Contacts of the strand formed by residues 222 - 229 (chain G) in PDB entry 3Q2K
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 222 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184G ALA* 4.4 0.9 - - - +
185G PHE* 5.0 0.2 - - - -
210G THR* 3.4 3.6 - - - -
211G ALA 2.9 27.7 + - - +
213G LEU* 3.8 5.8 - - + +
220G GLU* 3.3 8.0 - - - +
221G ASP* 1.3 102.1 + - - +
223G GLY* 1.3 61.5 + - - +
239G VAL* 3.4 6.7 - - - -
240G THR* 2.9 16.3 + - - +
242G LEU* 3.1 11.6 - - - +
154H TYR 3.7 13.2 - - - +
155H MET* 3.7 21.8 - - + -
234H MET* 3.5 22.1 - - + +
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Residues in contact with GLY 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G PHE* 3.5 18.6 - - - -
209G TYR 3.3 12.3 - - - -
210G THR* 4.0 1.6 - - - -
222G THR* 1.3 78.1 - - - +
224G VAL* 1.3 67.9 + - - +
239G VAL* 2.9 34.8 + - - +
155H MET* 3.6 1.7 - - - +
234H MET* 4.3 5.2 - - - -
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Residues in contact with VAL 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G PHE* 3.8 5.8 - - - -
207G TYR 4.1 0.2 - - - +
208G ALA* 3.2 3.8 - - - +
209G TYR* 2.9 35.4 + - + +
223G GLY* 1.3 79.3 - - - +
225G ALA* 1.3 72.9 + - - +
226G ALA 4.6 0.2 - - - +
236G SER* 4.7 0.2 - - - -
237G ILE 3.3 7.9 - - - +
238G ASN* 3.3 23.6 - - - +
155H MET* 4.0 9.9 - - + -
226H ALA* 4.2 11.0 - - + +
234H MET* 4.1 5.8 - - + -
235H GLY* 3.5 46.2 - - - +
236H SER* 4.1 7.4 - - - -
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Residues in contact with ALA 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G PHE* 4.8 0.7 - - + -
206G VAL* 4.8 1.3 - - + -
207G TYR 3.3 10.5 - - - +
208G ALA* 3.8 11.9 - - + -
224G VAL* 1.3 78.2 - - - +
226G ALA* 1.3 63.4 + - - +
227G LEU* 3.9 7.2 - - + +
236G SER* 3.0 6.8 - - - -
237G ILE* 2.9 49.4 + - + +
335G ILE* 3.9 22.2 - - + -
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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
----------------------------------------------------------
206G VAL* 3.2 6.4 - - - +
207G TYR* 2.9 38.7 + - + +
224G VAL* 5.9 0.2 - - + -
225G ALA* 1.3 73.5 - - - +
227G LEU* 1.3 58.8 + - - +
235G GLY 3.6 7.2 - - - -
236G SER* 4.3 2.9 - - - +
207H TYR* 4.7 4.9 - - + +
209H TYR* 3.5 20.6 - - + -
224H VAL* 4.3 13.5 - - + -
226H ALA* 4.1 23.7 - - + +
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Residues in contact with LEU 227 (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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156G VAL 5.1 0.2 - - - +
196G LEU* 3.9 30.3 - - + -
203G VAL* 4.8 9.0 - - + -
205G SER 3.6 6.1 - - - +
206G VAL* 3.7 24.5 - - + -
225G ALA* 3.9 14.8 - - + +
226G ALA* 1.3 79.3 - - - +
228G ARG* 1.3 62.2 + - - +
229G TRP* 3.7 30.7 - - + -
234G MET* 3.2 7.3 - - - +
235G GLY 3.1 26.1 + - - +
236G SER* 3.7 33.9 - - - +
237G ILE* 4.1 2.2 - - + +
331G LEU* 5.0 2.0 - - + -
335G ILE* 5.3 1.8 - - + -
209H TYR* 3.5 8.5 - - - -
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Residues in contact with ARG 228 (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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204E GLU* 5.6 3.0 + - - -
228E ARG* 6.0 1.6 - - - +
203G VAL* 3.7 1.5 - - - +
204G GLU* 2.8 65.3 + - - +
205G SER* 3.1 15.0 + - - +
227G LEU* 1.3 77.3 - - - +
229G TRP* 1.3 64.4 - - - +
232G GLY* 4.7 7.0 - - - +
233G ALA 3.5 9.2 - - - +
234G MET* 4.4 11.0 - - + -
344G ARG* 4.5 12.1 - - - +
209H TYR* 3.5 46.3 - - + +
210H THR 5.1 7.3 + - - +
339H ALA 5.7 3.6 + - - -
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Residues in contact with TRP 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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156G VAL* 3.8 22.4 - - + -
196G LEU* 3.1 40.5 + - + -
200G VAL* 3.4 22.7 - - + +
201G GLY 2.9 33.7 + - - -
202G PRO 3.4 13.0 - - - +
203G VAL* 3.7 10.8 - - + +
204G GLU* 3.9 3.2 - - - +
227G LEU* 3.7 25.8 - - + -
228G ARG* 1.3 86.0 - - - +
230G ARG* 1.3 63.6 + - - +
231G HIS* 3.4 26.9 - + + +
232G GLY* 3.0 11.3 + - - -
233G ALA* 2.9 27.5 + - + +
234G MET* 3.8 23.3 - - - -
235G GLY* 3.9 4.7 - - - -
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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