Contacts of the helix formed by residues 278 - 293 (chain G) in PDB entry 5UQ9
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 VAL 278 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268G ALA* 5.5 0.3 - - - +
271G ALA* 3.6 25.9 - - + +
276G VAL* 2.7 26.6 + - + -
277G PRO* 1.3 66.7 - - - +
279G THR* 1.3 61.8 + - - +
280G LEU 3.4 0.6 + - - -
281G ILE* 3.6 37.3 - - + +
282G GLY* 3.7 8.7 + - - -
334G SER 5.4 0.4 - - - +
337G GLN* 3.5 40.8 - - + +
338G GLY* 4.6 3.8 - - - +
341G LEU* 3.8 12.1 - - + -
286H PHE* 3.5 15.6 - - - -
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Residues in contact with THR 279 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G PRO* 2.8 22.1 + - + +
278G VAL* 1.3 72.6 - - - +
280G LEU* 1.3 65.7 + - - +
282G GLY* 3.4 0.9 + - - -
283G GLU* 3.2 26.5 + - - +
337G GLN* 2.9 19.5 + - - +
425G THR* 3.0 19.9 + - - +
429G PHE* 4.2 7.0 - - + +
283H GLU* 3.1 29.0 - - - +
286H PHE* 3.5 33.2 - - + -
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Residues in contact with LEU 280 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193G GLY* 3.8 22.0 - - - +
197G LEU* 4.4 7.0 - - + -
279G THR* 1.3 77.8 + - - +
281G ILE* 1.3 64.1 + - + +
283G GLU* 3.0 15.8 + - - +
284G ALA 3.1 8.7 + - - -
330G SER 4.7 1.1 - - - +
333G ILE* 5.4 0.4 - - + -
334G SER* 3.5 37.9 - - - +
337G GLN* 2.8 18.5 + - - +
422G CYS* 3.2 49.8 - - + +
425G THR* 3.6 12.1 - - + -
426G ALA* 3.8 15.3 - - + +
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Residues in contact with ILE 281 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G GLY* 3.3 31.4 - - - +
190G ILE* 4.4 9.4 - - + +
192G TYR* 5.2 0.2 - - + -
193G GLY* 4.7 4.0 - - - +
264G GLY 5.1 0.9 - - - +
267G THR* 3.5 50.0 - - + +
268G ALA* 3.9 6.1 - - + +
278G VAL* 3.6 32.5 + - + +
280G LEU* 1.3 77.1 - - + +
282G GLY* 1.3 61.4 + - - +
284G ALA* 3.6 8.5 - - + +
285G VAL* 2.9 37.2 + - + +
334G SER* 4.5 14.1 - - - +
338G GLY* 6.3 0.2 - - - -
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Residues in contact with GLY 282 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268G ALA* 4.2 18.4 - - - -
278G VAL 3.7 6.8 + - - -
279G THR 3.4 6.4 + - - -
280G LEU 3.1 1.4 - - - -
281G ILE* 1.3 83.8 - - - +
283G GLU* 1.3 59.8 + - - +
285G VAL* 4.1 1.9 - - - +
286G PHE* 3.1 39.0 + - - -
272H LEU* 5.0 0.6 - - - +
286H PHE* 4.9 8.5 - - - -
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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 THR 3.2 13.3 + - - +
280G LEU 3.0 9.0 + - - +
282G GLY* 1.3 76.2 - - - +
284G ALA* 1.3 53.9 + - - +
286G PHE* 3.5 2.6 - - - +
287G ALA* 2.6 36.9 + - - +
421G PRO* 3.4 37.8 - - + +
422G CYS* 4.2 4.3 - - - -
425G THR* 3.7 17.7 - - + -
279H THR* 3.8 21.4 - - - +
283H GLU* 2.7 20.1 - - - +
425H THR* 2.6 29.9 + - - +
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Residues in contact with ALA 284 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G TYR* 3.5 39.7 - - + +
193G GLY* 4.2 3.1 - - - +
196G GLN* 3.9 15.3 - - + +
280G LEU 3.1 11.9 + - - +
281G ILE* 3.1 10.0 + - - +
283G GLU* 1.3 77.7 - - - +
285G VAL* 1.3 61.7 + - - +
287G ALA* 3.2 8.4 + - - +
288G ARG* 3.1 27.4 + - - +
422G CYS* 4.2 1.7 - - - -
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Residues in contact with VAL 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G GLY* 6.2 0.2 - - - -
192G TYR* 3.8 22.0 - - + -
264G GLY* 3.2 29.2 - - - +
265G LYS* 3.7 33.4 - - + +
268G ALA* 4.6 4.3 - - + -
281G ILE* 2.9 23.6 + - + +
282G GLY 4.1 3.4 - - - +
284G ALA* 1.3 75.5 - - - +
286G PHE* 1.3 62.4 + - - +
288G ARG* 3.3 5.0 + - - +
289G CYS* 3.1 27.6 + - - -
272H LEU* 3.7 26.0 - - + -
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Residues in contact with PHE 286 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282G GLY* 3.1 25.7 + - - +
283G GLU* 3.8 4.3 - - - +
285G VAL* 1.3 76.2 - - - +
287G ALA* 1.3 57.2 + - - +
289G CYS* 3.7 7.4 - - - -
290G LEU* 3.0 27.7 + - - +
268H ALA* 4.3 6.3 - - + -
271H ALA* 4.0 11.9 - - + -
272H LEU* 3.5 38.6 - - + -
276H VAL 3.1 27.8 - - - -
277H PRO* 3.5 11.1 - - + +
278H VAL 3.4 22.4 - - - -
279H THR* 3.6 38.5 - - + +
282H GLY* 5.3 6.7 - - - -
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Residues in contact with ALA 287 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G GLN* 3.7 34.1 - - + +
283G GLU 2.6 22.6 + - - +
284G ALA 3.4 7.2 - - - +
285G VAL 3.2 0.6 - - - -
286G PHE* 1.3 71.5 - - - +
288G ARG* 1.3 59.8 + - - +
290G LEU* 3.2 9.8 + - - +
291G SER* 3.0 27.0 + - - -
421G PRO* 5.1 9.0 - - + -
438H LEU* 5.6 1.7 - - - +
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Residues in contact with ARG 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G TYR* 3.1 57.7 + - + +
195G MET* 3.3 35.2 - - - +
196G GLN* 5.7 2.5 - - - +
258G ALA* 3.6 21.3 + - + +
259G GLY 3.4 19.6 + - - +
265G LYS* 6.4 0.2 - - - -
284G ALA 3.1 12.9 + - - +
285G VAL* 3.3 7.1 + - - +
287G ALA* 1.3 76.9 - - + +
289G CYS* 1.3 60.5 + - - +
291G SER* 2.6 24.0 + - - -
292G SER* 3.1 13.3 + - - -
443H ILE* 3.6 25.8 - - + +
447H ARG* 3.1 29.1 - - - +
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Residues in contact with CYS 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259G GLY 4.8 0.2 - - - -
260G GLN* 3.6 35.0 + - - -
265G LYS* 3.9 11.0 - - - -
285G VAL* 3.1 24.1 + - - -
286G PHE* 3.7 15.5 - - - +
288G ARG* 1.3 77.9 - - - +
290G LEU* 1.3 61.8 + - - +
292G SER* 3.3 14.9 + - - -
293G LEU* 3.6 12.3 - - - +
272H LEU* 6.0 1.1 - - - -
275H GLY* 3.5 30.4 - - - +
276H VAL 4.6 0.2 - - - -
277H PRO* 4.3 10.3 - - + -
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Residues in contact with LEU 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G PHE 3.0 17.8 + - - +
287G ALA* 3.2 9.6 + - - +
289G CYS* 1.3 76.1 - - - +
291G SER* 1.3 61.3 + - - +
293G LEU* 3.2 19.7 + - + +
297G ARG* 3.0 26.0 + - - -
421G PRO* 6.5 1.1 - - + -
277H PRO* 4.2 9.6 - - + +
428H SER 5.3 0.9 - - - +
429H PHE* 3.9 31.0 - - + +
432H GLY* 3.7 28.3 - - - +
433H TYR* 3.8 34.1 - - + +
438H LEU* 4.6 5.8 - - + -
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Residues in contact with SER 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256G ASP 3.4 11.1 - - - +
257G SER* 3.8 5.5 + - - -
258G ALA* 3.2 17.5 + - - +
287G ALA 3.0 11.7 + - - -
288G ARG* 2.6 26.0 + - - -
290G LEU* 1.3 74.7 - - - +
292G SER* 1.3 63.0 + - - +
294G LYS* 3.5 3.1 + - - -
297G ARG* 2.8 27.9 + - - +
438H LEU* 4.5 6.3 - - - +
440H ALA* 3.5 28.0 - - - -
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Residues in contact with SER 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255G ARG* 5.6 0.5 + - - -
257G SER* 3.6 14.8 + - - -
259G GLY* 3.2 26.3 + - - -
260G GLN* 3.3 22.9 + - - -
288G ARG 3.1 12.7 + - - -
289G CYS 3.5 10.1 - - - -
290G LEU 3.2 0.8 - - - -
291G SER* 1.3 79.0 + - - +
293G LEU* 1.3 58.9 + - - +
294G LYS* 3.0 9.7 + - - +
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Residues in contact with LEU 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260G GLN* 4.4 12.8 - - - +
289G CYS 3.6 15.7 - - - +
290G LEU* 3.5 22.9 - - + +
291G SER 3.1 1.4 - - - -
292G SER* 1.3 75.9 - - - +
294G LYS* 1.3 57.0 + - - +
295G ASP 3.5 2.0 - - - -
296G GLU* 3.8 31.9 - - + +
297G ARG* 2.8 37.0 + - + +
277H PRO* 4.3 8.5 - - + -
340H MET* 3.7 30.3 - - + -
343H ARG* 4.7 9.4 - - - +
433H TYR* 4.7 2.5 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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