Contacts of the helix formed by residues 285 - 293 (chain A) in PDB entry 1G59
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 285 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ARG* 3.5 11.5 + - - +
284A PHE* 1.3 78.9 - - - +
286A LEU* 1.3 66.5 + - - +
287A GLU* 3.3 9.3 + - - +
288A GLU* 2.9 47.3 + - - +
289A PHE* 3.1 9.9 + - - +
317A TYR* 4.8 1.3 - - - +
321A VAL* 6.0 5.8 - - + -
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.8 26.0 - - + -
26A TYR* 3.2 46.0 - - + +
63A LEU 5.0 2.2 - - - +
64A GLY* 3.3 25.8 - - - +
65A LEU* 4.3 3.1 - - + -
267A ARG* 3.5 30.3 - - + +
285A THR* 1.3 73.6 - - - +
287A GLU* 1.3 65.5 + - - +
289A PHE* 3.0 10.2 + - + +
290A ILE* 2.9 28.7 + - + +
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 4.0 15.6 + - - -
30A ARG* 5.5 4.9 - - - -
285A THR* 3.2 8.1 + - - +
286A LEU* 1.3 83.4 - - - +
288A GLU* 1.3 63.4 + - + +
290A ILE* 3.2 21.3 + - - +
291A GLN* 2.9 52.2 + - - +
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Residues in contact with GLU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A MET* 3.6 12.6 - - + +
281A ARG* 3.6 22.8 + - - +
283A ILE 5.1 0.2 - - - +
284A PHE* 3.7 9.6 - - - +
285A THR* 2.9 47.5 + - - +
287A GLU* 1.3 75.8 - - + +
289A PHE* 1.3 57.0 + - - +
291A GLN* 3.4 10.2 + - - +
292A ALA* 2.8 32.4 + - - +
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Residues in contact with PHE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.7 29.8 - - + -
24A PHE* 3.8 28.0 - + - -
27A ALA* 3.6 22.0 - - + -
271A CYS* 3.8 25.6 - - + -
275A PHE* 3.1 44.4 - + + -
277A MET* 4.1 7.4 - - - +
284A PHE* 4.2 11.2 - + + -
285A THR 3.1 9.8 + - - +
286A LEU* 3.0 15.6 + - + +
288A GLU* 1.3 73.5 - - - +
290A ILE* 1.3 59.8 + - - +
291A GLN 2.8 4.9 + - - -
292A ALA* 3.0 0.7 + - - -
293A PHE* 2.8 46.0 + + - +
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 3.7 30.7 - - + -
27A ALA* 4.3 18.2 - - - +
30A ARG* 3.3 35.4 - - + +
31A ARG* 3.2 35.1 - - - +
286A LEU* 2.9 23.3 + - + +
287A GLU* 3.2 29.1 + - - +
289A PHE* 1.3 73.8 - - + +
291A GLN* 1.3 68.3 + - + +
293A PHE* 4.1 1.5 - - - +
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Residues in contact with GLN 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 3.4 22.1 + - - +
287A GLU* 2.9 45.5 + - - +
288A GLU* 3.6 8.2 - - - +
289A PHE 2.8 1.2 + - - -
290A ILE* 1.3 86.3 - - + +
292A ALA* 1.3 58.4 + - - +
293A PHE 3.2 4.0 - - - -
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 4.3 1.1 - - - -
275A PHE* 3.4 15.7 - - + -
277A MET* 3.4 28.7 - - + -
278A PRO* 4.7 9.8 - - + +
281A ARG* 5.8 0.7 - - - +
288A GLU 2.8 20.4 + - - +
289A PHE 4.2 0.4 - - - +
291A GLN* 1.3 73.5 - - - +
293A PHE* 1.3 64.5 + - - +
294A THR* 3.4 9.5 + - - -
297A ARG* 4.8 4.3 - - - -
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Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.6 31.2 - + - -
27A ALA* 4.1 4.7 - - + -
28A TRP* 3.6 52.4 - + + -
31A ARG* 2.4 38.0 + - + +
275A PHE* 4.1 7.9 - + - -
289A PHE* 2.8 35.4 + + - +
290A ILE* 4.1 13.0 - - - +
291A GLN 3.2 2.6 - - - -
292A ALA* 1.3 76.2 - - - +
294A THR* 1.3 62.8 + - - +
295A TRP* 3.8 41.5 - + - -
298A VAL* 4.0 12.6 - - + -
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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