Contacts of the helix formed by residues 179 - 189 (chain A) in PDB entry 2Z4U
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 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A GLU* 2.9 21.9 + - - +
176A ALA 3.0 15.2 - - - +
177A ALA 3.3 0.2 - - - -
178A ARG* 1.3 84.2 - - + +
180A LYS* 1.3 65.7 + - - +
181A TYR 4.1 0.2 - - - +
182A ILE* 2.9 36.4 + - + +
183A GLU 3.1 4.2 + - - -
203A LEU* 3.1 58.1 - - + -
204A GLU* 4.0 5.6 - - - -
207A TRP* 3.4 34.1 - + + -
210A ILE* 4.2 3.8 - - + -
247A ASP 3.2 16.6 - - - +
248A MET* 3.5 29.6 - - + -
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Residues in contact with LYS 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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24A ARG* 3.8 34.9 - - - +
179A PHE* 1.3 69.9 - - - +
181A TYR* 1.4 57.6 + - - +
183A GLU* 3.3 6.8 + - - +
184A ASN* 2.8 42.3 + - - +
245A LYS 5.7 0.4 + - - -
246A PRO* 3.5 22.4 - - + +
247A ASP* 2.9 5.3 + - - +
248A MET 3.4 22.4 + - - +
249A GLY* 3.6 7.9 - - - +
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Residues in contact with TYR 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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179A PHE 3.0 1.2 - - - -
180A LYS* 1.4 76.2 - - - +
182A ILE* 1.3 57.5 + - + +
184A ASN* 3.3 9.1 + - + +
185A GLN* 2.9 56.7 + - + +
197A ASN* 3.1 21.5 + - - -
199A LYS* 3.6 34.0 - - + +
200A VAL* 3.8 18.4 - - + -
203A LEU* 3.7 28.9 - - + -
231A ALA* 3.6 15.1 - - - +
247A ASP* 3.1 34.3 + - + +
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Residues in contact with ILE 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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139A LEU* 5.6 5.4 - - + -
171A GLN* 3.9 24.0 - - + +
175A GLU* 3.9 11.9 - - + -
176A ALA* 3.9 8.7 - - + -
179A PHE* 2.9 30.5 + - + +
181A TYR* 1.3 78.9 - - + +
183A GLU* 1.3 65.9 + - - +
185A GLN* 3.1 9.1 + - + +
186A VAL* 3.1 26.9 + - + +
194A PHE* 6.2 0.9 - - + -
200A VAL* 3.8 33.2 - - + +
203A LEU* 4.7 2.2 - - + -
204A GLU* 3.8 30.3 - - + +
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Residues in contact with GLU 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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16A TYR* 3.8 7.7 - - + -
17A ALA* 3.8 12.8 - - - +
20A MET* 3.8 19.4 - - + +
24A ARG* 2.8 40.3 + - - +
176A ALA* 3.9 14.1 - - - +
179A PHE 3.1 4.9 + - - -
180A LYS* 3.5 13.9 - - - +
182A ILE* 1.3 76.3 - - - +
184A ASN* 1.3 61.3 + - - +
186A VAL* 3.2 6.2 + - - +
187A LYS* 2.8 64.1 + - - +
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Residues in contact with ASN 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 LYS* 2.8 34.9 + - - +
181A TYR* 3.6 8.8 - - + +
183A GLU* 1.3 73.7 - - - +
185A GLN* 1.3 63.7 + - - +
187A LYS* 3.7 23.8 + - - +
188A THR* 2.8 37.6 + - - +
246A PRO 5.2 3.0 + - - -
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Residues in contact with GLN 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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181A TYR* 2.9 52.4 + - + +
182A ILE* 3.1 9.6 + - + +
184A ASN* 1.3 77.2 - - - +
186A VAL* 1.3 62.6 + - - +
188A THR* 3.5 7.7 + - - +
189A ASN* 2.9 41.6 + - - +
194A PHE* 3.9 22.0 - - + -
195A ASN 5.5 0.7 - - - +
197A ASN* 3.4 21.9 + - - +
200A VAL* 4.0 11.0 - - + +
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Residues in contact with VAL 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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16A TYR* 3.6 36.3 - - + +
139A LEU* 5.6 0.9 - - + -
140A GLY* 6.0 0.4 - - - -
141A ILE* 4.6 2.7 - - + +
172A MET* 3.9 32.5 - - + -
182A ILE* 3.1 18.1 + - + +
183A GLU 3.2 7.4 + - - +
185A GLN* 1.3 77.6 - - - +
187A LYS* 1.4 57.3 + - - +
189A ASN 3.2 3.6 + - - +
190A PHE* 2.9 46.2 + - + -
194A PHE* 3.9 24.6 - - + -
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Residues in contact with LYS 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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13A ILE* 3.7 37.3 - - + +
16A TYR* 4.1 11.2 - - + -
17A ALA* 3.6 32.9 - - - +
183A GLU* 2.8 52.4 + - - +
184A ASN* 3.3 20.8 + - - +
186A VAL* 1.4 74.4 - - - +
188A THR* 1.3 62.8 - - - +
190A PHE* 3.1 24.5 + - + +
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Residues in contact with THR 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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184A ASN* 2.8 24.8 + - - +
185A GLN* 3.9 11.4 + - - +
187A LYS* 1.3 72.8 - - - +
189A ASN* 1.4 68.2 + - - +
190A PHE 3.8 0.5 + - - -
191A ASN* 5.6 0.5 - - - +
192A ARG* 3.6 16.1 + - - +
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Residues in contact with ASN 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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140A GLY* 5.7 0.2 - - - -
185A GLN* 2.9 35.6 + - - +
186A VAL 3.2 3.5 - - - +
187A LYS 3.1 0.2 - - - -
188A THR* 1.4 87.2 - - - +
190A PHE* 1.3 63.0 + - - +
191A ASN* 3.2 2.9 - - - -
192A ARG* 2.8 53.8 + - + +
193A ALA 4.9 0.2 - - - +
194A PHE* 3.5 45.6 - - + +
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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