with SER 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229H LYS* 2.9 17.8 + - - +
230H ALA* 3.3 15.1 - - - -
232H PHE* 1.3 75.1 - - - +
234H GLN* 1.3 63.4 + - - +
235H PHE 2.8 1.9 + - - -
236H ASN* 2.9 18.5 + - - +
237H VAL 3.9 1.8 + - - -
238H GLU* 3.9 25.6 + - - +
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Residues in contact with GLN 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H LYS* 6.3 0.4 - - - +
159H LYS* 2.7 57.4 + - + +
160H ALA* 4.9 5.5 + - - +
212H LYS* 3.6 26.2 - - - +
230H ALA 3.4 13.5 - - - +
231H ILE* 3.4 27.0 - - - +
232H PHE 3.0 0.2 + - - -
233H SER* 1.3 76.5 - - - +
235H PHE* 1.3 67.2 + - + +
236H ASN* 5.1 2.7 + - - -
595H ASP* 4.5 0.3 - - - +
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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