Contacts of the helix formed by residues 243 - 255 (chain G) in PDB entry 2X86
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 PHE 243 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169G ASN* 5.2 2.9 - - - -
184G VAL* 3.6 36.9 - - + +
188G LEU* 5.7 0.2 - - - +
200G LEU* 3.9 19.9 - - + +
204G SER* 4.2 9.8 + - - +
207G PHE* 3.4 33.7 + - + -
208G LYS* 4.8 0.2 - - - -
209G ARG* 3.7 37.0 - - + -
211G PHE* 3.8 22.4 - + - -
242G SER* 1.3 72.8 - - - +
244G GLN* 1.3 64.2 + - - +
246G VAL* 3.1 7.7 + - + +
247G ALA* 3.0 21.7 + - - +
272G TYR* 3.7 10.5 - - - -
401G ADP 3.7 33.7 - + - -
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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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200G LEU* 4.2 7.7 - - + +
204G SER 4.5 7.5 + - - +
205G GLU* 5.6 5.6 - - - -
242G SER* 3.1 12.9 + - - +
243G PHE* 1.3 78.9 - - - +
245G ALA* 1.3 55.3 + - - +
247G ALA* 3.3 7.7 + - - +
248G ASP* 2.8 66.9 + - - +
259G ILE* 4.2 19.7 - - - +
261G TYR* 3.9 17.1 + - - +
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Residues in contact with ALA 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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241G GLU* 4.1 27.6 - - + +
242G SER* 2.9 22.7 + - - +
244G GLN* 1.3 73.8 - - - +
246G VAL* 1.3 65.1 + - - +
248G ASP* 3.2 13.4 + - - +
249G ALA* 3.0 23.6 + - - +
295G VAL* 4.0 6.9 - - + +
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Residues in contact with VAL 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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171G TYR* 6.4 0.2 - - + -
184G VAL* 4.9 7.0 - - + -
185G ALA* 4.2 34.8 - - + +
188G LEU* 4.6 5.4 - - + -
211G PHE* 3.7 47.1 - - + -
242G SER 4.2 2.7 - - - +
243G PHE* 3.1 8.4 + - - +
245G ALA* 1.3 76.1 - - - +
247G ALA* 1.3 64.8 + - - +
249G ALA* 3.2 4.9 + - - +
250G THR* 3.0 26.6 + - - +
295G VAL* 3.7 19.5 - - + -
299G VAL* 4.2 9.1 - - + +
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Residues in contact with ALA 247 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G LEU* 3.8 18.1 - - + +
200G LEU* 4.3 3.6 - - + -
243G PHE 3.0 12.3 + - - +
244G GLN* 3.4 14.8 - - - +
246G VAL* 1.3 76.6 - - - +
248G ASP* 1.3 52.6 + - - +
250G THR* 3.2 2.1 + - - -
251G LEU* 2.8 41.1 + - + +
259G ILE* 3.4 37.5 - - + -
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Residues in contact with ASP 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* 2.8 52.0 + - - +
245G ALA* 3.2 13.6 + - - +
247G ALA* 1.3 73.4 - - - +
249G ALA* 1.3 63.6 + - - +
251G LEU* 3.9 5.5 - - - +
252G ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 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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245G ALA 3.0 10.1 + - - +
246G VAL 3.2 8.0 + - - +
248G ASP* 1.3 78.5 - - - +
250G THR* 1.3 62.0 + - - +
252G ALA* 3.5 7.1 - - - +
253G TYR* 3.2 17.2 + - - +
295G VAL* 4.3 10.1 - - + +
296G ALA* 4.3 15.5 - - + +
299G VAL* 3.7 25.5 - - + +
300G THR* 3.8 15.8 - - + +
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Residues in contact with THR 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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185G ALA* 4.6 1.0 - - - -
188G LEU* 4.1 20.0 - - + +
189G ASN 4.5 1.3 - - - +
192G LEU* 3.9 22.2 - - + -
246G VAL* 3.0 18.2 + - - +
247G ALA* 3.5 10.8 - - - -
249G ALA* 1.3 73.7 - - - +
251G LEU* 1.3 66.0 + - + +
252G ALA 3.1 1.3 - - - -
253G TYR* 3.1 3.8 + - - +
254G HIS* 3.1 25.7 + - + +
299G VAL* 3.4 17.4 - - - +
303G MET* 3.6 30.0 - - + +
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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
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188G LEU* 5.5 1.6 - - + -
192G LEU* 3.8 22.4 - - + -
198G PRO* 3.9 18.6 - - + -
247G ALA* 2.8 29.1 + - + +
248G ASP* 4.2 4.5 - - - +
250G THR* 1.3 76.2 - - + +
252G ALA* 1.3 57.3 + - - +
254G HIS* 3.3 2.6 + - - +
255G LYS* 2.8 27.7 + - - -
256G LYS 3.5 18.1 + - - +
257G GLY 3.0 30.3 - - - +
258G GLN* 4.0 8.5 - - - +
259G ILE* 4.4 15.7 - - + +
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Residues in contact with ALA 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 ASP 3.0 19.6 + - - +
249G ALA* 3.5 8.7 - - - +
251G LEU* 1.3 79.5 - - - +
253G TYR* 1.3 62.3 + - - +
255G LYS* 3.2 25.9 - - - +
300G THR* 5.6 3.4 - - + -
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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
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249G ALA 3.2 10.0 + - - +
250G THR 3.1 9.0 + - - +
252G ALA* 1.3 80.7 - - - +
254G HIS* 1.3 75.9 + + - +
255G LYS* 3.2 11.4 + - - +
300G THR* 4.3 18.3 - - + +
303G MET* 3.5 40.2 + - + -
304G ALA* 3.4 31.5 + - + +
307G ASN* 4.0 23.4 - - + +
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Residues in contact with HIS 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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189G ASN* 2.8 33.5 + - - -
192G LEU* 3.8 37.3 - - + +
193G ASN* 3.4 24.3 + - - -
250G THR* 3.1 30.0 + - + +
251G LEU 4.0 3.1 - - - +
253G TYR* 1.3 89.7 - + - +
255G LYS* 1.3 68.5 + - - +
256G LYS* 3.0 28.0 + - + +
303G MET* 3.9 6.1 - - - -
307G ASN* 4.5 7.0 - - - -
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Residues in contact with LYS 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 2.8 9.4 + - - -
252G ALA* 3.2 25.1 + - - +
253G TYR 3.2 9.3 - - - +
254G HIS* 1.3 79.7 - - - +
256G LYS* 1.3 59.1 + - - +
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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