Contacts of the helix formed by residues 416 - 426 (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 ASN 416 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330G GLU* 2.3 31.0 + - - +
414G ALA 3.4 9.1 + - - -
415G ASN* 1.3 67.5 - - - +
417G PHE* 1.3 55.7 + - - +
419G MET* 3.3 0.7 - - - +
420G GLN* 2.7 35.2 + - - +
432G ARG* 2.7 27.6 + - - +
468G ARG* 3.7 13.9 + - - +
470G PHE* 3.2 18.6 - - + -
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Residues in contact with PHE 417 (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* 2.9 20.0 + - + -
333G ALA* 4.6 10.8 - - + -
334G THR* 4.0 23.1 - - + -
378G ARG* 3.7 44.9 - - + -
381G LEU* 4.0 32.3 - - + -
382G GLU* 4.7 4.3 - - + -
415G ASN* 3.0 7.2 - - - +
416G ASN* 1.3 77.5 - - - +
418G LEU* 1.3 70.3 + - + +
420G GLN* 3.8 3.9 - - + +
421G PHE* 2.8 53.9 + + + +
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Residues in contact with LEU 418 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G TYR* 4.9 2.9 - - + -
381G LEU* 3.8 29.2 - - + +
384G ILE* 4.1 33.9 - - + -
385G ALA* 4.3 21.3 - - + +
412G ALA* 4.6 20.4 - - + +
415G ASN* 2.6 30.4 + - + +
417G PHE* 1.3 83.6 - - + +
419G MET* 1.3 66.6 + - + +
421G PHE* 4.2 4.7 - - + -
422G GLN* 2.6 36.7 + - + +
504G ADP 5.7 1.3 - - + -
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Residues in contact with MET 419 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G TYR* 4.0 24.9 - - + +
408G VAL* 4.7 5.4 - - - -
413G VAL* 3.5 41.7 - - + +
415G ASN 2.5 25.1 + - - +
416G ASN 3.3 3.4 - - - +
418G LEU* 1.3 89.4 - - + +
420G GLN* 1.3 65.0 + - - +
422G GLN* 2.9 22.1 + - + +
423G SER* 2.9 20.1 + - - -
430G VAL* 4.3 19.7 - - + +
432G ARG* 3.9 4.3 - - - +
470G PHE* 3.6 26.7 - - + -
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Residues in contact with GLN 420 (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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416G ASN 2.7 20.6 + - - +
417G PHE* 3.8 4.5 - - + +
419G MET* 1.3 71.4 - - - +
421G PHE* 1.3 61.0 + - - +
423G SER* 2.6 26.0 + - - -
424G ASP* 2.7 44.5 + - - +
468G ARG* 5.1 2.8 + - - -
470G PHE* 3.7 24.6 - - + +
471G ARG 3.0 28.0 + - - +
473G GLY* 3.7 6.3 - - - +
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Residues in contact with PHE 421 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378G ARG* 4.7 4.9 - - - -
382G GLU* 3.5 45.5 - - + -
385G ALA* 3.6 28.0 - - + -
386G TYR* 3.8 8.1 - + - -
417G PHE* 2.8 50.3 + + + +
418G LEU* 3.6 8.1 - - + +
420G GLN* 1.3 75.0 - - - +
422G GLN* 1.3 63.1 + - - +
424G ASP* 3.7 12.3 - - + +
425G ILE* 2.9 50.8 + - + +
482G ARG* 5.0 16.2 - - - -
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Residues in contact with GLN 422 (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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265G TYR* 2.3 33.2 + - - +
385G ALA* 3.2 41.1 + - + +
388G THR* 3.1 19.8 + - - +
389G ARG 4.3 0.2 - - - +
406G LEU* 5.0 0.7 - - + -
418G LEU* 2.6 19.8 + - + +
419G MET* 2.9 20.8 + - + +
421G PHE* 1.3 73.2 - - - +
423G SER* 1.3 63.4 + - - +
425G ILE* 3.3 3.9 - - - +
426G LEU* 3.2 49.7 + - + +
430G VAL* 4.3 8.5 - - + -
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Residues in contact with SER 423 (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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419G MET 2.9 10.2 + - - -
420G GLN* 2.6 22.4 + - - -
422G GLN* 1.3 71.5 - - - +
424G ASP* 1.3 52.0 + - - -
426G LEU* 3.1 2.4 + - - +
427G GLY* 2.8 32.1 + - - -
428G THR 2.4 31.8 + - - -
430G VAL* 3.9 13.2 - - - -
470G PHE* 3.6 18.8 + - - -
472G PRO* 3.1 18.3 - - - +
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Residues in contact with ASP 424 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420G GLN* 2.7 47.3 + - - +
421G PHE* 3.7 14.6 - - + +
423G SER* 1.3 71.6 - - - +
425G ILE* 1.3 64.1 + - + +
426G LEU 3.0 1.4 + - - -
427G GLY 3.2 3.1 + - - -
472G PRO* 4.5 1.6 - - - -
473G GLY* 3.0 19.6 + - - -
475G GLU* 4.0 22.0 - - + +
476G THR* 3.0 43.3 + - - +
479G ARG* 3.6 5.4 - - - -
482G ARG* 6.0 3.1 - - - +
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Residues in contact with ILE 425 (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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385G ALA* 3.8 17.3 - - + +
386G TYR* 3.4 35.4 - - + -
389G ARG* 2.8 37.4 + - + +
421G PHE* 2.9 29.7 + - + +
422G GLN* 3.3 32.3 - - - +
424G ASP* 1.3 81.8 - - + +
426G LEU* 1.4 54.9 + - + +
479G ARG* 3.9 18.6 - - + +
482G ARG* 4.1 21.5 - - + +
483G TYR* 4.9 1.3 - - + +
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Residues in contact with LEU 426 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388G THR* 4.8 2.2 - - + -
389G ARG* 4.0 36.7 + - + +
392G LEU* 4.2 25.6 - - + -
406G LEU* 4.3 18.6 - - + -
422G GLN* 3.2 44.1 + - + +
423G SER 3.1 4.4 + - - +
424G ASP 3.0 0.6 - - - -
425G ILE* 1.4 78.1 - - + +
427G GLY* 1.4 64.0 - - - +
428G THR* 3.8 22.8 + - + +
430G VAL* 4.8 5.6 - - + -
479G ARG* 4.1 12.3 + - - -
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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