Contacts of the helix formed by residues 221 - 236 (chain k) in PDB entry 5GJQ
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 ASN 221 (chain k).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219k ILE 3.7 4.3 + - - +
220k LEU* 1.3 75.3 - - - +
222k PRO* 1.3 68.6 - - + +
223k GLU* 3.1 26.3 - - - +
224k GLU* 2.9 37.9 + - - +
225k ILE 3.1 8.5 + - - -
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Residues in contact with PRO 222 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203k GLY 6.0 1.1 - - - +
220k LEU 3.8 2.8 - - - +
221k ASN* 1.3 86.2 - - + -
223k GLU* 1.3 58.0 + - + +
225k ILE* 3.9 11.7 - - + +
226k GLU* 2.9 29.6 + - - +
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Residues in contact with GLU 223 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221k ASN* 2.9 16.3 + - - +
222k PRO* 1.3 81.3 - - + +
224k GLU* 1.3 59.3 + - - +
226k GLU* 3.3 6.9 + - - +
227k LYS* 2.9 28.5 + - - +
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Residues in contact with GLU 224 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220k LEU* 4.3 19.5 - - + -
221k ASN* 2.9 25.2 + - - +
223k GLU* 1.3 74.7 - - - +
225k ILE* 1.3 60.9 + - - +
227k LYS* 3.2 8.3 + - - +
228k TYR* 2.9 41.0 + - + -
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Residues in contact with ILE 225 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203k GLY* 4.6 15.7 - - - +
206k ILE* 5.1 8.3 - - + +
220k LEU* 4.4 18.7 - - + +
221k ASN 3.1 11.7 + - - +
222k PRO* 3.9 12.8 - - + +
224k GLU* 1.3 75.5 - - - +
226k GLU* 1.3 58.8 + - - +
228k TYR* 3.3 4.6 + - - +
229k VAL* 2.9 30.5 + - - +
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Residues in contact with GLU 226 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203k GLY* 6.5 0.7 - - - -
222k PRO 2.9 21.0 + - - +
223k GLU* 3.4 7.6 - - - +
225k ILE* 1.3 74.5 - - - +
227k LYS* 1.3 58.5 + - - +
229k VAL* 3.5 6.9 + - - +
230k ALA* 2.9 30.1 + - - +
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Residues in contact with LYS 227 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223k GLU 2.9 14.5 + - - +
224k GLU* 3.4 12.8 - - - +
226k GLU* 1.3 76.8 - - - +
228k TYR* 1.3 59.6 + - + +
230k ALA* 3.1 8.5 + - - +
231k GLU* 2.9 28.2 + - - +
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Residues in contact with TYR 228 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184k ASP* 5.5 0.3 - - - +
185k ASP* 4.2 40.3 + - + +
188k ILE* 5.1 17.7 - - + +
189k LYS* 5.5 10.1 - - + +
192k ILE* 5.6 10.3 - - + +
220k LEU* 4.1 24.0 - - + -
224k GLU* 2.9 28.6 + - + +
225k ILE* 3.8 5.4 - - - +
227k LYS* 1.3 78.2 - - + +
229k VAL* 1.3 57.6 + - - +
231k GLU* 3.5 13.5 + - + +
232k ILE* 2.9 27.1 + - - +
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Residues in contact with VAL 229 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192k ILE* 5.6 6.1 - - + +
203k GLY* 5.7 8.7 - - - -
225k ILE 2.9 16.9 + - - +
226k GLU* 3.8 6.5 - - - +
228k TYR* 1.3 75.7 - - - +
230k ALA* 1.3 57.4 + - - +
232k ILE* 3.3 8.6 - - - +
233k GLU* 2.9 28.2 + - - +
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Residues in contact with ALA 230 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226k GLU 2.9 15.8 + - - +
227k LYS* 3.1 13.7 - - - +
229k VAL* 1.3 74.0 - - - +
231k GLU* 1.3 59.6 + - - +
232k ILE 3.1 1.3 - - - -
233k GLU* 3.2 6.5 + - - +
234k LYS* 2.8 30.1 + - - +
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Residues in contact with GLU 231 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227k LYS 2.9 16.8 + - - +
228k TYR* 3.8 15.5 - - + +
230k ALA* 1.3 71.0 - - - +
232k ILE* 1.3 57.2 + - - +
234k LYS* 3.6 8.3 - - - +
235k GLU* 2.9 31.0 + - - +
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Residues in contact with ILE 232 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189k LYS* 5.5 12.6 - - + +
192k ILE* 5.6 6.7 - - + -
193k LYS* 5.8 6.5 - - + +
228k TYR 2.9 18.0 + - - +
229k VAL* 3.3 12.8 - - - +
231k GLU* 1.3 76.9 - - - +
233k GLU* 1.4 51.0 + - - +
235k GLU* 3.2 7.2 + - - +
236k LYS* 2.7 35.9 + - - +
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Residues in contact with GLU 233 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229k VAL 2.9 17.8 + - - +
230k ALA* 3.7 7.0 - - - +
232k ILE* 1.4 74.8 - - - +
234k LYS* 1.3 60.6 + - - +
236k LYS* 3.5 9.3 - - - +
237k GLU* 3.2 23.9 + - - +
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Residues in contact with LYS 234 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230k ALA 2.8 16.9 + - - +
231k GLU* 3.6 10.1 - - - +
233k GLU* 1.3 76.9 - - - +
235k GLU* 1.3 51.6 + - - +
237k GLU* 2.8 8.2 + - - +
238k GLU* 2.7 39.0 + - + +
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Residues in contact with GLU 235 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231k GLU 2.9 18.7 + - - +
232k ILE* 3.7 4.7 - - - +
234k LYS* 1.3 70.1 - - - +
236k LYS* 1.3 56.2 + - - +
237k GLU 3.1 7.9 + - - -
238k GLU* 4.3 7.2 - - - +
239k ASN* 3.4 28.5 + - + +
240k GLU* 4.0 1.7 + - - +
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Residues in contact with LYS 236 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232k ILE 2.7 17.4 + - - +
233k GLU* 3.5 12.1 - - - +
234k LYS 3.1 0.2 - - - -
235k GLU* 1.3 75.3 - - - +
237k GLU* 1.3 59.2 + - - +
238k GLU 3.8 0.2 - - - -
240k GLU* 3.6 24.6 - - + +
241k LYS* 4.2 2.4 + - - +
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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