Contacts of the helix formed by residues 183 - 194 (chain A) in PDB entry 2AEB
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 ASP 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ASN* 2.9 27.8 + - - +
136A THR* 5.1 8.6 + - - -
181A ASP* 4.1 8.2 + - - +
182A VAL* 1.3 77.6 - - - +
184A PRO* 1.3 76.5 - - + +
185A GLY 4.5 3.8 - - - +
186A GLU* 3.0 25.8 + - + +
187A HIS* 3.0 19.5 + - - +
551A ABH 2.9 21.8 + - - -
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Residues in contact with PRO 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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182A VAL 4.4 1.8 - - - +
183A ASP* 1.3 87.8 - - + +
185A GLY* 1.3 63.1 + - - +
187A HIS* 3.2 9.2 + - + +
188A TYR* 3.0 21.5 + - - +
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Residues in contact with GLY 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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130A ASN* 5.2 2.2 - - - -
134A THR* 5.0 17.6 - - - +
183A ASP* 3.4 2.8 - - - +
184A PRO* 1.3 78.3 - - - +
186A GLU* 1.3 55.1 + - - +
188A TYR* 3.4 10.4 + - - +
189A ILE* 3.0 36.2 + - - +
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Residues in contact with GLU 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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126A HIS* 6.0 0.2 - - - +
127A THR* 2.8 28.9 + - - +
128A ASP* 3.1 8.3 + - - -
129A ILE* 3.0 29.9 + - + +
130A ASN* 3.4 39.0 + - - +
142A GLY 4.1 0.5 - - - +
181A ASP 4.7 1.6 - - - +
182A VAL* 3.8 6.9 - - + -
183A ASP* 3.0 41.9 + - + +
185A GLY* 1.3 73.2 - - - +
187A HIS* 1.3 60.3 + - - +
189A ILE* 3.2 6.2 + - - +
190A LEU* 2.9 31.3 + - - +
551A ABH 3.7 7.6 + - - -
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Residues in contact with HIS 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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182A VAL* 3.7 14.3 - - + +
183A ASP 3.0 12.5 + - - +
184A PRO* 3.2 11.6 + - + +
186A GLU* 1.3 74.9 - - - +
188A TYR* 1.3 63.7 + - - +
190A LEU* 3.3 17.0 + - + +
191A LYS* 3.1 62.1 + - + +
197A TYR* 4.7 4.2 + + - -
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Residues in contact with TYR 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 PRO 3.0 12.7 + - - +
185A GLY* 3.4 14.6 - - - +
186A GLU 3.2 0.2 - - - -
187A HIS* 1.3 77.8 + - - +
189A ILE* 1.3 66.4 + - + +
191A LYS* 3.4 4.2 + - + +
192A THR* 2.8 65.6 + - + +
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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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129A ILE* 3.5 48.5 - - + +
131A THR* 4.4 17.3 - - + -
134A THR* 4.9 10.1 - - + +
152A LEU* 4.3 14.1 - - + -
185A GLY 3.0 20.9 + - - +
186A GLU* 3.2 8.7 + - - +
188A TYR* 1.3 85.1 - - + +
190A LEU* 1.3 66.0 + - - +
192A THR* 4.3 3.1 - - - -
193A LEU* 2.9 44.6 + - + +
195A ILE* 4.6 0.4 - - + -
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Residues in contact with LEU 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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127A THR* 4.1 21.1 - - + -
129A ILE* 5.2 3.1 - - + -
176A TYR* 3.8 20.4 - - + -
179A LEU* 4.3 8.3 - - + -
182A VAL* 4.6 4.5 - - + -
186A GLU 2.9 16.1 + - - +
187A HIS* 3.5 24.0 - - + +
189A ILE* 1.3 77.4 - - - +
191A LYS* 1.3 59.9 + - + +
194A GLY* 3.0 22.7 + - - -
195A ILE* 3.2 48.7 + - + +
197A TYR* 4.1 29.3 - - + -
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Residues in contact with LYS 191 (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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187A HIS* 3.1 46.0 + - + +
188A TYR* 3.9 4.7 - - + +
190A LEU* 1.3 74.4 - - + +
192A THR* 1.3 65.5 + - - +
193A LEU 3.5 0.2 + - - -
194A GLY* 3.6 8.5 + - - -
197A TYR* 2.9 34.9 + - + -
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Residues in contact with THR 192 (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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188A TYR* 2.8 60.0 + - + +
189A ILE* 3.8 4.7 - - - -
191A LYS* 1.3 80.3 - - - +
193A LEU* 1.3 74.5 + - + +
194A GLY 3.6 0.2 + - - -
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Residues in contact with LEU 193 (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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149A LEU* 4.4 16.8 - - + -
151A GLU* 4.1 33.7 - - + +
152A LEU* 4.1 17.0 - - + -
171A ALA* 3.9 23.4 - - + +
189A ILE* 2.9 37.3 + - + +
192A THR* 1.3 90.7 - - + +
194A GLY* 1.3 62.3 + - - +
195A ILE* 4.1 6.3 - - + -
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Residues in contact with GLY 194 (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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171A ALA* 5.1 1.7 - - - +
172A LYS* 5.7 0.7 - - - -
190A LEU 3.0 8.2 + - - -
191A LYS* 3.6 6.6 + - - -
192A THR 3.4 3.6 + - - -
193A LEU* 1.3 78.4 - - - +
195A ILE* 1.3 64.1 + - - +
196A LYS 3.6 2.1 + - - -
218A TYR* 4.4 8.5 + - - -
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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