Contacts of the helix formed by residues 183 - 194 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170O VAL 4.1 6.0 + - - -
171O TYR* 3.5 24.2 - - - +
175O GLU* 2.7 34.9 + - - -
181O MET 3.9 0.4 + - - -
182O ALA* 1.3 77.2 - - - +
184O VAL* 1.3 64.6 + - - +
185O ALA* 3.5 9.5 - - - +
186O PHE* 3.0 15.9 + - - +
187O HIS* 3.1 18.0 + - - -
211O PHE* 6.5 0.7 - - - -
302O TYR* 3.9 0.2 - - - -
401O ADP 5.2 2.2 - - - -
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Residues in contact with VAL 184 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183O SER* 1.3 70.4 - - - +
185O ALA* 1.3 66.5 + - - +
187O HIS* 3.1 9.5 + - + +
188O LEU* 2.9 44.2 + - + +
199O LYS 4.8 0.7 - - - +
200O LEU* 3.8 23.3 - - + -
211O PHE* 5.6 5.6 - - + -
243O PHE* 3.6 29.2 - - + -
246O VAL* 4.9 7.4 - - + -
401O ADP 3.5 40.3 - - + +
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Residues in contact with ALA 185 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171O TYR* 4.6 10.8 - - + -
183O SER* 3.5 11.4 + - - +
184O VAL* 1.3 78.6 - - - +
186O PHE* 1.3 63.9 + - - +
188O LEU* 3.3 3.0 + - - +
189O ASN* 3.0 23.7 + - - +
246O VAL* 4.2 22.6 - - + +
250O THR* 4.6 2.7 - - - -
299O VAL* 4.7 5.4 - - + -
302O TYR* 4.0 19.1 - - + -
303O MET* 3.6 18.1 - - + +
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Residues in contact with PHE 186 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175O GLU* 3.6 7.4 - - + +
176O GLY* 3.5 39.0 - - - -
179O GLY* 5.6 2.0 - - - -
182O ALA* 3.8 21.1 - - + -
183O SER* 3.0 16.4 + - - +
185O ALA* 1.3 80.1 - - - +
187O HIS* 1.3 71.6 + + - +
189O ASN* 3.2 6.5 + - - +
190O THR* 3.0 54.5 + - + +
302O TYR* 3.3 29.3 - - - +
306O LEU* 4.1 21.1 - - + -
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Residues in contact with HIS 187 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179O GLY 2.9 27.3 + - - -
180O SER* 3.8 10.9 - - - -
182O ALA* 3.1 23.6 + - - +
183O SER 3.1 12.7 + - - -
184O VAL* 3.1 12.6 + - + +
186O PHE* 1.3 88.7 - + - +
188O LEU* 1.3 60.1 + - + +
190O THR* 3.3 8.9 + - - -
191O GLN* 2.9 46.9 + - - +
199O LYS 6.1 0.4 - - - +
401O ADP 3.2 18.5 + - - -
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Residues in contact with LEU 188 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184O VAL* 2.9 35.9 + - + +
185O ALA* 3.7 3.8 - - - +
187O HIS* 1.3 77.1 - - + +
189O ASN* 1.3 64.0 + - - +
191O GLN* 3.4 15.7 + - - +
192O LEU* 2.9 31.5 + - + +
198O PRO* 3.8 13.9 - - + -
199O LYS 3.5 32.8 - - - +
200O LEU* 5.0 1.8 - - + -
246O VAL* 4.6 2.5 - - + -
247O ALA* 3.8 35.9 - - + +
250O THR* 4.1 19.1 - - + +
251O LEU* 5.4 1.1 - - + -
259O ILE* 4.7 4.3 - - + -
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Residues in contact with ASN 189 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185O ALA 3.0 13.2 + - - +
186O PHE 3.2 7.8 + - - +
188O LEU* 1.3 77.9 - - - +
190O THR* 1.3 68.7 + - - +
192O LEU* 3.3 2.6 + - - +
193O ASN* 3.0 43.2 + - - +
250O THR* 4.5 1.3 - - - +
254O HIS* 2.8 34.7 + - - -
303O MET* 3.6 9.7 - - - +
306O LEU* 3.6 39.1 + - + +
307O ASN* 3.4 13.3 + - - -
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Residues in contact with THR 190 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186O PHE* 3.0 48.2 + - + +
187O HIS* 3.4 12.8 + - - -
189O ASN* 1.3 84.4 - - - +
191O GLN* 1.3 68.0 + - - +
193O ASN* 3.4 7.0 + - - +
194O ASN* 3.1 38.2 + - - -
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Residues in contact with GLN 191 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187O HIS* 2.9 30.8 + - - +
188O LEU* 3.5 15.4 - - - +
190O THR* 1.3 79.1 + - - +
192O LEU* 1.3 58.4 + - - +
194O ASN* 3.3 6.1 + - - +
196O GLU* 2.9 54.1 + - - +
197O SER 3.9 14.6 - - - +
198O PRO* 3.3 6.9 - - + +
199O LYS* 3.0 50.2 + - + +
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Residues in contact with LEU 192 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188O LEU 2.9 21.2 + - - +
189O ASN 3.7 3.6 - - - +
191O GLN* 1.3 72.2 - - - +
193O ASN* 1.3 63.0 + - - +
194O ASN 3.1 5.2 - - - -
195O GLY* 3.2 6.4 + - - -
196O GLU 4.2 6.3 - - - +
198O PRO* 3.9 30.5 - - + -
250O THR* 3.9 9.2 - - + -
251O LEU* 3.8 21.8 - - + -
254O HIS* 3.8 37.9 - - + +
256O LYS* 2.8 42.7 + - - +
257O GLY* 4.1 18.2 - - - -
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Residues in contact with ASN 193 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189O ASN* 3.0 39.4 + - - +
190O THR* 3.8 8.1 - - - +
191O GLN 3.4 0.2 - - - -
192O LEU* 1.3 75.1 - - - +
194O ASN* 1.3 60.5 + - - +
195O GLY 3.3 2.1 + - - -
254O HIS* 3.4 17.9 + - - -
256O LYS* 5.2 0.2 - - - +
306O LEU 5.2 1.4 + - - -
307O ASN* 3.4 18.0 + - - +
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Residues in contact with ASN 194 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190O THR* 3.1 26.7 + - - +
191O GLN* 3.6 6.6 - - - +
192O LEU 3.1 1.4 - - - -
193O ASN* 1.3 80.6 - - - +
195O GLY* 1.3 55.3 + - - +
196O GLU* 3.0 32.7 + - - +
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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