Contacts of the helix formed by residues 183 - 194 (chain F) 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 SER 183 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170F VAL 4.1 5.4 + - - -
171F TYR* 3.5 24.9 - - - +
175F GLU* 2.7 34.9 + - - -
181F MET 3.9 0.6 + - - -
182F ALA* 1.3 77.8 - - - +
184F VAL* 1.3 64.8 + - - +
185F ALA* 3.5 9.3 - - - +
186F PHE* 3.0 15.9 + - - +
187F HIS* 3.1 18.0 + - - -
211F PHE* 6.5 0.4 - - - -
302F TYR* 3.9 0.2 - - - -
401F ADP 5.4 1.1 - - - -
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Residues in contact with VAL 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F ALA 3.7 0.2 + - - -
183F SER* 1.3 69.9 - - - +
185F ALA* 1.3 67.5 + - - +
187F HIS* 3.1 9.5 + - + +
188F LEU* 2.9 43.8 + - + +
199F LYS 4.8 0.7 - - - +
200F LEU* 3.8 23.1 - - + -
211F PHE* 5.6 5.8 - - + -
243F PHE* 3.6 32.5 - - + -
246F VAL* 4.9 8.5 - - + -
401F ADP 3.6 36.7 + - + +
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Residues in contact with ALA 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F TYR* 4.6 10.5 - - + -
183F SER* 3.2 11.3 - - - +
184F VAL* 1.3 78.9 - - - +
186F PHE* 1.3 64.5 + - - +
188F LEU* 3.3 3.0 + - - +
189F ASN* 3.0 24.1 + - - +
246F VAL* 4.2 22.5 - - + +
250F THR* 4.6 2.7 - - - -
299F VAL* 4.7 5.2 - - + -
302F TYR* 4.0 19.3 - - + -
303F MET* 3.6 18.1 - - + +
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Residues in contact with PHE 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F GLU* 3.6 7.2 - - + +
176F GLY* 3.5 40.6 - - - -
179F GLY* 5.6 2.2 - - - -
182F ALA* 3.8 20.4 - - + -
183F SER* 3.0 15.1 + - - +
185F ALA* 1.3 80.7 - - - +
187F HIS* 1.3 71.5 - + - +
189F ASN* 3.2 5.9 + - - +
190F THR* 3.0 54.7 + - + +
302F TYR* 3.3 29.3 - - - +
306F LEU* 4.1 20.4 - - + -
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Residues in contact with HIS 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179F GLY 2.9 26.9 + - - -
180F SER* 3.8 13.3 - - - -
182F ALA* 3.1 23.5 - - - +
183F SER 3.1 13.3 + - - -
184F VAL* 3.1 11.9 + - + +
186F PHE* 1.3 88.2 - + - +
188F LEU* 1.3 59.2 + - + +
190F THR* 3.3 9.2 + - - -
191F GLN* 2.9 48.6 + - - +
199F LYS 6.1 0.7 - - - +
401F ADP 3.1 18.9 + - - -
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Residues in contact with LEU 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F VAL* 2.9 35.9 + - + +
185F ALA 3.7 3.4 - - - +
187F HIS* 1.3 77.1 - - + +
189F ASN* 1.3 65.4 + - - +
191F GLN* 3.4 19.5 + - - +
192F LEU* 3.0 30.6 + - - +
198F PRO* 3.8 13.5 - - + -
199F LYS 3.5 28.5 - - - +
200F LEU* 5.0 2.0 - - + -
246F VAL* 4.6 2.5 - - + -
247F ALA* 3.8 36.3 - - + +
250F THR* 4.1 20.0 - - + +
251F LEU* 5.4 1.3 - - + -
259F ILE* 4.7 4.0 - - + -
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Residues in contact with ASN 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F ALA 3.0 13.4 + - - +
186F PHE 3.2 6.7 + - - +
188F LEU* 1.3 77.3 - - - +
190F THR* 1.3 68.5 + - - +
192F LEU* 3.3 3.5 + - - +
193F ASN* 3.0 42.4 + - - +
250F THR* 4.5 1.3 - - - +
254F HIS* 2.8 35.8 + - - -
303F MET* 3.6 9.5 - - - +
306F LEU* 3.6 39.2 + - + +
307F ASN* 3.4 12.8 + - - -
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Residues in contact with THR 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F PHE* 3.0 47.7 + - + +
187F HIS* 3.4 12.8 + - - -
189F ASN* 1.3 83.7 - - - +
191F GLN* 1.3 67.5 + - - +
193F ASN* 3.4 7.0 + - - +
194F ASN* 3.1 37.7 + - - -
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Residues in contact with GLN 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F HIS* 2.9 30.5 + - - +
188F LEU* 3.5 15.4 - - - +
190F THR* 1.3 79.2 + - - +
192F LEU* 1.3 58.9 + - - +
194F ASN* 3.3 5.8 + - - +
196F GLU* 2.9 53.6 + - - +
197F SER 3.9 14.4 - - - +
198F PRO* 3.3 6.7 - - + +
199F LYS* 3.0 49.3 + - + +
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Residues in contact with LEU 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F LEU 3.0 21.7 + - - +
189F ASN 3.7 3.8 - - - +
191F GLN* 1.3 72.9 - - - +
193F ASN* 1.3 62.2 + - - +
194F ASN 3.1 4.5 - - - -
195F GLY* 3.2 6.8 + - - -
196F GLU 4.2 5.8 - - - +
198F PRO* 3.9 31.0 - - + -
250F THR* 3.9 7.9 - - + -
251F LEU* 3.8 22.0 - - + -
254F HIS* 3.8 38.4 - - + +
256F LYS* 2.8 43.9 + - - +
257F GLY* 4.1 18.2 - - - -
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Residues in contact with ASN 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F ASN* 3.0 39.6 + - - +
190F THR* 3.9 7.4 - - - +
191F GLN 3.4 0.2 - - - -
192F LEU* 1.3 75.6 - - - +
194F ASN* 1.3 60.5 + - - +
195F GLY 3.3 1.9 + - - -
254F HIS* 3.4 17.5 + - - -
256F LYS* 5.2 0.2 - - - +
306F LEU 5.2 1.2 + - - -
307F ASN* 3.4 17.8 + - - +
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Residues in contact with ASN 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F THR* 3.1 28.5 + - - +
191F GLN* 3.6 6.1 - - - +
192F LEU 3.1 1.0 - - - -
193F ASN* 1.3 81.0 - - - +
195F GLY* 1.3 54.9 + - - +
196F GLU* 3.0 32.5 + - - +
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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
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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