Contacts of the helix formed by residues 183 - 194 (chain A) in PDB entry 5ABT
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 ASN 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ILE* 3.7 13.1 - - - +
172A ASP* 2.8 37.2 + - + +
175A ARG* 3.8 23.8 + - - +
182A SER* 1.3 69.9 - - - +
184A VAL* 1.3 64.5 + - - +
185A SER* 3.5 10.6 + - - -
186A LEU* 3.1 37.3 + - + +
187A TYR* 3.0 23.1 + - + -
203A GLY 4.6 1.0 + - - -
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Residues in contact with VAL 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 SER* 3.0 12.6 + - - +
183A ASN* 1.3 71.1 + - - +
185A SER* 1.3 64.2 + - - +
187A TYR* 3.1 4.3 + - - +
188A GLU* 3.0 40.9 + - - +
210A ASP 5.4 0.4 - - - +
213A ALA* 3.7 39.5 - - + +
214A LEU* 4.1 17.9 - - + -
217A THR* 3.9 9.1 - - + +
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Residues in contact with SER 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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183A ASN* 3.3 9.3 + - - -
184A VAL* 1.3 78.5 - - - +
186A LEU* 1.3 62.6 + - - +
188A GLU* 3.5 16.1 + - - +
189A GLU* 3.1 25.4 + - - +
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Residues in contact with LEU 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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130A VAL* 4.5 3.8 - - + -
132A ILE* 4.4 13.0 - - + -
138A LYS* 3.6 35.4 - - + +
170A CYS* 3.7 27.1 - - - -
172A ASP* 4.1 21.1 - - + -
183A ASN* 3.1 29.5 + - + +
185A SER* 1.3 78.4 - - - +
187A TYR* 1.3 79.7 + - + +
189A GLU* 3.4 5.0 + - - +
190A VAL* 3.0 39.5 + - + +
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Residues in contact with TYR 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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170A CYS* 2.6 39.9 + - + -
172A ASP* 3.8 8.1 + - - +
182A SER* 4.3 5.6 - - - -
183A ASN* 3.0 41.4 + - - -
184A VAL 3.1 4.7 + - - +
186A LEU* 1.3 89.0 - - + +
188A GLU* 1.3 66.2 + - - +
190A VAL* 3.8 11.2 - - + -
191A CYS* 2.9 30.0 + - - +
199A PHE* 5.4 2.2 - - + -
200A GLN 4.5 0.7 - - - -
201A SER* 3.7 25.8 - - - -
202A SER 3.1 18.7 + - - -
203A GLY 5.1 0.2 + - - -
214A LEU* 4.0 9.6 - - + -
217A THR* 4.0 10.5 - - + -
219A VAL* 3.6 29.2 - - + -
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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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184A VAL* 3.0 34.6 + - - +
185A SER* 3.7 17.5 + - - +
187A TYR* 1.3 78.2 - - - +
189A GLU* 1.3 63.0 + - - +
191A CYS* 4.4 0.7 - - - +
192A ALA* 3.4 21.5 + - - +
216A GLY 5.2 3.5 - - - +
217A THR* 3.7 28.9 - - + +
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Residues in contact with GLU 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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138A LYS* 3.1 33.0 + - - -
154A GLU* 4.1 3.6 - - - +
185A SER 3.1 15.8 + - - +
186A LEU* 3.7 4.8 - - - +
188A GLU* 1.3 80.4 - - - +
190A VAL* 1.3 67.0 + - + +
192A ALA* 3.3 4.6 + - - +
193A ARG* 3.0 39.3 + - + +
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Residues in contact with VAL 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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138A LYS* 4.1 14.8 - - - -
153A LEU* 4.1 20.9 - - + -
154A GLU* 5.1 2.0 - - - +
170A CYS* 5.4 2.7 - - - -
186A LEU* 3.0 37.7 + - + +
187A TYR* 3.8 18.2 - - + +
189A GLU* 1.3 78.9 - - + +
191A CYS* 1.3 65.9 + - - +
193A ARG* 3.3 5.7 + - - -
194A TYR* 3.0 24.9 + - + -
199A PHE* 3.5 40.1 - - + -
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Residues in contact with CYS 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 TYR 2.9 23.9 + - - +
190A VAL* 1.3 80.9 - - - +
192A ALA* 1.3 61.6 + - - +
194A TYR 3.4 18.0 - - - +
195A PRO* 3.4 8.3 - - - +
197A ILE 5.9 0.2 - - - -
199A PHE* 3.8 26.0 - - - -
217A THR 3.2 17.9 - - - +
218A GLY* 3.8 8.1 - - - +
219A VAL* 3.6 41.5 - - - -
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Residues in contact with ALA 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 GLU 3.4 17.7 + - - +
189A GLU* 3.3 4.0 + - - +
190A VAL 3.2 0.2 - - - -
191A CYS* 1.3 78.8 - - - +
193A ARG* 1.3 64.8 + - + +
194A TYR 3.5 0.3 + - - -
195A PRO* 3.5 15.5 - - - +
217A THR 5.0 0.2 + - - -
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Residues in contact with ARG 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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154A GLU* 5.7 8.1 - - - +
189A GLU* 3.0 36.4 + - + +
190A VAL* 3.3 6.0 + - - +
192A ALA* 1.3 79.8 - - + +
194A TYR* 1.3 95.8 + - + +
195A PRO* 3.4 7.4 - - - +
196A GLN* 4.3 1.0 + - - +
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Residues in contact with TYR 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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153A LEU* 4.9 3.1 - - + -
154A GLU* 3.9 29.2 + - + +
157A VAL* 3.6 34.8 - - + -
158A GLU* 2.8 37.5 + - - +
161A LEU* 3.9 15.3 - - + -
190A VAL* 3.0 21.0 + - + +
191A CYS 3.4 6.2 - - - +
193A ARG* 1.3 112.7 + - + +
195A PRO* 1.3 57.2 - - - +
196A GLN* 3.0 14.4 - - - +
197A ILE* 3.0 32.3 + - + +
199A PHE* 3.7 20.0 - + + -
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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