Contacts of the helix formed by residues 221 - 230 (chain i) 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 THR 221 (chain i).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218i ARG* 4.8 6.1 - - - +
219i ARG 3.6 2.0 + - - +
220i LEU* 1.3 76.2 - - - +
222i PRO* 1.4 75.0 - - - +
223i THR* 3.5 10.2 + - - -
224i GLU* 2.9 48.1 + - - +
225i VAL* 3.1 12.6 + - - +
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Residues in contact with PRO 222 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204i GLU* 3.4 29.6 - - + +
205i ASP* 4.0 20.6 - - - +
220i LEU 3.7 3.1 - - - +
221i THR* 1.4 87.2 - - - +
223i THR* 1.3 57.7 + - - +
225i VAL* 3.4 4.1 + - + +
226i LYS* 2.9 23.7 + - - +
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Residues in contact with THR 223 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87Q ARG* 5.5 1.3 - - - +
221i THR* 3.1 10.0 - - - +
222i PRO* 1.3 78.5 - - - +
224i GLU* 1.3 67.9 + - + +
226i LYS* 3.0 22.7 + - - +
227i ASP* 3.0 29.0 + - - +
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Residues in contact with GLU 224 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81Q SER* 5.4 12.9 - - - -
83Q ALA* 6.2 0.2 - - + -
218i ARG* 2.9 38.4 + - - -
220i LEU* 3.7 12.3 - - + -
221i THR* 2.9 49.0 + - - +
223i THR* 1.3 78.3 - - + +
225i VAL* 1.3 57.7 + - - +
227i ASP* 3.3 9.1 + - - +
228i TYR* 3.0 43.7 + - + -
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Residues in contact with VAL 225 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191i ILE* 5.0 2.0 - - + -
204i GLU* 4.1 10.3 - - - +
207i ILE* 3.8 23.6 - - + +
208i GLU* 5.8 0.2 - - - -
209i VAL* 3.8 26.0 - - + +
220i LEU* 3.8 20.0 - - + +
221i THR 3.1 13.6 + - - +
222i PRO* 3.6 11.7 - - + +
224i GLU* 1.3 74.0 - - - +
226i LYS* 1.3 56.3 + - - +
228i TYR* 3.4 7.0 + - - +
229i LEU* 2.7 62.1 + - + +
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Residues in contact with LYS 226 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87Q ARG* 4.3 19.1 - - - +
204i GLU* 2.2 48.0 + - + +
222i PRO 2.9 10.4 + - - +
223i THR* 3.0 23.2 + - - +
225i VAL* 1.3 74.5 - - - +
227i ASP* 1.3 64.9 + - - +
229i LEU* 3.0 7.7 + - + +
230i ALA* 3.0 24.6 + - - +
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Residues in contact with ASP 227 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81Q SER* 4.9 3.0 - - - -
83Q ALA* 3.8 21.9 - - + +
84Q LYS* 2.7 47.6 + - - +
86Q ALA* 5.4 2.4 - - - +
87Q ARG* 2.1 46.1 + - - +
223i THR* 3.0 17.3 + - - +
224i GLU* 3.4 12.6 - - - +
226i LYS* 1.3 76.7 - - - +
228i TYR* 1.3 61.4 + - - +
230i ALA* 3.4 15.8 + - - +
231i ALA 4.6 0.2 + - - -
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Residues in contact with TYR 228 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81Q SER* 6.1 1.8 - - - -
82Q LYS* 4.3 2.6 + - - +
83Q ALA* 3.1 34.2 + - + -
122Q ARG* 4.3 9.9 - - - -
184i GLU* 3.6 33.9 - - - +
187i ILE* 3.6 47.9 - - + +
188i HIS* 4.9 16.1 - + + -
191i ILE* 4.0 19.6 - - + +
220i LEU* 4.8 11.2 - - + -
224i GLU* 3.0 32.7 + - + +
225i VAL* 3.8 6.1 - - - +
227i ASP* 1.3 76.0 - - - +
229i LEU* 1.3 61.3 + - - +
230i ALA 3.1 3.7 + - - -
231i ALA* 3.7 13.2 + - - +
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Residues in contact with LEU 229 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191i ILE* 3.2 36.3 - - + -
202i MET* 3.8 22.0 - - + +
203i THR* 3.1 36.8 - - - +
204i GLU* 3.7 4.9 - - + -
207i ILE* 3.6 9.9 - - + -
225i VAL* 2.7 40.5 + - + +
226i LYS* 3.0 8.2 + - + +
228i TYR* 1.3 73.9 - - - +
230i ALA* 1.3 55.5 + - - +
231i ALA* 3.2 16.2 + - - -
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Residues in contact with ALA 230 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86Q ALA* 5.9 0.8 - - - -
87Q ARG* 3.7 34.9 - - + +
90Q ARG* 5.0 7.6 + - - +
226i LYS 3.0 9.7 + - - +
227i ASP 3.4 15.5 - - - +
228i TYR 3.1 1.6 - - - -
229i LEU* 1.3 76.6 - - - +
231i ALA* 1.3 59.0 + - - +
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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