Contacts of the helix formed by residues 211 - 220 (chain C) in PDB entry 1WZN
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 THR 211 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145C PHE* 4.3 3.1 - - - -
181C GLN* 5.6 0.4 - - - +
209C ILE* 5.9 3.8 - - + -
210C TYR* 1.3 77.1 - - - +
212C PRO* 1.3 75.5 - - - +
213C ARG* 3.5 9.8 + - - +
214C GLU* 3.1 44.8 + - - +
215C VAL* 3.2 13.3 + - - +
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Residues in contact with PRO 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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145C PHE* 4.0 12.8 - - + -
210C TYR 4.8 0.2 - - - +
211C THR* 1.3 86.7 - - - +
213C ARG* 1.3 61.8 + - - +
215C VAL* 3.5 3.1 + - - +
216C ARG 3.1 17.8 + - - -
228C ILE* 3.5 36.8 - - + +
236C LEU* 5.4 4.7 - - + -
243C TYR* 3.6 45.5 - - + -
245C ILE* 4.3 0.7 - - - +
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Residues in contact with ARG 213 (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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211C THR* 3.2 9.3 + - - +
212C PRO* 1.3 80.3 - - - +
214C GLU* 1.3 57.4 + - - +
216C ARG* 3.4 30.2 + - - +
217C LEU* 2.9 52.5 + - + +
228C ILE* 4.5 2.0 - - - +
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Residues in contact with GLU 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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181C GLN* 2.9 32.6 + - - -
210C TYR* 3.3 29.6 - - + -
211C THR* 3.1 38.7 + - - +
213C ARG* 1.3 76.9 - - + +
215C VAL* 1.3 67.4 + - - +
217C LEU* 3.0 12.3 + - + +
218C LEU* 2.9 31.8 + - + +
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Residues in contact with VAL 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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116C ILE* 4.0 13.2 - - + -
124C LEU* 5.3 2.0 - - + -
128C PHE* 4.2 19.2 - - + -
143C THR* 5.4 0.9 - - + -
145C PHE* 3.6 21.1 - - + -
210C TYR* 3.8 20.9 - - + -
211C THR 3.2 12.9 + - - +
212C PRO 3.8 5.6 - - - +
214C GLU* 1.3 74.8 - - - +
216C ARG* 1.3 53.1 + - - +
218C LEU* 3.1 9.6 + - - +
219C ALA* 2.7 34.2 + - + +
245C ILE* 3.2 37.0 - - + -
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Residues in contact with ARG 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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212C PRO 3.1 13.1 + - - +
213C ARG* 3.6 38.1 - - - +
215C VAL* 1.3 76.9 - - - +
217C LEU* 1.3 67.7 + - - +
220C GLU* 2.7 74.5 + - + +
226C VAL* 4.1 26.7 - - + -
228C ILE* 3.4 32.1 - - + +
245C ILE* 4.4 1.0 - - - +
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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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213C ARG* 2.9 41.1 + - + +
214C GLU* 3.0 12.3 + - + +
216C ARG* 1.3 94.2 - - - +
218C LEU* 1.3 63.8 + - + +
220C GLU* 4.0 13.7 + - - +
221C LYS* 3.6 25.6 + - - +
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Residues in contact with LEU 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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121C GLU* 3.8 26.2 - - + +
124C LEU* 4.1 25.4 - - + -
125C ARG* 3.7 35.7 - - + +
128C PHE* 4.0 14.1 - - + -
210C TYR* 4.2 16.8 - - + -
214C GLU* 2.9 24.9 + - + +
215C VAL* 3.6 4.5 - - - +
217C LEU* 1.3 81.3 - - + +
219C ALA* 1.3 60.4 + - - +
221C LYS* 3.9 13.3 - - - +
222C TYR* 3.4 25.3 - - - -
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Residues in contact with ALA 219 (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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128C PHE* 4.0 18.8 - - + -
141C PHE* 6.0 0.2 - - + -
215C VAL 2.7 21.3 + - - +
216C ARG 3.9 2.0 - - - +
218C LEU* 1.3 70.1 - - - +
220C GLU* 1.3 55.6 - - - +
221C LYS 3.0 5.4 - - - -
222C TYR* 2.8 22.2 + - - -
223C PHE* 3.1 26.4 + - + -
226C VAL* 3.7 22.2 - - + -
245C ILE* 4.6 10.3 - - + -
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Residues in contact with GLU 220 (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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216C ARG* 2.7 67.6 + - + +
217C LEU* 4.1 15.8 - - - +
218C LEU 3.6 0.2 - - - -
219C ALA* 1.3 71.5 - - - +
221C LYS* 1.3 61.8 + - + +
222C TYR 3.2 0.2 - - - -
223C PHE 3.2 15.5 - - - +
226C VAL* 3.6 23.2 + - + +
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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
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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