Contacts of the strand formed by residues 225 - 230 (chain G) in PDB entry 3GUT
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 GLU 225 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224G ILE* 1.3 81.2 - - - +
226G VAL* 1.3 64.1 + - - +
227G TYR* 5.8 0.2 - - + -
236G ARG* 2.8 38.6 + - + -
237G GLY 5.9 0.4 - - - +
239G PHE* 3.8 13.5 - - + -
272G LEU* 3.5 3.2 - - - -
273G ARG* 2.6 83.4 + - + +
275G PRO* 4.0 13.6 - - + +
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Residues in contact with VAL 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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214G LEU* 4.8 7.4 - - + -
225G GLU* 1.3 72.8 - - - +
227G TYR* 1.3 60.4 + - - +
228G PHE* 3.7 12.7 + - + -
236G ARG* 3.0 10.0 - - - +
237G GLY 3.0 25.9 + - - +
239G PHE* 3.9 17.2 - - + -
250G ILE* 4.7 6.3 - - + -
252G PHE* 3.6 55.4 - - + -
270G MET* 4.1 14.6 - - + -
271G GLN 3.6 8.1 - - - +
272G LEU* 4.8 8.7 - - + -
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Residues in contact with TYR 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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225G GLU* 3.6 1.0 + - + -
226G VAL* 1.3 70.1 - - - +
228G PHE* 1.3 61.5 + - - +
229G THR* 3.4 18.2 + - - -
234G GLU* 3.1 32.6 + - + -
235G ALA 3.6 4.5 - - - -
236G ARG* 3.0 42.0 - - + -
271G GLN* 2.6 68.1 + - + +
273G ARG* 3.7 26.3 + - + -
280G LEU* 3.7 21.3 - - + -
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Residues in contact with PHE 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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226G VAL* 3.7 30.5 - - + -
227G TYR* 1.3 72.8 - - - +
229G THR* 1.3 59.8 + - - +
233G TRP* 3.9 18.6 - + + -
234G GLU* 3.4 3.3 - - - +
235G ALA 2.6 38.8 + - - +
237G GLY 4.1 3.4 - - - -
252G PHE* 3.7 13.0 - + - -
254G THR* 3.5 24.5 - - + -
255G PRO* 3.4 31.9 - - + -
268G VAL* 4.7 4.0 - - + -
269G SER 3.2 5.8 - - - +
270G MET* 4.1 19.1 - - + +
286G PHE* 4.3 19.3 - + - -
288G TYR* 3.6 23.8 - + - -
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Residues in contact with THR 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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227G TYR* 3.4 22.9 + - - -
228G PHE* 1.3 71.0 - - - +
230G GLY* 1.3 68.2 + - - +
233G TRP* 3.9 6.6 + - - -
234G GLU* 4.6 2.0 - - - +
268G VAL* 3.0 5.1 - - - +
269G SER* 2.4 79.9 + - - +
271G GLN* 3.8 15.0 - - - +
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Residues in contact with GLY 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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229G THR* 1.3 83.3 + - - +
231G PRO* 1.3 70.9 - - - +
232G GLY 3.0 9.1 + - - -
233G TRP* 3.1 31.0 + - - +
268G VAL* 4.5 4.3 - - - -
269G SER* 4.9 1.6 - - - -
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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