Contacts of the helix formed by residues 183 - 194 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170R VAL 4.1 5.6 + - - -
171R TYR* 3.5 23.6 - - - +
175R GLU* 2.7 35.5 + - - -
181R MET 3.9 0.6 + - - -
182R ALA* 1.3 78.6 - - - +
184R VAL* 1.3 63.1 + - - +
185R ALA* 3.5 10.1 - - - +
186R PHE* 3.0 16.3 + - - +
187R HIS* 3.1 18.2 + - - -
211R PHE* 6.5 0.9 - - - -
401R ADP 5.3 1.3 - - - -
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Residues in contact with VAL 184 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182R ALA 3.7 0.2 + - - -
183R SER* 1.3 70.6 - - - +
185R ALA* 1.3 67.2 + - - +
187R HIS* 3.1 10.1 + - + +
188R LEU* 2.9 44.5 + - + +
199R LYS 4.8 1.3 - - - +
200R LEU* 3.9 23.1 - - + -
211R PHE* 5.6 6.0 - - + -
243R PHE* 3.6 33.0 - - + -
246R VAL* 4.9 8.3 - - + -
401R ADP 3.8 34.9 + - + +
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Residues in contact with ALA 185 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171R TYR* 4.6 10.5 - - + -
183R SER* 3.5 10.7 - - - +
184R VAL* 1.3 79.1 - - - +
186R PHE* 1.3 63.9 + - - +
188R LEU* 3.3 2.7 + - - +
189R ASN* 3.0 24.1 + - - +
246R VAL* 4.2 22.0 - - + +
250R THR* 4.6 3.4 - - - +
299R VAL* 4.7 5.2 - - + -
302R TYR* 4.0 20.2 - - + -
303R MET* 3.6 17.7 - - + +
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Residues in contact with PHE 186 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175R GLU* 3.6 7.6 - - + +
176R GLY* 3.5 38.6 - - - -
179R GLY* 5.5 2.0 - - - -
182R ALA* 3.8 20.0 - - + -
183R SER* 3.0 16.4 + - - +
185R ALA* 1.3 79.8 - - - +
187R HIS* 1.3 71.8 + + - +
189R ASN* 3.2 6.0 + - - +
190R THR* 3.1 54.9 + - + +
302R TYR* 3.3 28.4 - - - +
306R LEU* 4.1 20.4 - - + -
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Residues in contact with HIS 187 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179R GLY 2.9 26.8 + - - -
180R SER* 3.8 12.7 - - - -
182R ALA* 3.1 24.6 + - - +
183R SER 3.1 12.9 + - - -
184R VAL* 3.1 12.0 + - + +
186R PHE* 1.3 88.2 - + - +
188R LEU* 1.3 59.4 + - + +
190R THR* 3.3 9.2 + - - -
191R GLN* 2.9 47.6 + - - +
199R LYS 6.1 0.2 - - - +
401R ADP 3.2 17.3 + - - -
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Residues in contact with LEU 188 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184R VAL* 2.9 38.0 + - + +
185R ALA 3.7 3.6 - - - +
187R HIS* 1.3 76.9 - - + +
189R ASN* 1.3 64.0 + - - +
191R GLN* 3.4 18.8 + - - +
192R LEU* 3.0 32.1 + - + +
198R PRO* 3.8 13.0 - - + -
199R LYS 3.5 30.3 - - - +
200R LEU* 5.0 1.8 - - + -
246R VAL* 4.7 2.5 - - + -
247R ALA* 3.8 35.9 - - + +
250R THR* 4.1 18.6 - - + +
251R LEU* 5.4 1.1 - - + -
259R ILE* 4.7 4.5 - - + -
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Residues in contact with ASN 189 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185R ALA 3.0 14.0 + - - +
186R PHE 3.6 7.2 - - - +
188R LEU* 1.3 77.4 - - - +
190R THR* 1.3 66.9 + - - +
192R LEU* 3.3 2.8 + - - +
193R ASN* 3.0 42.8 + - - +
250R THR* 4.5 1.3 - - - +
254R HIS* 2.8 34.5 + - - -
303R MET* 3.6 9.7 - - - +
306R LEU* 3.6 41.0 + - + +
307R ASN* 3.4 12.8 + - - -
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Residues in contact with THR 190 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186R PHE* 3.1 49.2 + - + +
187R HIS* 3.4 12.8 + - - -
189R ASN* 1.3 85.2 - - - +
191R GLN* 1.3 66.2 + - - +
193R ASN* 3.4 7.1 + - - +
194R ASN* 3.1 36.8 + - - -
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Residues in contact with GLN 191 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187R HIS* 2.9 30.4 + - - +
188R LEU* 3.4 15.9 - - - +
189R ASN 3.3 0.2 - - - -
190R THR* 1.3 79.0 + - - +
192R LEU* 1.3 59.0 + - - +
194R ASN* 3.3 6.1 + - - +
196R GLU* 2.9 54.4 + - + +
197R SER 3.9 14.4 - - - +
198R PRO* 3.3 7.0 - - + +
199R LYS* 3.0 48.2 + - + +
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Residues in contact with LEU 192 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188R LEU* 3.0 21.7 + - + +
189R ASN 3.7 3.6 - - - +
191R GLN* 1.3 74.7 - - - +
193R ASN* 1.3 61.7 + - - +
194R ASN 3.1 4.7 - - - -
195R GLY* 3.2 6.4 + - - -
196R GLU 4.2 5.4 - - - +
198R PRO* 3.9 31.2 - - + -
250R THR* 3.9 7.9 - - + -
251R LEU* 3.8 22.2 - - + -
254R HIS* 3.8 38.1 - - + +
256R LYS* 2.8 43.7 + - - +
257R GLY* 4.1 18.4 - - - -
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Residues in contact with ASN 193 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189R ASN* 3.0 41.1 + - - +
190R THR* 3.9 6.8 - - - +
192R LEU* 1.3 75.2 - - - +
194R ASN* 1.3 60.8 + - - +
195R GLY 3.3 2.1 + - - -
254R HIS* 3.4 18.2 + - - -
306R LEU 5.2 1.6 + - - -
307R ASN* 3.4 17.6 + - - +
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Residues in contact with ASN 194 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190R THR* 3.1 27.5 + - - +
191R GLN* 3.6 6.4 - - - +
192R LEU 3.1 1.2 - - - -
193R ASN* 1.3 80.9 - - - +
195R GLY* 1.3 55.5 + - - +
196R GLU* 3.0 32.1 + - - +
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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