Contacts of the helix formed by residues 183 - 194 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170K VAL 4.1 5.6 - - - -
171K TYR* 3.5 24.0 - - - +
175K GLU* 2.7 35.8 + - - -
181K MET 3.9 0.6 + - - -
182K ALA* 1.3 78.5 - - - +
184K VAL* 1.3 63.8 - - - +
185K ALA* 3.5 9.8 - - - +
186K PHE* 3.0 16.3 + - - +
187K HIS* 3.1 18.2 + - - -
211K PHE* 6.5 0.4 - - - -
302K TYR* 3.9 0.2 - - - -
401K ADP 5.2 2.0 - - - -
402K BMA 5.6 1.5 + - - -
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Residues in contact with VAL 184 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K ALA 3.7 0.2 + - - -
183K SER* 1.3 69.5 - - - +
185K ALA* 1.3 66.1 + - - +
187K HIS* 3.1 10.4 + - + +
188K LEU* 2.9 42.7 + - + +
199K LYS 4.8 1.1 - - - +
200K LEU* 3.9 23.1 - - + -
211K PHE* 5.5 6.2 - - + -
243K PHE* 3.6 33.4 - - + +
246K VAL* 4.9 8.1 - - + -
401K ADP 3.7 35.8 - - + +
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Residues in contact with ALA 185 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171K TYR* 4.6 10.5 - - + -
183K SER* 3.5 11.4 - - - +
184K VAL* 1.3 77.7 - - - +
186K PHE* 1.3 63.1 + - - +
188K LEU* 3.3 2.9 + - - +
189K ASN* 3.0 24.1 + - - +
246K VAL* 4.2 22.9 - - + +
250K THR* 4.6 2.5 - - - -
299K VAL* 4.7 5.8 - - + -
302K TYR* 4.0 19.3 - - + -
303K MET* 3.6 18.5 - - + +
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Residues in contact with PHE 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175K GLU* 3.6 7.9 - - + +
176K GLY* 3.5 38.6 - - - -
179K GLY* 5.5 2.2 - - - -
182K ALA* 3.7 20.4 - - + -
183K SER* 3.0 14.9 + - - +
185K ALA* 1.3 80.3 - - - +
187K HIS* 1.3 71.6 + + - +
189K ASN* 3.2 5.7 + - - +
190K THR* 3.0 54.5 + - + +
302K TYR* 3.3 28.4 - - - +
306K LEU* 4.1 21.3 - - + -
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Residues in contact with HIS 187 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179K GLY 2.9 26.7 + - - -
180K SER* 3.8 12.9 - - - -
182K ALA* 3.1 23.1 - - - +
183K SER 3.1 14.3 + - - -
184K VAL* 3.1 11.6 + - + +
186K PHE* 1.3 85.8 - + - +
188K LEU* 1.3 59.4 + - + +
190K THR* 3.3 9.5 + - - -
191K GLN* 2.9 48.8 + - - +
199K LYS 6.1 0.2 - - - +
401K ADP 3.2 20.1 + - - -
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Residues in contact with LEU 188 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184K VAL* 2.9 36.6 + - + +
185K ALA 3.7 3.1 - - - +
187K HIS* 1.3 76.2 - - + +
189K ASN* 1.3 64.6 + - - +
191K GLN* 3.4 19.8 + - - +
192K LEU* 3.0 31.2 + - + +
198K PRO* 3.8 13.0 - - + -
199K LYS 3.5 29.4 - - - +
200K LEU* 5.0 2.0 - - + -
246K VAL* 4.6 2.2 - - + -
247K ALA* 3.8 35.4 - - + +
250K THR* 4.1 19.7 - - + +
251K LEU* 5.5 1.3 - - + -
259K ILE* 4.8 4.0 - - + -
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Residues in contact with ASN 189 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185K ALA 3.0 13.4 + - - +
186K PHE 3.6 7.2 - - - +
188K LEU* 1.3 77.7 - - - +
190K THR* 1.3 68.6 + - - +
192K LEU* 3.3 2.4 + - - +
193K ASN* 3.0 43.8 + - - +
250K THR* 4.5 1.7 - - - +
254K HIS* 2.8 35.1 + - - -
303K MET* 3.6 10.2 - - - +
306K LEU* 3.6 39.7 + - + +
307K ASN* 3.4 12.8 + - - -
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Residues in contact with THR 190 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186K PHE* 3.0 48.9 + - + +
187K HIS* 3.4 12.8 + - - -
188K LEU 3.3 0.2 - - - -
189K ASN* 1.3 83.1 - - - +
191K GLN* 1.3 67.9 + - - +
193K ASN* 3.4 6.5 + - - +
194K ASN* 3.1 36.9 + - - -
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Residues in contact with GLN 191 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187K HIS* 2.9 30.1 + - - +
188K LEU* 3.4 15.4 - - - +
190K THR* 1.3 78.6 + - - +
192K LEU* 1.3 58.0 + - - +
194K ASN* 3.3 6.1 + - - +
196K GLU* 2.9 54.2 + - - +
197K SER 3.9 14.8 - - - +
198K PRO* 3.3 6.8 - - + +
199K LYS* 3.0 49.3 + - + +
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Residues in contact with LEU 192 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188K LEU 3.0 21.5 + - - +
189K ASN 3.7 4.3 - - - +
190K THR 3.2 0.2 - - - -
191K GLN* 1.3 72.9 - - - +
193K ASN* 1.3 62.8 + - - +
194K ASN 3.1 4.9 - - - -
195K GLY* 3.2 6.8 + - - -
196K GLU 4.2 5.6 - - - +
198K PRO* 3.9 31.4 - - + -
250K THR* 3.9 7.6 - - + -
251K LEU* 3.8 22.4 - - + -
254K HIS* 3.8 38.8 - - + +
256K LYS* 2.8 42.9 + - - +
257K GLY* 4.1 18.2 - - - -
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Residues in contact with ASN 193 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189K ASN* 3.0 39.7 + - - +
190K THR* 3.8 7.8 - - - +
192K LEU* 1.3 76.8 - - - +
194K ASN* 1.3 60.5 + - - +
195K GLY 3.3 1.7 + - - -
254K HIS* 3.4 18.1 + - - -
256K LYS* 5.2 0.2 - - - +
306K LEU 5.2 1.4 + - - -
307K ASN* 3.4 17.9 + - - +
157P GLU* 4.9 1.4 - - - +
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Residues in contact with ASN 194 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190K THR* 3.1 27.3 + - - +
191K GLN* 3.6 6.0 - - - +
192K LEU 3.1 1.0 - - - -
193K ASN* 1.3 79.5 - - - +
195K GLY* 1.3 55.8 + - - +
196K GLU* 3.0 32.1 + - - +
157P GLU* 3.1 14.0 - - - +
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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