Contacts of the helix formed by residues 326 - 335 (chain G) in PDB entry 1GLE
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 ALA 326 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313G ILE* 3.1 33.4 - - + -
314G GLN* 6.0 0.2 - - - -
317G ARG* 4.4 15.9 - - - +
323G ILE* 4.0 3.3 - - - +
325G ASP* 1.3 73.7 - - - +
327G TYR* 1.3 57.2 + - - +
328G ASP 3.2 0.2 - - - -
329G SER* 2.4 27.4 + - - -
504G ADP 3.4 38.2 - - + +
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Residues in contact with TYR 327 (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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325G ASP* 2.9 15.9 - - + +
326G ALA* 1.3 84.4 - - - +
328G ASP* 1.3 72.1 + - - +
329G SER* 3.1 1.6 + - - -
330G GLU* 3.3 32.2 + - + +
414G ALA* 5.5 7.0 - - + -
504G ADP 3.7 21.5 + - - +
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Residues in contact with ASP 328 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323G ILE* 4.5 5.2 - - + -
324G ASN* 4.0 13.5 + - - +
325G ASP* 3.2 35.7 + - - +
327G TYR* 1.3 83.8 - - - +
329G SER* 1.3 66.1 + - - +
330G GLU 3.1 0.2 - - - -
331G TYR* 2.8 21.1 + - - +
332G PHE* 3.0 35.4 + - + -
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Residues in contact with SER 329 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313G ILE* 5.0 5.4 - - - -
316G LEU* 5.9 0.2 - - - -
323G ILE* 4.9 14.1 - - - +
325G ASP 3.9 1.6 + - - -
326G ALA* 2.4 29.9 + - - -
327G TYR 3.6 0.5 + - - -
328G ASP* 1.3 75.7 - - - +
330G GLU* 1.3 56.6 + - - +
332G PHE* 4.6 3.4 - - - +
333G ALA* 2.8 35.9 + - - +
377G ILE* 4.1 16.9 - - - +
381G LEU* 4.0 21.1 - - - -
415G ASN* 3.8 1.4 + - - -
504G ADP 3.8 12.5 + - - -
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Residues in contact with GLU 330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327G TYR* 3.3 27.5 + - + +
328G ASP 2.9 2.0 + - - -
329G SER* 1.3 77.5 + - - +
331G TYR* 1.3 65.7 + - - +
333G ALA* 3.8 2.4 - - - +
334G THR* 2.6 33.3 + - + +
381G LEU* 4.9 0.2 - - - -
414G ALA 4.6 2.3 - - - +
415G ASN* 3.5 26.6 - - - +
416G ASN* 2.3 55.7 + - - +
417G PHE* 2.9 14.3 + - + -
504G ADP 5.8 0.7 - - - +
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Residues in contact with TYR 331 (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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327G TYR 4.6 0.2 + - - -
328G ASP* 2.8 14.5 + - - +
330G GLU* 1.3 79.5 - - - +
332G PHE* 1.3 95.4 + + - +
334G THR* 3.0 17.2 + - - -
335G LYS* 3.4 31.4 + - + +
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Residues in contact with PHE 332 (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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322G LEU 5.2 5.4 - - - -
323G ILE* 4.4 16.6 - - + -
328G ASP* 3.0 42.0 + - + +
329G SER 4.4 0.9 - - - +
331G TYR* 1.3 99.7 - + - +
333G ALA* 1.3 64.4 + - - +
334G THR 2.8 1.2 + - - -
335G LYS* 3.0 30.6 + - + +
374G ASN* 3.1 38.0 - - - +
377G ILE* 4.0 15.5 - - + -
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Residues in contact with ALA 333 (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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329G SER 2.8 25.4 + - - +
330G GLU 4.0 1.8 - - - +
332G PHE* 1.3 76.3 - - - +
334G THR* 1.3 59.8 + - - +
336G VAL* 3.4 6.2 + - - +
374G ASN 4.6 3.8 - - - -
377G ILE* 4.1 4.2 - - + +
378G ARG* 3.2 64.9 + - + +
381G LEU* 4.1 11.0 - - + -
417G PHE* 4.6 9.0 - - + -
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Residues in contact with THR 334 (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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330G GLU* 2.6 27.3 + - + +
331G TYR* 3.0 12.4 + - - -
332G PHE 2.8 0.2 - - - -
333G ALA* 1.3 78.2 - - - +
335G LYS* 1.3 56.9 + - - +
336G VAL 2.9 10.2 + - - -
337G GLN* 4.5 5.2 + - - +
378G ARG* 4.8 2.9 - - - +
417G PHE* 4.0 33.0 - - + -
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Residues in contact with LYS 335 (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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331G TYR* 3.4 35.8 + - + +
332G PHE* 3.0 27.0 + - + +
334G THR* 1.3 79.8 - - - +
336G VAL* 1.4 67.6 + - + +
337G GLN* 5.1 4.2 - - - +
374G ASN* 3.8 20.6 - - - +
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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