Contacts of the helix formed by residues 269 - 281 (chain G) in PDB entry 4E2I
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 SER 269 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267G GLN 3.9 2.0 + - - -
268G VAL* 1.3 73.2 - - - +
270G TRP* 1.3 62.5 + - - +
271G LYS* 3.7 6.8 + - - +
272G LEU* 3.3 42.4 + - - +
273G VAL* 3.3 9.4 + - - +
323G ASN* 2.6 32.9 + - - -
336G ILE* 4.6 0.9 - - - +
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Residues in contact with TRP 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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268G VAL* 3.6 22.9 - - + +
269G SER* 1.3 72.5 + - - +
271G LYS* 1.3 57.7 + - - +
272G LEU 3.1 2.0 - - - -
273G VAL* 3.2 2.9 + - - +
274G THR* 2.8 37.3 + - - +
332G ASN* 5.1 8.1 - - + -
335G THR* 3.6 33.0 - - + -
336G ILE* 3.6 47.6 - - + +
339G GLN* 3.1 39.7 - - + +
328H ALA 5.5 3.4 - - - +
329H ASP* 5.9 3.8 - - - -
330H SER 4.9 4.5 - - - +
331H LYS* 3.0 68.3 - - + +
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Residues in contact with LYS 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269G SER* 3.6 6.9 + - - +
270G TRP* 1.3 81.5 - - - +
272G LEU* 1.3 58.4 + - + +
274G THR* 3.7 7.0 - - - -
275G GLU* 2.9 37.8 + - - +
296H GLN* 4.2 24.2 - - - +
297H TYR* 6.1 2.2 - - - -
328H ALA* 4.4 23.5 + - + +
329H ASP* 3.9 28.4 - - - +
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Residues in contact with LEU 272 (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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269G SER* 3.3 21.7 + - - +
270G TRP 3.1 0.6 - - - -
271G LYS* 1.3 78.4 - - + +
273G VAL* 1.3 59.8 + - - +
275G GLU* 3.1 20.1 + - - +
276G TYR* 3.0 24.8 + - - +
319G LYS* 4.9 8.5 - - + +
320G HIS* 3.2 28.7 - - + +
322G ALA* 5.8 2.9 - - + -
323G ASN* 3.5 34.5 - - + +
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Residues in contact with VAL 273 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269G SER 3.3 9.4 - - - +
270G TRP 3.2 5.3 + - - +
272G LEU* 1.3 74.6 - - - +
274G THR* 1.3 58.0 + - - +
276G TYR* 3.3 4.7 + - - +
277G ALA* 3.0 26.3 + - - +
288G LEU* 5.1 5.1 - - + +
292G TYR* 3.6 29.8 - - + -
323G ASN* 3.2 26.0 - - - +
327G PHE* 4.8 2.0 - - + -
336G ILE* 3.6 33.7 - - + +
337G CYS* 4.2 24.2 - - - -
340G ALA* 4.4 3.8 - - + -
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Residues in contact with THR 274 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G TRP 2.8 22.6 + - - -
271G LYS* 3.7 8.9 - - - -
273G VAL* 1.3 73.7 - - - +
275G GLU* 1.3 60.7 + - - +
277G ALA* 3.2 2.3 + - - +
278G MET* 2.9 31.3 + - + +
336G ILE 5.3 1.0 + - - -
339G GLN* 4.2 13.0 + - - -
340G ALA* 3.9 18.8 + - - +
343G THR* 3.5 41.4 + - + +
333H GLN* 5.1 7.3 + - - +
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Residues in contact with GLU 275 (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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271G LYS* 2.9 27.7 + - + +
272G LEU* 3.1 27.7 + - - +
274G THR* 1.3 77.7 - - - +
276G TYR* 1.3 62.7 + - - +
278G MET* 3.1 10.2 + - + +
279G GLU* 3.0 34.6 + - + +
319G LYS* 3.2 36.0 + - - -
320G HIS* 3.9 4.8 - - + -
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Residues in contact with TYR 276 (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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272G LEU 3.0 9.1 + - - +
273G VAL* 3.6 6.3 - - + +
275G GLU* 1.3 76.3 - - - +
277G ALA* 1.3 61.2 + - - +
279G GLU* 3.2 6.5 + - - +
280G THR* 3.1 46.7 + - + +
288G LEU* 4.1 23.1 - - + -
291G MET* 3.8 23.0 - - + +
292G TYR* 3.6 20.9 - + + -
295G PHE* 3.8 19.8 - + - -
312G SER* 2.7 36.5 + - - -
316G TYR* 3.6 33.9 - + + -
320G HIS* 3.2 25.1 + + + +
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Residues in contact with ALA 277 (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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273G VAL 3.0 14.1 + - - +
274G THR 3.3 9.4 - - - +
276G TYR* 1.3 78.4 - - - +
278G MET* 1.3 53.0 + - - +
280G THR* 4.2 1.3 - - - -
281G LYS* 2.8 35.0 + - - -
282G CYS 3.3 3.7 + - - +
288G LEU* 3.8 20.2 - - + -
340G ALA* 3.6 23.8 - - + +
344G VAL* 3.7 19.9 - - + +
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Residues in contact with MET 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 THR* 2.9 23.1 + - + +
275G GLU* 3.1 9.8 + - + +
277G ALA* 1.3 75.5 - - - +
279G GLU* 1.3 66.2 + - - +
281G LYS* 3.7 16.8 - - - +
343G THR* 3.5 46.9 - - + +
344G VAL* 4.3 7.6 - - - -
347G LYS* 3.9 33.0 - - + +
293H LEU* 6.1 1.6 - - + -
297H TYR* 5.2 9.9 - - - +
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Residues in contact with GLU 279 (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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275G GLU* 3.0 31.4 + - + +
276G TYR* 3.3 9.4 - - - +
278G MET* 1.3 80.5 - - - +
280G THR* 1.3 63.1 + - + +
281G LYS* 3.0 16.0 + - - +
316G TYR* 3.5 44.4 + - + +
319G LYS* 5.5 6.5 - - - -
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Residues in contact with THR 280 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G TYR* 3.1 41.1 + - + +
277G ALA* 3.8 1.2 + - - -
279G GLU* 1.3 76.6 - - - +
281G LYS* 1.3 71.6 + - - +
282G CYS* 3.1 20.7 + - - +
312G SER* 3.6 32.1 - - - -
316G TYR* 4.6 7.9 - - + +
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Residues in contact with LYS 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 ALA 2.8 12.3 + - - -
278G MET* 3.7 11.9 - - - +
279G GLU 3.0 13.9 - - - +
280G THR* 1.3 78.8 - - - +
282G CYS* 1.3 63.8 + - - +
283G ASP* 3.1 9.0 + - - +
344G VAL* 3.6 15.0 - - + +
348G LYS* 3.7 20.9 + - - +
363G ASN* 5.7 3.4 - - - +
367G ASP* 3.5 30.9 + - - -
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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