Contacts of the helix formed by residues 211 - 220 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A PHE* 4.3 2.5 - - - -
181A GLN* 5.8 0.9 - - - +
209A ILE* 6.1 2.0 - - + -
210A TYR* 1.3 78.5 - - - +
212A PRO* 1.3 75.0 - - - +
213A ARG* 3.7 6.9 + - - +
214A GLU* 2.8 47.1 + - - +
215A VAL* 3.2 14.0 + - - +
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Residues in contact with PRO 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A PHE* 4.0 10.8 - - + -
210A TYR 4.7 0.7 - - - +
211A THR* 1.3 89.8 - - + +
213A ARG* 1.3 62.1 + - - +
215A VAL* 3.3 4.2 + - - +
216A ARG 3.0 17.8 + - - -
228A ILE* 3.4 36.3 - - + +
236A LEU* 5.6 4.3 - - + -
243A TYR* 3.6 45.8 - - + -
245A ILE* 4.1 0.9 - - - +
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Residues in contact with ARG 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A THR* 3.2 7.7 + - - +
212A PRO* 1.3 80.3 - - - +
214A GLU* 1.3 57.2 + - + +
216A ARG* 3.3 30.8 + - - +
217A LEU* 2.9 49.7 + - + +
228A ILE* 4.4 4.0 - - - +
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Residues in contact with GLU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A GLN* 2.6 31.3 + - - +
210A TYR* 2.8 27.2 - - + +
211A THR* 2.8 47.0 + - - +
213A ARG* 1.3 77.7 - - + +
215A VAL* 1.3 62.7 + - - +
217A LEU* 3.2 11.5 + - + +
218A LEU* 3.0 32.6 + - + +
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Residues in contact with VAL 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ILE* 4.1 13.0 - - + -
124A LEU* 5.2 2.7 - - + -
128A PHE* 4.0 22.8 - - + -
143A THR* 5.4 1.1 - - + -
145A PHE* 3.5 19.5 - - + -
210A TYR* 3.8 21.5 - - + -
211A THR 3.2 14.0 + - - +
212A PRO 3.8 5.8 - - - +
214A GLU* 1.3 75.0 - - - +
216A ARG* 1.3 57.5 + - - +
218A LEU* 3.2 9.0 + - - +
219A ALA* 2.8 27.9 + - - +
245A ILE* 3.3 33.0 - - + -
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Residues in contact with ARG 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A PRO 3.0 5.7 + - - -
213A ARG* 3.5 39.2 - - - +
214A GLU 3.2 0.2 - - - -
215A VAL* 1.3 77.4 - - - +
217A LEU* 1.3 68.9 + - - +
219A ALA 3.2 0.2 + - - -
220A GLU* 2.8 76.3 + - + +
226A VAL* 4.0 25.6 - - + -
228A ILE* 3.5 38.5 - - + +
245A ILE* 4.4 1.7 - - - +
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Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ARG* 2.9 37.0 + - + +
214A GLU* 3.2 10.5 + - + +
216A ARG* 1.3 94.0 - - - +
218A LEU* 1.3 62.6 + - + +
220A GLU* 3.9 12.7 + - - +
221A LYS* 3.3 28.1 + - - +
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Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLU* 3.9 27.1 - - + +
124A LEU* 4.0 26.7 - - + -
125A ARG* 3.5 39.7 - - + +
128A PHE* 3.8 13.5 - - + -
210A TYR* 4.1 16.6 - - + -
214A GLU* 3.0 26.2 + - + +
215A VAL* 3.7 4.3 - - - +
216A ARG 3.2 0.2 - - - -
217A LEU* 1.3 78.8 - - + +
219A ALA* 1.3 61.2 + - - +
221A LYS* 3.7 9.8 - - - +
222A TYR* 3.3 26.5 - - - -
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Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PHE* 3.8 19.7 - - + -
141A PHE* 6.1 0.2 - - + -
215A VAL 2.8 17.4 + - - +
216A ARG 3.8 2.5 - - - +
218A LEU* 1.3 76.0 - - - +
220A GLU* 1.3 56.2 + - - +
221A LYS 2.9 5.4 - - - -
222A TYR* 2.8 20.2 + - - -
223A PHE* 3.2 25.8 + - + -
226A VAL* 3.7 21.5 - - + -
245A ILE* 4.5 9.6 - - + -
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Residues in contact with GLU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ARG* 2.8 69.5 + - + +
217A LEU* 4.3 13.2 - - - +
218A LEU 3.6 0.4 - - - -
219A ALA* 1.3 72.0 - - - +
221A LYS* 1.3 60.3 + - + +
222A TYR 3.1 0.4 - - - -
223A PHE 3.3 16.1 - - - +
224A GLU 6.1 0.2 - - - +
225A LYS* 6.2 0.2 - - - -
226A VAL* 3.7 23.1 + - + +
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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