Contacts of the helix formed by residues 212 - 216 (chain C) in PDB entry 2WZJ
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 212 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B LEU* 3.8 22.9 - - - +
175C ASP* 2.7 27.3 + - - -
176C LEU 6.0 0.2 - - - -
177C LYS* 2.8 24.6 + - - -
209C PHE* 3.3 14.6 + - - +
210C CYS 3.3 0.8 - - - -
211C GLY* 1.3 78.0 - - - +
213C PRO* 1.3 72.9 - - - +
215C TYR* 3.1 16.9 + - - +
216C ALA* 3.5 6.8 + - - -
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Residues in contact with PRO 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLU 4.2 7.2 - - - +
209B PHE* 4.1 6.5 - - + -
213B PRO* 3.7 25.6 - - + -
255B LEU* 3.8 16.2 - - + -
209C PHE 3.9 8.5 - - - +
211C GLY 3.7 0.9 - - - -
212C SER* 1.3 92.5 - - - +
214C PRO* 1.3 68.9 - - + +
215C TYR 3.0 1.8 + - - -
216C ALA* 3.0 17.9 + - + +
221C PHE* 4.7 7.0 - - + -
255C LEU* 3.8 16.4 - - + -
258C LEU* 3.5 26.7 - - + +
262C VAL* 5.2 1.7 - - - +
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Residues in contact with PRO 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ASP 3.7 23.1 - - - +
209B PHE* 3.8 12.6 - - + -
211C GLY 3.1 21.3 - - - +
212C SER 3.2 0.4 - - - -
213C PRO* 1.3 97.4 - - + +
215C TYR* 1.3 61.6 + - + +
216C ALA 3.5 1.8 - - - +
234C TRP* 5.4 0.2 + - - -
238C VAL* 3.6 18.4 - - - +
248C LEU* 3.7 26.7 - - + -
249C PRO* 5.3 0.3 - - - +
250C PHE* 4.2 19.8 - - - +
258C LEU* 4.0 13.9 - - + -
262C VAL* 5.2 2.0 - - - +
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Residues in contact with TYR 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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206B LEU* 5.3 2.8 - - - +
138C PHE* 5.4 1.6 - - - -
176C LEU 3.5 23.1 - - - +
177C LYS* 3.5 13.0 - - + -
178C ALA* 3.1 38.2 + - + +
179C GLU* 4.1 5.8 + - - -
211C GLY* 2.9 30.3 - - - -
212C SER* 3.1 5.7 + - - +
213C PRO 3.0 1.0 - - - -
214C PRO* 1.3 88.3 - - + +
216C ALA* 1.3 63.9 + - - +
234C TRP* 3.5 11.7 - - - -
235C SER* 2.8 28.2 + - - +
238C VAL* 3.4 32.5 - - + -
239C ILE* 3.9 21.3 - - + -
242C THR* 4.4 6.4 - - + +
248C LEU* 4.3 16.1 - - + +
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Residues in contact with ALA 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 4.3 9.4 - - + -
212C SER 3.5 3.2 + - - +
213C PRO 3.0 17.0 + - - +
214C PRO 5.0 0.3 - - - +
215C TYR* 1.3 78.4 - - - +
217C ALA* 1.3 63.3 + - - +
218C PRO 3.9 0.5 - - - -
220C LEU* 3.5 31.4 - - + -
221C PHE* 4.0 9.4 - - + -
226C TYR* 3.6 8.7 - - - +
234C TRP* 3.2 12.0 + - - -
235C SER* 4.8 0.2 - - - -
262C VAL* 4.0 14.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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