Contacts of the strand formed by residues 293 - 298 (chain R) in PDB entry 1G0Y
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 PHE 293 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229R LEU* 3.8 25.4 - - + -
243R TRP* 3.7 9.0 - + + -
244R LYS 3.8 5.6 - - - -
245R TRP* 3.9 32.3 - + + -
250R ILE* 5.3 0.9 - - + -
257R LEU* 4.3 11.4 - - + -
279R LEU* 3.6 24.0 - - + -
281R ILE* 3.9 18.4 - - + -
288R PHE* 3.9 36.1 - + + -
291R HIS 5.0 2.0 - - - -
292R PRO* 1.3 72.7 - - - +
294R THR* 1.3 59.8 + - - +
307R TYR* 3.1 3.6 - - - +
308R ILE 2.9 34.6 + - - +
310R LEU* 3.9 32.5 - - + -
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Residues in contact with THR 294 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243R TRP* 3.2 5.9 - - - -
244R LYS* 2.8 39.8 + - - -
292R PRO* 3.8 13.5 + - - +
293R PHE* 1.3 77.9 + - - +
295R CYS* 1.3 67.7 + - - +
296R PHE* 3.6 25.6 - - + -
305R ALA* 4.4 4.9 - - + -
306R ALA* 2.9 30.1 - - - +
307R TYR* 3.6 11.2 - - + +
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Residues in contact with CYS 295 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211R ILE* 3.9 10.5 - - + -
214R PRO* 4.1 6.1 - - + -
231R CYS* 2.0 52.7 - - + -
241R ALA* 4.5 2.9 - - - -
242R TYR 3.7 14.6 - - - -
243R TRP* 3.3 15.8 - - + -
294R THR* 1.3 76.1 - - - +
296R PHE* 1.3 84.1 + - - +
305R ALA* 3.5 4.0 - - - -
306R ALA 2.9 30.2 + - - +
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Residues in contact with PHE 296 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211R ILE* 4.3 0.4 - - - -
240R ILE 3.2 0.7 - - - +
241R ALA* 3.2 6.4 - - - -
242R TYR* 2.8 64.3 + + + +
244R LYS* 3.5 38.4 - - + -
294R THR* 3.6 35.9 - - + -
295R CYS* 1.3 80.6 - - - +
297R ALA* 1.3 59.2 + - - +
303R ILE* 4.2 16.2 - - + -
304R ASP 3.6 4.3 - - - -
305R ALA* 3.9 20.0 - - + -
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Residues in contact with ALA 297 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209R PRO* 3.1 33.9 - - + +
211R ILE* 4.2 9.0 - - + -
233R VAL* 4.0 24.0 - - + -
240R ILE 2.8 12.3 - - - +
296R PHE* 1.3 77.6 - - - +
298R LYS* 1.3 59.8 + - - +
303R ILE* 3.3 5.8 - - - +
304R ASP* 3.1 26.4 + - + +
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Residues in contact with LYS 298 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209R PRO* 4.1 0.9 - - - -
239R ASP* 3.5 6.8 - - - +
240R ILE* 3.3 47.9 + - + +
242R TYR* 4.8 9.3 - - + +
297R ALA* 1.3 74.6 - - - +
299R ASN* 1.3 74.9 + - - +
300R THR* 3.9 26.5 - - + +
302R GLY 3.8 10.1 - - - +
303R ILE* 4.1 22.8 - - + +
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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