Contacts of the helix formed by residues 268 - 284 (chain G) in PDB entry 5X8X
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 268 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267G LEU* 1.3 82.9 + - + +
269G GLU* 1.3 77.3 + - - +
271G GLU* 3.2 18.2 + - - +
272G HIS* 3.1 35.6 + - - -
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Residues in contact with GLU 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267G LEU 4.9 6.5 - - - +
268G THR* 1.3 88.3 + - - +
270G ILE* 1.3 63.6 + - + +
272G HIS* 3.2 25.0 + - - +
273G LEU* 3.3 11.8 + - - +
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Residues in contact with ILE 270 (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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267G LEU* 3.3 19.3 + - + +
269G GLU* 1.3 78.6 - - + +
271G GLU* 1.3 66.8 + - + +
273G LEU* 3.1 11.4 + - + +
274G VAL* 3.0 24.7 + - + +
445G ASN 5.2 1.8 - - - +
448G LEU* 3.9 38.8 - - + +
449G ALA* 3.9 26.1 - - + +
452G HIS* 4.3 26.0 - - + -
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Residues in contact with GLU 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267G LEU* 3.2 35.9 + - + +
268G THR* 3.2 16.2 + - - +
270G ILE* 1.3 76.0 - - + +
272G HIS* 1.4 65.4 + - - +
274G VAL* 3.2 7.5 + - + +
275G GLN* 3.0 36.0 + - + +
452G HIS* 5.4 7.9 + - + +
456G LYS* 5.1 10.0 + - - +
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Residues in contact with HIS 272 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268G THR* 3.1 38.4 + - - -
269G GLU* 3.2 19.3 + - - +
271G GLU* 1.4 74.4 - - - +
273G LEU* 1.3 58.1 + - - +
275G GLN* 3.9 4.1 - - - +
276G SER* 2.9 32.3 + - - -
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Residues in contact with LEU 273 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269G GLU 3.3 7.6 + - - +
270G ILE* 3.1 13.0 + - + +
272G HIS* 1.3 76.8 - - - +
274G VAL* 1.3 59.9 + - - +
276G SER* 2.8 20.5 + - - +
277G VAL* 3.0 24.9 + - + +
339G SER* 3.3 31.9 - - - +
419G LEU* 5.5 0.4 - - + -
445G ASN* 3.7 42.4 - - + +
446G LEU* 4.1 22.4 - - + +
449G ALA* 4.4 6.3 - - + -
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Residues in contact with VAL 274 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G ILE* 3.0 17.1 + - + +
271G GLU* 3.2 8.9 + - - +
273G LEU* 1.3 73.5 - - - +
275G GLN* 1.3 76.9 + - - +
277G VAL* 3.3 3.1 + - - +
278G CYS* 3.0 35.7 + - - -
415G ASP* 5.4 2.2 - - - +
419G LEU* 4.6 19.0 - - + +
449G ALA* 3.7 35.0 - - + +
452G HIS* 6.0 2.7 - - + -
453G HIS* 4.6 21.8 - - + +
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Residues in contact with GLN 275 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271G GLU* 3.0 24.9 + - + +
272G HIS* 4.1 3.6 - - - +
274G VAL* 1.3 87.1 - - - +
276G SER* 1.3 58.2 + - - +
278G CYS* 3.3 9.5 + - - +
279G LYS* 2.8 32.5 + - - +
282G ARG* 5.4 2.8 + - - -
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Residues in contact with SER 276 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G HIS 2.9 16.9 + - - -
273G LEU* 2.8 21.3 + - - +
275G GLN* 1.3 78.4 - - - +
277G VAL* 1.3 60.7 + - - +
279G LYS* 3.3 8.9 + - - +
280G SER* 3.0 26.7 + - - -
337G ARG 5.3 4.6 + - - +
339G SER* 3.9 16.9 + - - -
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Residues in contact with VAL 277 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273G LEU* 3.0 22.1 + - + +
274G VAL 3.3 0.4 + - - +
276G SER* 1.3 83.9 + - - +
278G CYS* 1.3 58.8 + - - +
280G SER* 2.8 19.8 + - - -
281G TYR* 3.1 16.1 + - - +
334G PHE* 3.9 6.6 - - + -
338G LEU* 4.3 13.2 - - + -
339G SER 6.1 1.1 - - - +
418G ALA* 3.4 32.5 - - + +
419G LEU* 3.8 18.8 - - + -
422G ALA* 4.1 8.7 - - + -
446G LEU* 3.9 25.4 - - + -
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Residues in contact with CYS 278 (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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274G VAL* 3.0 30.2 + - - +
275G GLN* 3.8 9.2 - - - +
277G VAL* 1.3 73.7 - - - +
279G LYS* 1.3 65.6 + - - +
281G TYR* 3.2 3.3 + - + +
282G ARG* 3.0 46.5 + - + +
414G GLU 5.3 0.4 - - - -
415G ASP* 3.3 46.7 - - - +
418G ALA* 4.1 12.6 - - - -
419G LEU* 5.1 3.8 - - - -
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Residues in contact with LYS 279 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G GLN 2.8 21.9 + - - +
276G SER* 3.5 8.3 - - - +
278G CYS* 1.3 72.0 - - - +
280G SER* 1.3 57.5 + - - +
282G ARG* 3.4 22.1 + - - +
283G GLU* 2.9 65.3 + - + +
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Residues in contact with SER 280 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G SER 3.0 11.1 + - - -
277G VAL* 2.8 21.0 + - - -
279G LYS* 1.3 78.7 - - - +
281G TYR* 1.3 58.6 + - - +
283G GLU* 3.4 11.2 + - - +
284G THR* 3.0 31.9 + - - +
334G PHE* 3.8 13.3 - - - -
337G ARG* 3.5 35.4 + - - -
338G LEU* 4.1 5.4 - - - +
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Residues in contact with TYR 281 (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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277G VAL 3.1 10.4 + - - +
278G CYS* 3.2 2.7 + - - +
280G SER* 1.3 73.1 + - - +
282G ARG* 1.3 70.5 + - + +
284G THR* 3.2 5.6 + - - -
285G CYS* 3.0 50.1 + - - -
334G PHE* 3.7 12.3 - + + -
364G ARG* 3.8 26.6 + - + -
367G ARG* 2.8 33.8 + - - -
414G GLU* 3.2 37.9 + - + -
417G ILE* 3.6 29.3 - - + +
418G ALA* 3.5 36.8 - - + -
421G THR* 4.5 5.4 - - - -
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Residues in contact with ARG 282 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G GLN* 5.4 2.8 + - - -
278G CYS* 3.0 38.2 + - - +
279G LYS* 3.7 25.8 - - - +
281G TYR* 1.3 86.3 - - + +
283G GLU* 1.3 62.8 + - + +
284G THR 3.2 0.7 + - - -
285G CYS* 3.3 19.7 + - - +
288G ARG* 6.1 1.4 - - - +
414G GLU* 4.9 16.8 - - + +
415G ASP* 4.8 5.5 + - - -
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Residues in contact with GLU 283 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G LYS* 2.9 62.1 + - + +
280G SER* 3.6 10.6 - - - +
282G ARG* 1.3 73.2 - - + +
284G THR* 1.3 63.2 + - + +
285G CYS 3.9 4.7 + - - +
330G TYR* 5.4 2.3 - - - -
337G ARG* 3.8 26.0 + - - +
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Residues in contact with THR 284 (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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280G SER 3.0 19.1 + - - +
281G TYR 3.4 1.0 + - - -
282G ARG 3.2 0.2 - - - -
283G GLU* 1.3 79.3 - - - +
285G CYS* 1.3 63.1 + - - +
330G TYR* 3.2 34.3 - - - +
333G GLU* 3.8 10.8 - - + -
334G PHE* 3.5 24.8 - - - +
337G ARG* 3.7 24.5 - - - +
364G ARG* 2.7 44.6 + - - -
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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