Contacts of the helix formed by residues 242 - 256 (chain G) in PDB entry 2NN6
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 242 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A GLU* 4.5 3.1 + - - -
240G ALA 4.1 0.7 - - - -
241G LYS* 1.3 80.4 - - - +
243G ILE* 1.3 72.7 + - + +
244G GLN* 2.9 28.9 - - + +
245G GLN* 2.2 59.5 + - - +
246G THR* 2.5 19.8 + - - -
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Residues in contact with ILE 243 (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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13A PHE* 5.1 7.9 - - + -
16A ARG 5.4 0.2 - - - -
17A ALA* 4.0 18.4 - - + -
20A GLU* 3.2 44.2 - - + +
22A LYS* 3.1 37.0 - - + -
242G THR* 1.3 81.4 + - + +
244G GLN* 1.3 65.4 + - + +
246G THR* 2.8 9.9 - - - -
247G LEU* 2.5 60.7 + - + +
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Residues in contact with GLN 244 (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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22A LYS* 4.4 23.1 - - - +
242G THR* 2.9 14.7 + - + +
243G ILE* 1.3 78.6 - - + +
245G GLN* 1.3 56.6 + - + +
246G THR 2.5 5.5 + - - -
247G LEU* 2.4 53.1 + - - +
248G ILE* 2.9 33.2 + - + +
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Residues in contact with GLN 245 (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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223G LEU* 5.4 5.0 - - + +
240G ALA* 4.2 10.4 - - + +
241G LYS* 3.3 21.6 - - + +
242G THR* 2.2 70.8 + - - +
244G GLN* 1.3 74.3 - - + +
246G THR* 1.3 57.6 + - - +
248G ILE* 3.7 14.8 - - + +
249G LEU* 3.0 29.8 + - - +
271G LEU* 4.3 10.9 - - + +
274G SER* 5.6 15.3 - - - +
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Residues in contact with THR 246 (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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13A PHE* 5.3 4.9 - - + -
196G GLY* 5.8 1.1 - - - -
197G LEU* 4.9 4.5 - - + +
238G VAL* 3.4 31.5 - - + +
239G LYS* 4.1 3.6 - - - +
240G ALA* 2.9 38.0 + - - +
242G THR 2.5 17.5 + - - -
243G ILE* 2.8 15.5 - - - +
244G GLN 2.5 3.8 + - - -
245G GLN* 1.3 73.3 - - - +
247G LEU* 1.3 68.8 + - + +
249G LEU* 3.3 6.3 + - - +
250G ALA* 3.1 21.7 + - - +
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Residues in contact with LEU 247 (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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13A PHE* 3.9 27.4 - - + -
17A ALA* 5.7 1.8 - - + -
22A LYS* 5.7 3.6 - - + -
23A ARG 5.2 2.9 - - - +
24A LEU* 4.8 24.2 - - + +
197G LEU* 5.4 6.3 - - + -
243G ILE* 2.5 48.2 + - + +
244G GLN* 2.4 32.3 + - - +
246G THR* 1.3 73.4 - - + +
248G ILE* 1.3 71.6 + - - +
250G ALA* 3.2 6.3 + - + +
251G ASN* 2.9 26.2 + - - +
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Residues in contact with ILE 248 (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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244G GLN* 2.9 32.2 + - + +
245G GLN* 3.7 13.0 - - + +
247G LEU* 1.3 75.0 - - - +
249G LEU* 1.3 66.3 + - - +
251G ASN* 2.7 11.2 + - + +
252G ILE* 2.6 32.4 + - + +
271G LEU* 3.1 47.1 - - + -
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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
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220G VAL* 5.1 14.4 - - + -
223G LEU* 4.1 20.0 - - + -
226G LEU* 4.3 28.9 - - + -
228G ILE* 4.9 7.2 - - + -
238G VAL* 5.5 3.6 - - + -
240G ALA* 5.5 3.1 - - + -
245G GLN 3.0 16.1 + - - +
246G THR* 3.4 6.3 - - - +
248G ILE* 1.3 80.0 - - - +
250G ALA* 1.3 58.1 + - - +
252G ILE* 2.7 34.9 - - + +
253G LEU* 2.8 28.4 + - + +
268G PHE* 4.6 8.7 - - + -
271G LEU* 3.5 24.7 - - + -
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Residues in contact with ALA 250 (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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197G LEU* 3.9 21.3 - - + -
199G PHE* 3.7 30.8 - - + -
238G VAL* 5.0 2.4 - - + +
246G THR 3.1 10.3 + - - +
247G LEU* 3.6 8.3 - - + +
249G LEU* 1.3 78.8 - - - +
251G ASN* 1.3 53.3 + - - +
253G LEU* 2.7 10.2 + - - +
254G GLU* 2.7 40.8 + - - +
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Residues in contact with ASN 251 (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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24A LEU 4.8 8.7 - - - +
25A ASP 5.9 0.5 - - - -
26A GLY* 5.6 3.8 + - - -
247G LEU* 2.9 16.0 + - - +
248G ILE* 2.7 17.8 + - + +
250G ALA* 1.3 72.5 - - - +
252G ILE* 1.3 60.7 + - - +
254G GLU* 3.1 43.8 + - - +
255G ALA* 3.3 9.9 + - - +
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Residues in contact with ILE 252 (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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248G ILE* 2.6 22.3 + - + +
249G LEU* 2.7 28.9 - - + +
251G ASN* 1.3 73.5 - - - +
253G LEU* 1.3 56.1 + - + +
255G ALA* 3.2 6.1 + - - +
256G CYS* 2.8 33.4 + - - -
259G MET* 4.2 6.1 - - + +
267G ILE* 3.5 36.3 - - + +
268G PHE* 3.3 30.7 - - + -
271G LEU* 3.3 27.4 - - + -
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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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199G PHE* 3.9 22.0 - - + -
201G VAL* 5.4 5.9 - - + +
205G LEU* 4.5 6.4 - - - +
209G LEU* 4.9 7.2 - - + +
216G ILE* 4.8 9.0 - - + -
220G VAL* 5.2 5.2 - - + -
228G ILE* 5.8 1.6 - - + -
230G PHE* 5.7 8.7 - - + -
236G ILE* 5.0 8.3 - - + -
238G VAL* 5.1 2.5 - - + -
249G LEU* 2.8 38.8 + - + +
250G ALA* 2.7 14.9 + - - +
252G ILE* 1.3 78.4 - - + +
254G GLU* 1.3 51.3 + - - -
255G ALA 2.7 16.4 + - - -
256G CYS* 2.8 52.3 + - - +
268G PHE* 4.2 9.2 - - + -
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Residues in contact with GLU 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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199G PHE* 4.6 14.7 - - + -
200G LYS 6.0 0.9 - - - +
201G VAL* 5.5 8.1 - - - -
205G LEU* 4.4 11.3 - - - +
250G ALA* 2.7 20.8 + - - +
251G ASN* 3.1 46.7 + - - +
253G LEU* 1.3 71.8 - - - +
255G ALA* 1.3 55.9 + - + +
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Residues in contact with ALA 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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205G LEU* 5.2 0.7 - - - -
251G ASN 3.3 7.1 + - - +
252G ILE* 3.2 8.3 + - - +
253G LEU 2.7 4.8 + - - -
254G GLU* 1.3 77.7 - - - +
256G CYS* 1.3 53.5 + - - +
257G GLU* 2.6 23.9 + - - +
258G HIS* 3.7 9.5 + - - +
259G MET* 3.8 11.6 - - + +
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Residues in contact with CYS 256 (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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205G LEU* 5.2 0.9 - - + -
209G LEU* 3.8 21.3 - - + -
216G ILE* 5.0 1.6 - - - -
252G ILE 2.8 13.2 + - - -
253G LEU* 2.8 60.6 - - - +
255G ALA* 1.3 73.8 - - - +
257G GLU* 1.3 68.0 + - - +
259G MET* 3.3 22.6 - - - +
264G ARG* 3.4 19.4 + - - +
268G PHE* 4.2 14.1 - - - -
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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