Contacts of the helix formed by residues 222 - 231 (chain G) in PDB entry 5LS6
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 LYS 222 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G LYS* 3.5 39.7 - - - +
12G PRO* 4.9 10.1 + - - +
15G TRP* 4.1 29.2 - - + +
220G SER* 3.5 6.1 - - - -
221G ASP* 1.3 77.7 - - - +
223G ILE* 1.3 60.0 + - + +
224G PHE 3.3 0.7 - - - -
225G GLU* 3.1 42.5 + - - +
226G ALA* 3.6 18.8 + - - +
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Residues in contact with ILE 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G TRP* 3.2 39.9 - - + -
175G VAL* 4.5 23.6 - - + +
178G LEU* 3.5 37.2 - - + +
179G GLY* 5.8 0.9 - - - +
220G SER* 3.8 35.0 - - - +
221G ASP 3.6 0.2 - - - -
222G LYS* 1.3 74.5 - - + +
224G PHE* 1.3 82.5 + - + +
225G GLU 3.2 0.2 - - - -
226G ALA* 3.3 8.6 + - - +
227G ILE* 3.2 25.9 + - + +
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Residues in contact with PHE 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171G PHE* 4.5 1.3 - + - -
175G VAL* 4.3 22.2 - - + -
216G ARG 4.0 8.3 - - - -
220G SER 3.7 23.3 - - - -
221G ASP* 4.7 6.5 + - - +
222G LYS 3.3 0.8 - - - -
223G ILE* 1.3 85.6 - - + +
225G GLU* 1.3 57.1 + - - +
227G ILE* 3.8 10.4 - - + +
228G SER* 3.3 28.6 + - - -
237G ALA* 3.5 23.1 - - + +
240G LEU* 3.4 27.9 - - + +
241G LYS* 3.5 49.6 - - + -
244G TYR* 3.7 28.7 - + + -
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Residues in contact with GLU 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221G ASP 3.0 23.7 - - - +
222G LYS* 3.1 34.9 + - - +
224G PHE* 1.3 77.9 - - - +
226G ALA* 1.3 59.9 + - - +
227G ILE 3.5 0.2 - - - -
228G SER* 3.6 4.9 + - - -
229G SER* 3.4 20.1 + - - -
237G ALA* 3.8 20.0 - - + -
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Residues in contact with ALA 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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12G PRO 5.6 0.4 - - - +
15G TRP* 3.6 40.2 - - + +
16G ARG* 4.0 10.6 - - + +
19G VAL* 4.7 7.0 - - + +
222G LYS* 3.6 11.6 + - - +
223G ILE* 3.3 12.6 + - - +
225G GLU* 1.3 81.2 - - - +
227G ILE* 1.3 57.7 + - - +
229G SER* 2.5 25.9 + - - -
230G MET* 3.8 5.7 + - - +
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Residues in contact with ILE 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G VAL* 3.8 24.0 - - + -
171G PHE* 3.5 32.3 - - + -
174G LEU* 4.4 13.2 - - + -
175G VAL* 4.5 5.4 - - + -
178G LEU* 3.4 32.5 - - + -
223G ILE* 3.2 12.0 + - + +
224G PHE* 3.8 21.1 - - + +
226G ALA* 1.3 72.4 - - - +
228G SER* 1.3 63.9 + - - +
229G SER 3.2 1.8 - - - -
230G MET* 4.1 1.6 - - - +
231G PHE* 3.1 34.5 + - + +
240G LEU* 3.7 20.3 - - + +
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Residues in contact with SER 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224G PHE 3.3 20.9 + - - -
225G GLU* 3.6 7.6 + - - -
226G ALA 3.5 0.4 - - - -
227G ILE* 1.3 75.0 - - - +
229G SER* 1.3 64.2 + - - +
230G MET 3.5 0.2 - - - -
231G PHE 3.2 20.0 - - - +
232G PRO* 3.3 8.0 - - - +
235G GLY* 3.7 24.0 - - - -
236G THR* 4.1 1.7 - - - -
237G ALA* 3.5 16.3 + - - +
240G LEU* 3.7 12.8 - - - -
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Residues in contact with SER 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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16G ARG* 3.0 48.8 + - - +
162G GLU* 4.5 5.4 - - - +
225G GLU 3.4 12.0 + - - -
226G ALA* 2.5 23.8 + - - -
228G SER* 1.3 81.2 + - - +
230G MET* 1.3 65.9 + - - +
231G PHE 3.5 0.3 + - - -
232G PRO* 3.6 12.7 - - - +
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Residues in contact with MET 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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16G ARG* 4.3 27.4 - - + +
19G VAL* 4.7 13.5 - - + -
20G LYS* 3.7 23.8 - - + -
161G ARG* 3.4 25.5 - - - +
162G GLU* 3.7 41.2 + - + +
163G CYS* 3.4 27.0 + - - -
226G ALA 3.8 7.0 + - - +
227G ILE* 3.8 2.7 + - - +
228G SER 3.5 0.4 - - - -
229G SER* 1.3 88.1 + - - +
231G PHE* 1.3 79.2 + - + +
232G PRO* 3.5 3.1 - - - +
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Residues in contact with PHE 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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19G VAL* 5.3 3.1 - - + -
23G TYR* 4.7 7.0 - + - -
161G ARG* 3.2 30.1 - - - +
163G CYS* 3.4 23.3 - - + -
165G PHE 3.6 10.1 - - - -
166G ILE* 3.3 47.8 - - + -
174G LEU* 4.7 13.9 - - + -
227G ILE* 3.1 30.1 + - + +
228G SER* 3.2 8.0 - - - +
229G SER 3.2 0.8 - - - -
230G MET* 1.3 94.7 - - + +
232G PRO* 1.4 57.8 - - - +
233G ASP 3.2 3.6 - - - -
234G LYS* 3.0 20.6 + - + +
235G GLY 3.0 22.0 + - - -
240G LEU* 5.3 0.4 - - + -
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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