Contacts of the helix formed by residues 479 - 493 (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 ARG 479 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F ASP* 3.2 29.3 + - - -
39F VAL* 4.5 13.9 - - - +
40F VAL* 3.1 28.4 - - - +
389G ARG* 3.9 6.5 - - - +
424G ASP 3.6 13.7 - - - +
425G ILE* 3.9 33.9 - - + +
426G LEU 4.1 11.5 + - - -
427G GLY 4.4 2.9 - - - +
475G GLU 3.7 4.0 + - - -
476G THR* 2.9 31.8 + - - +
477G THR* 4.7 1.6 + - - +
478G GLU* 1.3 76.3 - - - +
480G ASN* 1.3 93.5 + - - +
481G TYR 3.1 0.2 + - - -
482G ARG* 3.2 6.4 + - - +
483G TYR* 2.9 25.1 + - - +
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Residues in contact with ASN 480 (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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38F ASP* 4.7 5.5 + - - -
94F ASP* 4.4 18.3 + - - +
389G ARG* 3.3 24.5 + - - +
477G THR 4.6 4.4 + - - -
478G GLU 3.1 1.8 + - - -
479G ARG* 1.3 114.8 + - - +
481G TYR* 1.3 64.6 + - - +
483G TYR* 3.4 4.6 + - + +
484G ALA* 3.0 19.6 + - - +
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Residues in contact with TYR 481 (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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94F ASP* 5.4 4.9 + - - -
96F VAL* 4.0 43.5 - - + -
97F GLU* 4.2 27.1 - - + -
99F LYS* 4.1 29.1 + - - +
478G GLU* 3.1 10.0 + - + +
480G ASN* 1.3 74.6 - - - +
482G ARG* 1.3 67.7 + - + +
484G ALA* 2.6 32.1 + - + +
485G GLY* 3.1 7.8 + - - -
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Residues in contact with ARG 482 (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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337G GLN 5.6 3.8 + - - -
343G TYR* 2.9 25.2 + - - -
378G ARG* 5.6 5.1 - - - +
382G GLU* 5.4 5.0 + - - -
386G TYR* 3.6 26.4 - - - +
421G PHE* 5.0 13.9 - - - -
424G ASP* 6.0 3.4 - - - +
425G ILE* 4.1 13.7 - - + +
475G GLU* 3.9 31.1 + - - +
478G GLU* 3.4 34.7 - - + +
479G ARG* 3.2 9.3 + - - +
481G TYR* 1.3 89.8 - - + +
483G TYR* 1.3 60.7 + - - +
485G GLY 3.3 1.0 + - - -
486G TRP 3.4 4.0 + - - -
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Residues in contact with TYR 483 (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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386G TYR* 3.8 28.5 - + + -
389G ARG* 3.6 55.3 - - + +
390G ASP* 2.5 38.8 + - - -
393G GLU* 4.1 12.8 + - - +
425G ILE* 5.0 1.3 - - + -
479G ARG 2.9 16.4 + - - +
480G ASN* 4.1 5.4 - - + +
482G ARG* 1.3 76.8 - - - +
484G ALA* 1.3 69.0 + - - +
485G GLY 2.9 2.0 - - - -
486G TRP* 3.3 12.7 - + - +
487G LYS* 2.7 51.3 + - + +
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Residues in contact with ALA 484 (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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480G ASN 3.0 12.3 + - - +
481G TYR* 2.6 16.6 + - + +
483G TYR* 1.3 81.4 - - - +
485G GLY* 1.3 66.2 + - - +
487G LYS* 3.1 7.2 + - - +
488G LYS* 3.1 20.3 + - - +
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Residues in contact with GLY 485 (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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343G TYR* 3.0 34.3 - - - -
481G TYR 3.1 8.2 + - - -
482G ARG 3.3 0.4 + - - -
483G TYR 2.9 1.0 - - - -
484G ALA* 1.3 80.7 - - - +
486G TRP* 1.3 64.8 - - - +
488G LYS* 2.8 22.9 + - - +
489G ALA 3.1 9.5 + - - -
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Residues in contact with TRP 486 (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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343G TYR* 3.2 17.7 - + - -
344G VAL 3.9 21.5 - - - -
345G VAL* 4.3 9.6 - - + -
346G PRO* 4.3 9.0 - - + -
351G LEU* 6.3 0.9 - - + -
355G TYR* 3.5 8.2 + + - -
383G SER* 4.0 10.3 - - - -
386G TYR* 3.3 42.5 - + + +
387G GLN* 3.5 38.8 - - + -
390G ASP* 3.0 23.8 + - - -
482G ARG 3.4 2.6 + - - +
483G TYR* 3.3 30.1 - + - +
485G GLY* 1.3 72.6 - - - +
487G LYS* 1.3 73.5 + - + +
489G ALA* 3.1 6.9 + - + +
490G VAL* 2.9 48.2 + - + +
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Residues in contact with LYS 487 (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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355G TYR* 3.8 24.7 + - - +
390G ASP* 3.6 5.0 + - - +
393G GLU* 4.9 4.2 + - - -
483G TYR* 2.7 56.9 + - + +
484G ALA* 3.1 6.9 + - - +
485G GLY 3.0 1.0 + - - -
486G TRP* 1.3 89.5 - - + +
488G LYS* 1.3 61.2 + - - +
490G VAL* 3.8 4.0 - - + +
491G LYS* 3.3 23.0 + - - +
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Residues in contact with LYS 488 (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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343G TYR* 5.9 4.3 - - + -
484G ALA 3.1 8.2 + - - +
485G GLY* 2.8 17.4 + - - +
487G LYS* 1.3 73.3 - - - +
489G ALA* 1.3 70.2 + - - +
491G LYS* 3.3 9.3 + - - +
492G ARG* 3.3 43.7 + - - +
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Residues in contact with ALA 489 (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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343G TYR* 4.0 26.0 - - + -
345G VAL* 3.6 18.3 - - + +
365G PHE* 3.4 33.4 - - + -
485G GLY 3.1 10.0 + - - +
486G TRP* 3.3 11.9 - - + +
488G LYS* 1.3 80.3 - - - +
490G VAL* 1.3 64.6 + - - +
492G ARG* 2.9 11.5 + - - +
493G ALA 3.4 0.9 + - - -
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Residues in contact with VAL 490 (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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345G VAL* 3.9 15.0 - - + -
351G LEU* 4.1 16.6 - - + +
355G TYR* 3.9 30.5 - - + +
486G TRP* 2.9 58.7 + - + +
487G LYS* 3.8 6.5 - - - +
489G ALA* 1.3 76.2 - - - +
491G LYS* 1.3 61.2 + - + +
492G ARG 2.6 12.0 + - - -
493G ALA* 2.8 15.2 + - - +
494G MET* 3.4 14.1 + - - +
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Residues in contact with LYS 491 (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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487G LYS 3.3 14.5 + - - +
488G LYS* 3.8 6.7 - - - +
489G ALA 3.3 0.4 - - - -
490G VAL* 1.3 83.7 - - + +
492G ARG* 1.3 61.6 + - + +
494G MET* 4.0 28.2 - - + +
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Residues in contact with ARG 492 (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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365G PHE* 3.5 29.2 - - + -
488G LYS* 3.3 32.8 + - - +
489G ALA* 2.9 10.6 + - - +
490G VAL 2.6 7.1 + - - -
491G LYS* 1.3 79.8 - - + +
493G ALA* 1.3 58.6 + - - +
494G MET 3.3 6.3 - - - +
496G TRP* 5.4 6.8 - - - -
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Residues in contact with ALA 493 (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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345G VAL* 3.7 29.2 - - + -
351G LEU* 5.6 0.4 - - + -
360G ALA* 3.1 20.0 - - + -
361G ARG 3.2 25.8 + - - +
363G ALA* 3.8 18.8 - - + -
489G ALA 3.4 3.5 + - - +
490G VAL 2.8 4.7 + - - +
492G ARG* 1.3 75.8 - - - +
494G MET* 1.3 66.3 + - - +
496G TRP* 3.6 10.3 + - - +
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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