Contacts of the helix formed by residues 227 - 237 (chain G) in PDB entry 2R9R
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 VAL 227 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223G GLU* 2.9 38.5 + - - +
226G GLU* 1.3 81.9 - - - +
228G GLN* 1.3 71.8 + - + +
229G LEU 3.6 0.4 - - - -
230G PRO* 3.5 8.2 - - - +
231G GLU* 4.7 5.9 + - - +
359G PRO* 3.8 22.4 - - + +
360G TYR 3.8 16.6 - - - +
361G SER* 4.4 20.0 - - - +
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Residues in contact with GLN 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191G SER* 4.9 4.9 - - - -
192G SER* 3.8 36.6 + - - +
223G GLU* 3.1 27.0 + - - +
224G LYS* 3.3 32.4 + - + +
227G VAL* 1.3 82.1 - - + +
229G LEU* 1.3 64.0 + - + +
230G PRO 3.7 0.2 - - - -
231G GLU* 3.8 14.4 + - - +
232G LEU* 4.2 8.7 + - - +
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Residues in contact with LEU 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G SER* 5.3 3.4 - - - -
195G ILE* 4.3 4.3 - - + -
213G GLU* 3.9 34.5 - - + -
215G ALA* 4.1 15.7 - - + -
224G LYS* 3.0 33.8 + - + +
225G VAL* 4.0 13.9 - - + +
228G GLN* 1.3 69.3 - - + +
230G PRO* 1.3 69.9 - - + +
231G GLU 3.2 2.9 - - - -
232G LEU* 3.0 36.5 + - + +
233G PHE* 3.2 11.3 + - - +
238G VAL* 4.8 3.1 - - + +
239G GLY 5.6 0.2 - - - +
240G ALA* 3.9 27.4 - - + -
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Residues in contact with PRO 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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225G VAL 3.2 23.6 - - - +
226G GLU* 3.4 15.5 - - - +
227G VAL 3.5 15.9 - - - +
229G LEU* 1.3 89.4 - - - +
231G GLU* 1.3 60.1 + - - +
233G PHE* 3.2 14.4 + - + +
234G HIS* 3.2 30.7 + - + +
314G ASN* 6.2 0.9 - - - +
316G GLY* 5.8 9.2 - - - -
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Residues in contact with GLU 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227G VAL 4.7 5.4 + - - +
228G GLN 3.8 10.5 + - - +
229G LEU 3.2 0.8 - - - -
230G PRO* 1.3 79.4 - - - +
232G LEU* 1.3 65.0 + - + +
234G HIS* 3.3 3.2 + - - -
235G LYS* 2.9 51.6 + - + +
62H PRO* 4.1 23.3 - - - +
65H ARG* 5.3 3.1 + - - -
66H MET* 3.8 20.1 - - + +
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Residues in contact with LEU 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G SER* 3.9 36.8 - - - +
195G ILE* 3.8 36.8 - - + -
196G MET* 4.6 13.9 - - + -
228G GLN 4.3 4.9 - - - +
229G LEU* 3.0 20.0 + - + +
231G GLU* 1.3 86.2 - - + +
233G PHE* 1.3 58.6 + - - +
235G LYS* 4.5 4.5 - - + +
236G ILE* 2.9 46.4 + - + +
237G GLY 3.2 5.7 + - - -
238G VAL* 3.5 15.6 + - + +
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Residues in contact with PHE 233 (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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43G GLY* 3.8 30.1 - - - -
44G LYS* 3.5 27.6 - - + -
229G LEU 3.2 10.1 + - - +
230G PRO* 3.2 11.1 + - + +
232G LEU* 1.3 76.6 - - - +
234G HIS* 1.3 88.2 + + - +
237G GLY* 3.1 20.1 + - - -
238G VAL 3.2 24.6 + - - +
239G GLY* 4.1 10.3 - - - -
315G GLU 5.4 8.5 - - - -
316G GLY* 4.9 20.2 - - - +
318G SER* 5.4 1.8 - - - -
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Residues in contact with HIS 234 (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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44G LYS* 3.2 20.4 + - - +
230G PRO* 3.2 31.7 + - + +
231G GLU* 4.0 5.2 - - - +
233G PHE* 1.3 100.6 - + - +
235G LYS* 1.3 59.8 + - - +
66H MET* 4.1 20.7 - - + +
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Residues in contact with LYS 235 (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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44G LYS* 4.9 1.4 + - - -
196G MET* 3.6 28.9 - - + +
231G GLU* 2.9 37.8 + - + +
232G LEU* 4.4 4.5 - - + +
234G HIS* 1.3 79.8 - - - +
236G ILE* 1.3 61.9 + - + +
237G GLY 3.7 0.4 - - - -
33H GLU* 4.7 7.9 + - - -
65H ARG* 5.5 2.8 - - - +
66H MET* 3.9 21.3 - - + +
69H PHE* 3.6 40.0 - - + -
71H PRO* 3.6 21.0 - - - +
76H TYR* 3.3 28.6 + - - -
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Residues in contact with ILE 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G LYS* 5.2 0.4 - - - -
195G ILE* 4.5 7.0 - - + +
196G MET* 4.2 9.9 - - - -
199G TYR* 3.6 64.7 - - + -
209G PRO* 6.1 0.5 - - - +
210G PRO 5.3 1.6 - - - +
232G LEU* 2.9 37.1 + - + +
235G LYS* 1.3 82.8 - - + +
237G GLY* 1.3 61.2 + - - +
238G VAL* 3.2 27.6 + - + +
69H PHE* 4.1 9.0 - - + -
71H PRO* 4.6 7.6 - - - -
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Residues in contact with GLY 237 (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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43G GLY* 3.4 0.9 - - - -
44G LYS* 3.0 52.4 + - - +
45G SER 4.8 0.2 + - - -
211G ILE* 4.0 5.7 - - - +
232G LEU 3.2 0.2 + - - -
233G PHE* 3.1 21.0 + - - -
235G LYS 3.7 0.8 - - - -
236G ILE* 1.3 76.1 - - - +
238G VAL* 1.3 62.5 + - - +
239G GLY 3.3 1.2 + - - -
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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