Contacts of the helix formed by residues 179 - 190 (chain A) in PDB entry 1EZW
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 GLY 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A GLN* 1.3 89.3 + - - +
180A PRO* 1.3 70.9 - - - +
181A ILE 3.4 2.2 + - - -
182A MET* 3.4 8.3 + - - +
183A LEU* 3.0 32.5 + - - +
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Residues in contact with PRO 180 (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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179A GLY* 1.3 82.6 - - - +
181A ILE* 1.3 66.0 + - + +
183A LEU* 3.9 8.7 - - + +
184A LYS* 3.0 31.9 + - - +
209A LYS* 4.7 25.6 - - + +
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Residues in contact with ILE 181 (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 ALA* 4.0 22.0 - - + -
179A GLY 3.4 0.8 - - - -
180A PRO* 1.3 85.9 - - + +
182A MET* 1.3 64.4 + - + +
184A LYS* 3.4 4.3 + - - +
185A THR* 2.8 32.5 + - - +
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Residues in contact with MET 182 (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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97A PRO* 4.1 13.9 - - + -
127A PRO* 3.6 18.6 - - + -
128A ALA* 3.3 44.2 - - + +
131A ILE* 3.9 21.3 - - + -
175A MET* 3.9 11.7 - - - +
176A GLY 4.3 4.7 - - - +
177A ALA* 3.7 23.6 - - + +
178A GLN 4.3 2.7 - - - +
179A GLY* 3.4 9.4 + - - +
180A PRO 3.4 0.4 - - - -
181A ILE* 1.3 79.9 - - + +
183A LEU* 1.3 58.3 + - - +
185A THR* 3.4 2.7 + - - -
186A ALA* 2.9 30.7 + - - +
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Residues in contact with LEU 183 (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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177A ALA* 3.7 26.7 - - + +
178A GLN 3.6 15.9 - - - +
179A GLY 3.0 28.4 + - - +
180A PRO* 3.9 4.7 - - + +
182A MET* 1.3 77.3 - - - +
184A LYS* 1.3 63.8 + - - +
186A ALA* 3.4 3.8 + - - +
187A GLY 3.1 17.2 + - - -
193A VAL* 4.2 4.0 - - + -
195A VAL* 4.2 3.8 - - + -
205A VAL* 5.1 3.6 - - + +
206A ALA* 3.7 34.8 - - + +
209A LYS* 4.1 18.4 - - + -
210A ILE* 3.6 37.4 - - + +
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Residues in contact with LYS 184 (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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180A PRO 3.0 18.6 + - - +
181A ILE* 3.8 5.4 - - - +
183A LEU* 1.3 77.9 - - - +
185A THR* 1.3 61.2 + - - +
187A GLY 3.2 2.1 + - - -
188A GLU* 3.1 24.3 + - - +
209A LYS* 3.6 19.8 + - + +
212A GLU* 3.0 30.3 - - + +
213A GLY* 3.4 25.4 - - - +
216A GLU* 2.5 43.8 + - - +
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Residues in contact with THR 185 (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 ALA* 3.8 21.8 - - + +
132A ARG* 4.0 38.6 + - + +
175A MET* 3.9 11.7 - - + -
181A ILE* 2.8 25.3 + - - +
182A MET* 3.7 5.8 - - - -
184A LYS* 1.3 77.1 - - - +
186A ALA* 1.3 58.6 + - - +
188A GLU* 3.1 4.1 + - - +
189A ILE* 2.9 48.5 + - + +
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Residues in contact with ALA 186 (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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175A MET* 3.7 31.2 - - + -
177A ALA* 4.6 0.9 - - + -
182A MET 2.9 17.1 + - - +
183A LEU 3.7 3.6 - - - +
184A LYS 3.2 0.2 - - - -
185A THR* 1.3 78.4 - - - +
187A GLY* 1.3 58.6 + - - +
190A ALA* 2.8 34.1 + - + +
193A VAL* 3.7 33.4 - - + +
224A ILE* 4.6 0.9 - - - +
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Residues in contact with GLY 187 (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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183A LEU 3.1 11.7 + - - -
184A LYS 3.2 2.4 + - - -
186A ALA* 1.3 76.2 - - - +
188A GLU* 1.3 57.4 + - - +
210A ILE* 3.4 28.6 - - - +
214A ALA* 3.2 22.1 - - - -
219A ARG* 2.9 19.6 + - - -
224A ILE* 3.5 14.4 - - - +
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Residues in contact with GLU 188 (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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132A ARG* 3.0 39.6 + - - -
184A LYS* 3.1 15.1 + - + +
185A THR* 3.1 8.5 + - - +
187A GLY* 1.3 80.2 - - - +
189A ILE* 1.3 62.4 + - + +
213A GLY* 3.5 16.8 - - - +
216A GLU* 5.1 10.5 - - + +
217A ALA* 3.5 27.8 - - + +
219A ARG* 3.6 9.9 + - - -
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Residues in contact with ILE 189 (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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131A ILE* 4.5 1.8 - - + -
132A ARG* 3.5 51.1 - - + +
135A LYS* 2.8 52.9 + - + +
173A PHE* 4.2 5.8 - - + +
175A MET* 3.8 24.7 - - - -
185A THR* 2.9 24.9 + - + +
188A GLU* 1.3 91.3 - - + +
190A ALA* 1.3 63.2 + - - +
191A ASN* 5.7 0.2 + - - -
219A ARG* 4.1 2.9 - - - -
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Residues in contact with ALA 190 (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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173A PHE* 3.5 18.6 - - + +
175A MET* 4.2 8.5 - - + +
186A ALA* 2.8 28.0 + - - +
189A ILE* 1.3 81.2 - - - +
191A ASN* 1.3 63.4 + - - +
192A GLY 3.3 22.9 - - - +
219A ARG* 2.8 29.8 + - - +
224A ILE* 4.0 4.7 - - - +
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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