Contacts of the helix formed by residues 183 - 194 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170T VAL 4.1 5.6 + - - -
171T TYR* 3.5 23.2 - - - +
175T GLU* 2.7 35.5 + - - -
181T MET 3.9 0.4 + - - -
182T ALA* 1.3 77.7 - - - +
184T VAL* 1.3 64.4 + - - +
185T ALA* 3.5 9.5 - - - +
186T PHE* 3.0 15.8 + - - +
187T HIS* 3.1 17.8 + - - -
211T PHE* 6.5 0.4 - - - -
401T ADP 4.6 1.8 - - - -
402T BMA 5.8 0.4 + - - -
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Residues in contact with VAL 184 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182T ALA 3.7 0.4 + - - -
183T SER* 1.3 70.6 - - - +
185T ALA* 1.3 65.8 + - - +
187T HIS* 3.1 9.1 + - + +
188T LEU* 2.9 44.5 + - + +
199T LYS 4.8 0.4 - - - +
200T LEU* 3.9 23.1 - - + -
211T PHE* 5.5 5.8 - - + -
243T PHE* 3.6 33.7 - - + -
246T VAL* 4.9 8.1 - - + -
401T ADP 3.6 37.1 + - + +
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Residues in contact with ALA 185 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171T TYR* 4.6 10.3 - - + -
183T SER* 3.5 11.4 - - - +
184T VAL* 1.3 78.3 - - - +
186T PHE* 1.3 64.0 + - - +
188T LEU* 3.3 3.1 + - - +
189T ASN* 3.0 23.6 + - - +
246T VAL* 4.2 23.3 - - + +
250T THR* 4.6 2.9 - - - -
299T VAL* 4.7 5.6 - - + -
302T TYR* 4.0 19.5 - - + -
303T MET* 3.6 16.9 - - + +
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Residues in contact with PHE 186 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175T GLU* 3.6 7.6 - - + +
176T GLY* 3.5 38.6 - - - -
179T GLY* 5.5 1.8 - - - -
182T ALA* 3.8 20.6 - - + -
183T SER* 3.0 16.7 + - - +
185T ALA* 1.3 80.0 - - - +
187T HIS* 1.3 72.0 + + - +
189T ASN* 3.2 5.7 + - - +
190T THR* 3.1 54.3 + - + +
302T TYR* 3.3 28.8 - - - +
306T LEU* 4.1 21.5 - - + -
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Residues in contact with HIS 187 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179T GLY 2.9 26.2 + - - -
180T SER* 3.8 14.0 - - - -
182T ALA* 3.1 24.0 + - - +
183T SER 3.1 12.7 + - - -
184T VAL* 3.1 11.8 + - + +
186T PHE* 1.3 88.2 - + - +
188T LEU* 1.3 59.6 + - + +
190T THR* 3.3 9.3 + - - -
191T GLN* 2.9 48.0 + - - +
199T LYS 6.1 0.2 - - - +
401T ADP 3.4 15.7 + - - -
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Residues in contact with LEU 188 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184T VAL* 2.9 36.1 + - + +
185T ALA 3.7 3.6 - - - +
187T HIS* 1.3 77.5 - - + +
189T ASN* 1.3 63.1 + - - +
191T GLN* 3.4 19.9 + - - +
192T LEU* 2.9 31.6 + - + +
198T PRO* 3.8 13.2 - - + -
199T LYS 3.5 29.6 - - - +
200T LEU* 5.0 1.8 - - + -
243T PHE 5.7 0.2 - - - +
246T VAL* 4.6 2.5 - - + -
247T ALA* 3.8 36.3 - - + +
250T THR* 4.1 19.3 - - + +
251T LEU* 5.5 0.7 - - + -
259T ILE* 4.8 4.3 - - + -
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Residues in contact with ASN 189 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185T ALA 3.0 13.4 + - - +
186T PHE 3.6 7.4 - - - +
188T LEU* 1.3 77.4 - - - +
190T THR* 1.3 68.3 + - - +
192T LEU* 3.3 2.6 + - - +
193T ASN* 3.0 43.2 + - - +
250T THR* 4.5 1.5 - - - +
254T HIS* 2.8 34.8 + - - -
303T MET* 3.6 10.1 - - - +
306T LEU* 3.6 39.9 + - + +
307T ASN* 3.4 12.6 + - - -
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Residues in contact with THR 190 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186T PHE* 3.1 49.1 + - + +
187T HIS* 3.4 13.0 + - - -
188T LEU 3.3 0.2 - - - -
189T ASN* 1.3 84.2 - - - +
191T GLN* 1.3 67.9 + - - +
193T ASN* 3.4 7.0 + - - +
194T ASN* 3.1 37.4 + - - -
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Residues in contact with GLN 191 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187T HIS* 2.9 31.6 + - - +
188T LEU* 3.4 15.4 - - - +
190T THR* 1.3 79.2 + - - +
192T LEU* 1.3 59.8 + - - +
194T ASN* 3.3 5.3 + - - +
196T GLU* 2.9 54.3 + - - +
197T SER 3.9 14.4 - - - +
198T PRO* 3.3 6.5 - - + +
199T LYS* 3.0 49.3 + - + +
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Residues in contact with LEU 192 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188T LEU 2.9 20.8 + - - +
189T ASN 3.7 3.6 - - - +
190T THR 3.2 0.2 - - - -
191T GLN* 1.3 74.0 - - - +
193T ASN* 1.3 62.1 + - - +
194T ASN 3.1 4.7 - - - -
195T GLY* 3.2 6.6 + - - -
196T GLU 4.2 6.5 - - - +
198T PRO* 3.9 32.8 - - + -
250T THR* 3.9 9.2 - - + -
251T LEU* 3.8 21.5 - - + -
254T HIS* 3.8 38.6 - - + +
256T LYS* 2.8 42.4 + - - +
257T GLY* 4.1 18.2 - - - -
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Residues in contact with ASN 193 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189T ASN* 3.0 40.3 + - - +
190T THR* 3.8 7.6 - - - +
191T GLN 3.4 0.2 - - - -
192T LEU* 1.3 76.4 - - - +
194T ASN* 1.3 61.1 + - - +
195T GLY 3.3 2.3 + - - -
254T HIS* 3.4 18.5 + - - -
306T LEU 5.2 1.2 + - - -
307T ASN* 3.4 18.2 + - - +
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Residues in contact with ASN 194 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190T THR* 3.1 27.3 + - - +
191T GLN* 3.6 5.8 - - - +
192T LEU 3.1 0.8 - - - -
193T ASN* 1.3 81.6 - - - +
195T GLY* 1.3 56.2 + - - +
196T GLU* 3.0 31.9 + - - +
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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