Contacts of the helix formed by residues 293 - 301 (chain O) in PDB entry 5GJQ
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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292O THR* 1.3 77.4 - - - +
294O GLU* 1.3 60.5 + - - +
296O ILE* 3.3 4.0 + - - +
297O ALA* 2.9 28.4 + - - +
304O VAL* 4.5 9.8 - - + +
307O VAL* 3.9 34.5 - - + +
308O GLU* 4.4 22.2 - - + -
311O VAL* 6.2 0.4 - - + -
324O ILE* 3.7 23.1 - - + -
325O ASP 4.2 2.2 - - - -
326O GLU* 4.2 10.8 - - + -
329O LYS* 3.3 45.4 + - + +
330O ARG 3.6 8.5 - - - -
331O VAL* 3.6 28.5 - - + -
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Residues in contact with GLU 294 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292O THR* 2.7 30.6 + - - +
293O PHE* 1.3 77.2 - - - +
295O GLU* 1.3 71.4 + - + +
297O ALA* 3.0 8.8 + - - +
298O LYS* 2.9 50.6 + - - +
304O VAL* 5.2 4.6 - - - +
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Residues in contact with GLU 295 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284O ARG* 3.9 37.0 + - - +
291O LEU* 4.1 6.1 - - + -
292O THR* 2.9 30.9 + - - +
293O PHE 3.3 0.2 - - - -
294O GLU* 1.3 87.5 - - + +
296O ILE* 1.3 58.4 + - - +
298O LYS* 3.5 5.2 + - - +
299O SER* 2.9 31.7 + - - -
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Residues in contact with ILE 296 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277O LEU* 3.8 30.7 - - + -
291O LEU* 3.5 28.0 - - + -
292O THR 3.6 12.3 + - - +
293O PHE 3.3 2.1 + - - +
294O GLU 3.3 0.6 - - - -
295O GLU* 1.3 73.2 - - - +
297O ALA* 1.3 60.0 + - - +
299O SER* 3.8 5.3 - - - -
300O ALA* 2.8 32.6 + - + +
302O ILE* 6.2 1.1 - - + -
307O VAL* 3.6 31.6 - - + +
310O LEU* 4.4 18.2 - - + -
311O VAL* 4.1 12.6 - - + -
331O VAL* 4.1 15.7 - - + -
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Residues in contact with ALA 297 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293O PHE 2.9 14.0 + - - +
294O GLU* 3.0 13.2 + - - +
296O ILE* 1.3 77.5 - - - +
298O LYS* 1.3 55.5 + - + +
301O LYS* 2.5 34.8 + - - -
302O ILE* 3.0 31.8 + - - +
303O THR* 5.1 0.2 - - - -
304O VAL* 4.2 17.3 - - + +
307O VAL* 4.9 2.6 - - + +
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Residues in contact with LYS 298 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294O GLU* 2.9 43.3 + - + +
295O GLU* 4.1 4.0 - - - +
297O ALA* 1.3 77.9 - - + +
299O SER* 1.3 63.7 + - - +
301O LYS* 3.4 17.9 + - - +
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Residues in contact with SER 299 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245O VAL* 3.0 21.5 - - - +
246O GLU* 4.7 1.2 + - - +
276O CYS* 3.3 9.9 - - - -
277O LEU* 6.0 1.3 - - - -
280O MET* 3.9 35.9 - - - -
284O ARG* 5.9 1.1 - - - -
295O GLU 2.9 20.2 + - - -
296O ILE* 3.8 5.8 - - - -
298O LYS* 1.3 80.9 - - - +
300O ALA* 1.3 57.6 + - - +
301O LYS* 3.8 1.7 + - - +
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Residues in contact with ALA 300 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245O VAL* 3.2 18.7 - - - +
273O GLN* 2.6 61.3 + - - +
276O CYS* 4.7 2.7 - - + -
277O LEU* 5.5 1.8 - - + +
296O ILE* 2.8 21.9 + - + +
299O SER* 1.3 71.4 - - - +
301O LYS* 1.3 66.0 + - - +
302O ILE* 4.3 2.9 - - + +
310O LEU* 4.5 7.2 - - + -
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Residues in contact with LYS 301 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245O VAL* 4.3 10.8 - - + -
246O GLU* 4.7 17.9 - - + -
249O GLN* 6.0 7.2 - - + -
273O GLN* 3.9 1.8 + - - -
297O ALA 2.5 16.2 + - - -
298O LYS* 3.4 14.6 + - - +
299O SER 3.4 2.4 - - - +
300O ALA* 1.3 77.2 - - - +
302O ILE* 1.3 57.0 + - - +
303O THR 4.1 1.3 + - - -
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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