Contacts of the helix formed by residues 211 - 218 (chain C) in PDB entry 5XVO
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 PHE 211 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C LEU* 3.8 37.2 - - + -
73C PRO* 4.5 3.4 - - + -
184C LEU* 4.1 22.7 - - + -
188C ALA* 3.8 25.4 - - + -
198C THR* 3.3 19.1 - - - -
209C ASN* 3.0 19.4 + - - +
210C ASP* 1.3 89.3 - - + +
212C ASN* 1.3 65.7 + - - +
213C LEU 3.2 2.7 - - - -
214C ALA* 2.9 22.8 + - + -
215C SER* 3.0 11.3 + - - -
81D TYR* 3.5 32.3 - + - -
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Residues in contact with ASN 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C THR 3.2 3.0 + - - -
199C GLN 3.2 21.4 + - - +
200C LEU* 5.0 1.4 - - - +
201C GLY* 3.6 17.7 - - - +
203C LYS 5.9 2.0 - - - +
204C HIS* 4.8 9.6 + - - -
207C GLN* 3.4 28.0 + - - +
209C ASN* 3.5 25.2 + - - +
210C ASP 3.7 0.8 - - - -
211C PHE* 1.3 75.9 - - - +
213C LEU* 1.3 62.2 + - - +
215C SER* 3.2 10.9 + - - -
216C ASP* 3.0 26.2 + - - +
87D SER* 4.7 2.6 + - - -
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Residues in contact with LEU 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C GLN* 3.8 13.9 - - - +
96C TRP* 4.2 13.5 - - + -
191C LEU* 3.7 28.2 - - + +
196C CYS* 4.4 2.5 - - + -
197C PHE 3.5 18.8 - - - +
198C THR* 3.0 18.1 + - - +
200C LEU 3.8 8.7 - - - +
201C GLY* 3.8 9.8 - - - -
202C LEU* 3.9 37.7 - - + +
212C ASN* 1.3 78.4 - - - +
214C ALA* 1.3 62.6 + - - +
216C ASP* 3.4 4.4 + - - +
217C LEU* 3.1 28.8 + - + +
276C LEU* 5.4 1.3 - - + -
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Residues in contact with ALA 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C LEU* 3.6 19.3 - - + +
187C PHE* 4.2 4.6 - - - +
188C ALA* 3.8 31.0 - - - +
191C LEU* 3.6 12.3 - - + +
198C THR* 4.3 1.9 + - - -
211C PHE* 2.9 17.7 + - + +
213C LEU* 1.3 77.0 - - - +
215C SER* 1.3 66.0 + - - +
217C LEU* 3.2 3.2 + - - +
218C MET* 3.1 25.1 + - - +
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Residues in contact with SER 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C LEU* 3.6 12.9 - - - +
209C ASN* 3.7 14.2 + - - -
211C PHE 3.0 12.4 + - - -
212C ASN* 3.2 11.3 + - - -
214C ALA* 1.3 78.4 - - - +
216C ASP* 1.3 65.4 + - - +
218C MET* 3.1 26.5 - - - +
219C GLU* 3.3 15.9 - - - +
222C ARG* 3.9 6.7 + - - -
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Residues in contact with ASP 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C TRP* 3.6 29.5 + - + -
108C ILE* 3.6 12.7 - - + +
201C GLY* 3.5 7.8 - - - -
202C LEU* 2.7 45.0 + - + -
203C LYS* 3.8 5.3 + - - +
212C ASN* 3.0 13.8 + - - +
213C LEU* 3.5 9.6 - - + +
215C SER* 1.3 77.9 - - - +
217C LEU* 1.3 63.9 + - + +
219C GLU* 3.2 27.2 + - - +
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Residues in contact with LEU 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ILE* 4.2 13.4 - - + +
187C PHE* 4.1 13.2 - - + -
191C LEU* 3.8 19.3 - - + -
202C LEU* 4.9 3.6 - - + -
213C LEU* 3.1 27.2 + - + +
214C ALA* 3.2 4.5 + - - +
216C ASP* 1.3 84.6 - - + +
218C MET* 1.3 60.2 + - - +
219C GLU 3.1 1.6 + - - -
220C PRO* 3.4 11.4 - - - +
221C PHE* 4.0 5.2 - - - -
268C TYR* 3.9 16.3 - - + -
269C THR* 3.6 42.8 - - + +
272C VAL* 3.8 33.0 - - + -
273C VAL* 5.4 0.9 - - + -
276C LEU* 5.5 0.9 - - + -
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Residues in contact with MET 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C TYR* 3.5 28.3 - - + +
183C LEU* 3.8 15.5 - - + +
184C LEU* 3.8 35.0 - - - -
187C PHE* 3.8 28.5 - - + -
214C ALA 3.1 12.0 + - - +
215C SER* 3.1 19.1 - - - +
217C LEU* 1.3 76.2 - - - +
219C GLU* 1.3 59.0 + - - +
220C PRO* 3.3 2.0 - - - -
221C PHE* 2.9 26.2 + - - +
222C ARG* 3.5 46.8 + - + +
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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