Contacts of the strand formed by residues 284 - 289 (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 MET 284 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196G ILE* 4.1 28.3 - - + +
197G CYS 6.0 1.1 - - - -
198G ARG* 4.9 4.3 - - - +
199G VAL* 3.8 36.1 - - + +
202G ASN* 5.6 6.3 - - + +
269G SER* 5.3 0.7 - - - -
270G MET* 2.8 49.0 + - + +
282G GLU* 4.9 1.1 - - - +
283G PRO* 1.3 77.1 - - - +
285G GLU* 1.3 74.9 + - - +
286G PHE 3.4 0.5 + - - -
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Residues in contact with GLU 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202G ASN* 3.4 22.9 - - - +
267G ARG* 5.4 14.8 - - + -
268G VAL 3.8 6.7 - - - +
269G SER* 5.5 0.2 - - - +
270G MET* 4.9 1.6 - - - +
283G PRO* 4.5 11.3 - - - +
284G MET* 1.3 79.7 - - - +
286G PHE* 1.3 60.6 + - - +
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Residues in contact with PHE 286 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201G ARG 4.0 7.2 - - - -
202G ASN* 3.2 22.4 - - - -
203G SER 3.4 13.0 - - - -
204G GLY* 3.3 30.1 - - - -
212G ILE* 4.7 6.5 - - + -
228G PHE* 4.3 12.6 - + + -
254G THR* 3.6 26.7 - - + -
267G ARG* 3.4 2.9 - - - -
268G VAL* 2.5 49.5 + - + +
270G MET* 4.1 28.3 - - + -
284G MET 3.4 5.6 + - - +
285G GLU* 1.3 75.0 - - - +
287G GLN* 1.3 62.0 + - - +
288G TYR* 4.0 35.4 - + - -
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Residues in contact with GLN 287 (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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202G ASN 2.8 14.3 + - - +
203G SER* 3.2 31.5 + - - -
204G GLY 3.2 3.3 + - - -
265G PRO* 3.2 24.0 - - + +
266G VAL 3.6 10.8 - - - +
267G ARG* 3.6 34.8 + - - +
286G PHE* 1.3 75.6 - - - +
288G TYR* 1.3 65.3 + - - +
289G LEU* 3.6 15.9 - - + +
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Residues in contact with TYR 288 (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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204G GLY 3.5 1.6 - - - -
205G SER 3.0 27.8 - - - -
206G CYS* 3.5 9.4 - - + -
208G GLY* 4.6 1.8 - - - -
228G PHE* 3.6 11.5 - + - -
233G TRP* 3.3 29.6 - + - -
254G THR* 4.7 3.8 - - - -
255G PRO* 2.3 49.7 + - - +
257G TYR* 3.6 26.9 - + + -
262G LEU* 4.0 7.2 - - + +
265G PRO* 3.5 1.7 - - - +
266G VAL* 3.1 39.4 + - + -
268G VAL* 3.9 15.5 - - + -
286G PHE* 4.0 21.9 - + - -
287G GLN* 1.3 75.2 - - - +
289G LEU* 1.3 64.1 + - - +
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Residues in contact with LEU 289 (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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203G SER* 3.0 26.5 - - - +
204G GLY* 2.6 23.3 + - - +
205G SER* 3.6 2.6 - - - -
206G CYS* 2.9 27.2 + - - +
262G LEU* 4.8 1.6 - - - -
265G PRO* 3.8 25.8 - - + -
287G GLN* 3.6 15.3 - - + +
288G TYR* 1.3 83.6 - - - +
290G PRO* 1.3 80.4 - - + +
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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