Contacts of the helix formed by residues 239 - 255 (chain G) in PDB entry 6MZL
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 LEU 239 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G ILE* 4.3 22.0 - - + -
236G LEU* 3.1 55.0 + - + +
238G GLN* 1.3 79.9 - - + +
240G PHE* 1.3 64.9 + - - +
241G TYR 3.4 0.2 - - - -
242G PRO* 3.4 6.6 - - - +
243G LEU* 3.3 26.0 + - + +
307G LEU* 4.3 15.7 - - + -
309G ILE* 4.2 16.6 - - + -
317G LEU* 6.0 7.0 - - + -
337G LEU* 6.4 0.7 - - + -
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Residues in contact with PHE 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218G TYR* 3.3 23.1 + + - -
222G LYS* 3.6 51.4 - - + -
225G ILE* 3.6 34.1 - - + -
226G GLU* 4.3 13.9 - - + -
233G ARG* 5.2 8.3 - - + -
236G LEU 3.5 16.4 - - - -
237G SER* 3.2 30.3 - - - +
238G GLN 3.3 1.6 - - - -
239G LEU* 1.3 78.3 - - + +
241G TYR* 1.3 65.2 + - - +
243G LEU* 4.0 3.5 - - - +
244G PHE* 3.4 8.8 + - - +
270G ASP* 5.9 0.7 - - + +
271G GLN* 3.3 22.4 + - - +
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Residues in contact with TYR 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237G SER 5.8 0.2 - - - +
238G GLN* 4.1 3.7 + - - +
240G PHE* 1.3 75.6 - - - +
242G PRO* 1.3 74.8 - - + +
244G PHE* 3.0 10.7 + + - +
245G VAL* 2.9 51.7 + - + +
271G GLN* 3.0 33.8 + - + +
275G TYR* 3.5 57.6 + + + +
278G ASP* 3.2 34.3 + - - +
279G LEU* 4.2 13.8 - - + +
282G LEU* 5.6 1.8 - - + +
300G PHE* 4.6 18.1 - + - -
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Residues in contact with PRO 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238G GLN 3.2 21.5 - - - +
239G LEU* 3.4 4.9 - - - +
241G TYR* 1.3 99.5 - - + +
243G LEU* 1.3 58.6 + - - +
245G VAL* 3.6 10.1 - - + +
246G HIS* 2.8 32.7 + - - +
300G PHE* 5.6 8.5 - - + -
304G LYS 5.1 4.3 - - - +
305G PHE* 4.2 28.8 - - + -
306G VAL 6.1 2.0 - - - +
307G LEU* 6.4 1.6 - - + -
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Residues in contact with LEU 243 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218G TYR* 3.8 25.8 - - + -
221G LEU* 4.3 23.3 - - + -
222G LYS 6.4 0.2 - - - +
225G ILE* 5.7 6.1 - - + -
239G LEU* 3.3 21.7 + - + +
240G PHE* 4.0 3.6 - - - +
242G PRO* 1.3 81.1 - - - +
244G PHE* 1.3 57.5 + - - +
246G HIS* 3.4 3.0 + - - +
247G MET* 2.9 38.1 + - + +
305G PHE* 5.4 4.4 - - - -
329G ILE* 4.7 15.9 - - + -
332G ILE* 3.7 37.0 - - + -
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Residues in contact with PHE 244 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218G TYR* 3.5 32.1 - + - +
240G PHE 3.4 4.6 + - - +
241G TYR* 3.0 14.8 + + - +
243G LEU* 1.3 79.4 - - - +
245G VAL* 1.3 61.6 + - + +
247G MET* 3.4 4.5 + - - +
248G TYR* 2.9 34.5 + + + +
263G PHE* 3.6 34.8 - + - -
264G PHE* 3.6 45.8 - + + -
267G PHE* 3.7 31.2 - - + -
268G HIS* 4.4 3.1 - - - -
271G GLN* 4.9 4.9 - - + +
279G LEU* 6.1 2.0 - - + -
282G LEU* 4.0 15.7 - - + -
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Residues in contact with VAL 245 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241G TYR* 2.9 55.9 + - + +
242G PRO* 3.7 9.9 - - + +
243G LEU 3.2 0.4 - - - -
244G PHE* 1.3 82.1 - - + +
246G HIS* 1.3 58.5 + - - +
248G TYR* 3.2 6.7 + - - +
249G LEU* 2.9 26.5 + - - +
282G LEU* 4.6 15.9 - - + +
300G PHE* 4.3 11.9 - - + -
301G ARG* 3.4 41.1 + - + +
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Residues in contact with HIS 246 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242G PRO 2.8 18.5 + - - +
243G LEU* 4.0 2.7 - - - +
245G VAL* 1.3 75.8 - - - +
247G MET* 1.3 59.4 + - - +
249G LEU* 3.3 18.9 + - + +
250G GLU* 2.9 29.1 + - + +
301G ARG* 3.7 30.1 + - + +
305G PHE* 5.2 7.7 - + + -
328G GLN* 5.3 5.8 + - - -
332G ILE* 3.5 36.2 - - + +
336G HIS* 3.3 37.0 + + - -
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Residues in contact with MET 247 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211G PRO* 5.1 2.7 - - + +
214G TYR* 3.7 38.1 - - + +
215G GLU* 5.3 1.8 - - + +
218G TYR* 5.1 9.9 - - + -
243G LEU* 2.9 29.2 + - + +
244G PHE* 3.7 6.5 - - - +
246G HIS* 1.3 78.1 - - - +
248G TYR* 1.3 57.2 + - - +
250G GLU* 3.1 33.6 + - + +
251G LEU* 2.8 37.8 + - + +
263G PHE* 5.1 13.2 - - + -
328G GLN* 4.6 5.2 - - + -
329G ILE* 5.7 7.0 - - + -
332G ILE* 3.8 24.7 - - + -
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Residues in contact with TYR 248 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G PHE* 2.9 25.4 + + + +
245G VAL* 3.7 5.6 - - - +
247G MET* 1.3 73.9 - - - +
249G LEU* 1.3 61.5 + - - +
251G LEU* 3.4 20.3 - - + +
252G VAL* 2.9 44.1 + - + +
260G ALA* 3.5 34.5 - - + +
261G LYS* 5.3 1.9 + - - -
263G PHE* 5.9 0.4 - - + -
264G PHE* 4.0 19.1 - + + +
282G LEU* 3.1 54.7 + - + -
283G SER* 4.7 3.1 + - - -
285G LEU* 3.6 27.1 + - + -
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Residues in contact with LEU 249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245G VAL 2.9 14.6 + - - +
246G HIS* 3.3 23.6 - - + +
248G TYR* 1.3 77.9 - - - +
250G GLU* 1.3 57.3 + - - +
252G VAL* 4.9 3.8 - - + -
253G TYR* 2.8 35.5 + - + +
282G LEU* 5.9 0.2 - - - +
285G LEU* 6.4 1.1 - - - -
291G MET* 4.2 25.6 - - + -
297G MET* 3.2 39.9 - - + +
298G LEU* 4.0 12.8 - - + -
301G ARG* 3.7 26.5 - - + +
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Residues in contact with GLU 250 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211G PRO* 5.7 1.3 - - + -
214G TYR* 3.7 16.7 - - - -
246G HIS* 2.9 16.6 + - + +
247G MET* 3.1 39.8 + - + +
249G LEU* 1.3 76.3 - - - +
251G LEU* 1.3 52.4 + - + +
253G TYR* 3.5 9.3 - - + +
254G ASN* 2.6 58.3 + - - +
328G GLN* 3.3 32.3 + - - +
332G ILE* 5.4 0.2 - - - +
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Residues in contact with LEU 251 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211G PRO* 3.8 29.6 - - + +
215G GLU* 3.9 18.8 - - + +
247G MET* 2.8 20.2 + - + +
248G TYR* 3.4 23.8 - - + +
249G LEU 3.2 0.4 - - - -
250G GLU* 1.3 78.3 - - + +
252G VAL* 1.3 58.4 + - - +
254G ASN* 3.2 6.7 + - - +
255G GLN 3.0 20.4 + - - -
256G HIS* 3.5 15.4 + - + +
259G GLU* 5.5 2.7 - - + -
260G ALA* 3.6 33.9 - - + +
263G PHE* 3.8 31.2 - - + -
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Residues in contact with VAL 252 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248G TYR* 2.9 47.7 + - + +
249G LEU* 4.2 6.1 - - + +
251G LEU* 1.3 75.4 - - - +
253G TYR* 1.3 57.5 + - - +
255G GLN* 3.0 27.1 + - - +
256G HIS 5.2 0.4 - - - +
260G ALA* 4.9 3.8 - - + -
285G LEU* 4.0 22.7 - - + +
286G THR 3.3 29.5 - - - +
287G LYS* 4.1 12.0 - - - +
288G LYS* 5.7 0.3 - - - +
291G MET* 5.4 5.0 - - + +
297G MET* 4.9 9.2 - - + -
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Residues in contact with TYR 253 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249G LEU* 2.8 24.3 + - + +
250G GLU* 3.5 9.4 - - + +
252G VAL* 1.3 78.1 - - - +
254G ASN* 1.3 66.1 + - - +
255G GLN* 3.4 11.9 + - - +
288G LYS* 4.0 27.6 + - - +
291G MET* 3.6 37.0 - - + -
298G LEU* 5.8 1.3 - - + -
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Residues in contact with ASN 254 (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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211G PRO* 3.9 24.9 - - + +
250G GLU* 2.6 48.2 + - - +
251G LEU* 3.2 6.4 + - - +
253G TYR* 1.3 78.1 - - - +
255G GLN* 1.3 69.0 + - - +
256G HIS* 3.2 29.1 + - + +
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Residues in contact with GLN 255 (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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251G LEU 3.0 2.2 + - - -
252G VAL* 3.0 25.2 + - - +
253G TYR 3.7 6.3 - - - +
254G ASN* 1.3 81.8 - - - +
256G HIS* 1.3 64.4 + - - +
257G GLU* 3.9 3.2 + - - -
286G THR 4.8 4.9 - - - -
287G LYS* 4.3 36.5 + - + +
288G LYS* 3.4 40.8 - - - +
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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