Contacts of the helix formed by residues 242 - 256 (chain G) in PDB entry 6CM9
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 ASP 242 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188G HIS* 3.3 34.7 - - - +
226G LEU* 4.0 11.6 - - + +
235G HIS* 3.0 39.3 + - + +
240G ILE 3.3 1.2 + - - -
241G SER* 1.3 75.7 - - - +
243G PRO* 1.3 68.3 - - - +
244G PHE* 4.1 0.7 + - - -
245G LEU* 3.6 23.7 + - - +
246G GLN* 3.3 17.2 + - - +
126S THR* 3.6 19.8 + - - +
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Residues in contact with PRO 243 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235G HIS 3.7 9.6 - - - +
237G VAL* 3.8 13.9 - - + -
240G ILE* 3.9 6.5 - - + +
241G SER 3.8 1.1 - - - +
242G ASP* 1.3 89.5 - - - +
244G PHE* 1.3 68.3 + - + +
246G GLN* 3.2 0.8 + - - +
247G VAL* 3.0 34.3 + - - +
284G VAL* 3.6 23.3 - - + +
287G ALA* 6.1 0.4 - - + -
288G ILE* 3.6 18.0 - - + +
79S LEU* 4.2 4.5 - - + -
82S GLU* 3.2 30.1 - - - +
86S ARG* 5.1 0.2 - - - +
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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
----------------------------------------------------------
192G HIS* 3.2 19.8 - - - +
237G VAL* 4.6 0.2 - - + -
242G ASP* 3.4 1.5 + - - -
243G PRO* 1.3 87.1 - - + +
245G LEU* 1.3 59.4 + - - +
247G VAL* 4.2 1.1 - - - +
248G ARG* 3.2 18.0 + - - +
79S LEU* 3.6 32.4 - - + +
82S GLU* 4.0 30.1 - - + -
83S ILE* 3.6 29.2 - - + -
86S ARG* 3.3 45.3 - - + -
117S PHE* 5.2 3.4 - + - -
123S ILE* 4.8 10.3 - - + -
126S THR* 3.7 32.8 - - + -
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Residues in contact with LEU 245 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G HIS* 3.5 34.8 - - + -
191G LEU* 3.7 23.8 - - + +
192G HIS* 3.7 37.0 - - + +
195G VAL* 4.6 3.4 - - + -
226G LEU* 3.7 16.4 - - + -
242G ASP* 3.6 21.4 + - - +
243G PRO 3.2 0.4 - - - -
244G PHE* 1.3 78.6 - - - +
246G GLN* 1.3 59.9 + - - +
247G VAL 3.3 0.2 - - - -
248G ARG* 3.4 0.8 + - + -
249G ILE* 2.9 49.7 + - + +
126S THR* 4.7 1.8 - - + +
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Residues in contact with GLN 246 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223G LEU* 3.8 26.0 - - + +
226G LEU* 4.0 18.3 + - + +
227G ILE* 4.2 21.8 - - - +
240G ILE* 4.8 4.9 - - - +
241G SER* 2.8 28.2 + - - +
242G ASP 3.3 12.7 + - - +
243G PRO* 3.2 5.1 + - - +
245G LEU* 1.3 78.4 - - - +
247G VAL* 1.3 56.8 + - - +
249G ILE* 3.4 1.4 + - - +
250G LEU* 2.9 37.0 + - + +
274G VAL* 5.3 2.0 - - - +
288G ILE* 3.3 37.4 - - + +
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Residues in contact with VAL 247 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243G PRO 3.0 19.9 + - - +
244G PHE 4.5 1.1 - - - +
246G GLN* 1.3 76.6 - - - +
248G ARG* 1.3 58.6 + - + +
250G LEU* 3.3 2.1 + - - -
251G ARG* 2.9 52.8 + - - +
287G ALA* 4.3 6.1 - - + +
288G ILE* 3.7 18.4 - - + -
291G GLU* 3.8 16.0 - - + +
76S ASN* 3.5 32.5 - - + +
79S LEU* 3.6 21.5 - - + -
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Residues in contact with ARG 248 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G HIS* 3.3 24.4 + - + +
195G VAL* 3.5 20.0 - - + +
196G VAL* 4.2 16.5 - - + +
199G THR* 4.5 12.2 + - - +
244G PHE 3.2 20.5 + - - +
245G LEU* 3.4 4.6 + - + +
246G GLN 3.4 0.4 - - - -
247G VAL* 1.3 77.4 - - + +
249G ILE* 1.3 57.1 + - - +
251G ARG* 3.0 42.3 - - - +
252G LEU* 2.9 28.4 + - - +
1S MET* 4.5 12.9 - - - +
71S ILE* 5.7 3.2 - - - +
79S LEU* 5.3 12.9 - - + +
83S ILE* 5.6 3.0 - - - +
121S GLY 5.5 0.2 + - - -
122S GLU* 4.1 33.6 - - - +
123S ILE* 4.9 9.5 - - - +
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Residues in contact with ILE 249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191G LEU* 5.3 1.1 - - + -
195G VAL* 4.0 19.7 - - + -
219G LEU* 3.7 28.5 - - + +
222G ILE* 3.9 25.8 - - + -
223G LEU* 3.8 29.8 - - + -
226G LEU* 4.1 8.7 - - + -
245G LEU* 2.9 46.5 + - + +
246G GLN 4.0 2.9 - - - +
248G ARG* 1.3 75.1 - - - +
250G LEU* 1.3 58.5 + - - +
252G LEU* 3.3 4.5 + - - +
253G LEU* 2.9 28.8 + - + +
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Residues in contact with LEU 250 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223G LEU* 3.7 25.8 - - + -
246G GLN* 2.9 23.8 + - + +
247G VAL* 5.0 0.2 - - - -
249G ILE* 1.3 75.8 - - - +
251G ARG* 1.3 57.6 + - - +
253G LEU* 3.3 9.8 + - + +
254G ARG* 2.9 21.8 + - - +
270G ILE* 5.6 0.4 - - + -
271G LEU* 3.7 27.8 - - + -
274G VAL* 4.8 7.9 - - + -
288G ILE* 4.0 22.4 - - + +
291G GLU* 3.8 13.0 - - + -
292G THR* 3.5 27.1 - - - +
295G THR* 3.2 22.4 + - + +
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Residues in contact with ARG 251 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G THR* 4.7 19.1 - - + +
247G VAL* 2.9 28.2 + - - +
248G ARG* 3.0 47.7 - - - +
249G ILE 3.3 0.4 - - - -
250G LEU* 1.3 74.4 - - - +
252G LEU* 1.3 60.8 + - - +
254G ARG* 3.1 26.8 + - - +
255G ILE* 3.0 33.1 + - + +
291G GLU* 3.7 14.4 + - - +
74S GLN* 5.9 1.1 - - - -
75S ASP* 3.0 38.2 + - - +
76S ASN* 3.0 35.2 + - - +
79S LEU* 5.2 3.8 - - - +
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Residues in contact with LEU 252 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G VAL* 4.2 15.9 - - + -
198G LEU* 3.9 45.1 - - + +
199G THR* 4.1 7.5 + - - +
202G CYS* 4.4 4.0 - - - -
215G LEU* 5.2 0.7 - - + -
219G LEU* 3.7 28.3 - - + -
248G ARG 2.9 16.5 + - - +
249G ILE* 3.3 6.3 + - - +
251G ARG* 1.3 77.8 - - - +
253G LEU* 1.3 55.6 + - - +
255G ILE* 3.4 23.8 - - + +
256G LEU* 3.0 53.5 + - + +
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Residues in contact with LEU 253 (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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216G VAL* 4.4 15.3 - - + -
219G LEU* 3.7 27.4 - - + -
220G VAL* 4.8 1.1 - - + -
249G ILE* 2.9 25.4 + - + +
250G LEU* 3.7 17.0 - - + +
251G ARG 3.2 0.2 - - - -
252G LEU* 1.3 73.5 - - - +
254G ARG* 1.3 60.4 + - - +
256G LEU* 2.8 23.0 - - + +
267G MET* 3.4 49.7 - - + +
270G ILE* 3.8 29.2 - - + -
271G LEU* 5.5 2.7 - - + -
295G THR* 4.1 7.8 - - + +
299G ILE* 3.9 2.9 - - - +
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Residues in contact with ARG 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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250G LEU 2.9 13.6 + - - +
251G ARG* 3.1 29.4 + - - +
253G LEU* 1.3 77.4 - - - +
255G ILE* 1.3 66.9 + - + +
256G LEU 3.0 14.5 - - - +
258G ARG* 4.0 16.8 + - - +
291G GLU* 3.6 17.1 + - - -
294G LEU* 3.3 57.2 - - - +
295G THR* 4.2 11.4 - - - +
298G ASP* 3.8 23.2 - - + +
299G ILE* 4.1 5.8 - - - +
334G LYS* 4.1 12.3 - - - +
74S GLN* 2.6 35.9 + - - +
75S ASP 5.5 0.4 + - - -
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Residues in contact with ILE 255 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G THR* 3.6 46.9 - - + +
202G CYS* 3.8 19.7 - - + +
203G GLU* 4.5 9.6 - - + +
209G LEU* 4.3 12.3 - - - +
213G ARG* 5.3 0.7 + - - -
251G ARG* 3.0 19.1 + - + +
252G LEU* 3.4 20.6 - - + +
254G ARG* 1.3 87.6 - - + +
256G LEU* 1.3 62.3 + - - +
257G GLY 4.4 0.2 + - - -
258G ARG* 4.6 25.3 - - - +
74S GLN* 6.1 0.9 - - - +
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Residues in contact with LEU 256 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202G CYS* 3.8 14.8 - - - -
209G LEU* 3.7 27.6 - - + -
212G PHE 3.5 27.6 - - - +
213G ARG* 4.6 11.0 - - + +
215G LEU* 5.5 0.2 - - + -
216G VAL* 4.1 20.2 - - + -
219G LEU* 5.2 5.4 - - + -
252G LEU* 3.0 40.6 + - + +
253G LEU* 2.8 26.2 - - + +
254G ARG 3.0 8.0 - - - +
255G ILE* 1.3 75.7 - - - +
257G GLY* 1.3 64.6 + - - +
258G ARG 3.2 3.4 - - - -
267G MET* 4.1 8.1 - - + +
299G ILE* 3.9 2.3 - - - +
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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
------------------------------------------------------------
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