Contacts of the helix formed by residues 180 - 191 (chain A) in PDB entry 2HXO
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 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A GLU* 1.3 80.3 + - - +
182A PHE* 3.4 7.4 - - - +
183A LEU* 3.9 24.7 + - - +
184A ASP* 3.7 18.9 + - - +
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Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A ASP* 1.3 91.0 + - - +
182A PHE* 1.3 67.3 + - + +
184A ASP* 3.7 5.1 + - - +
185A THR* 2.8 27.5 + - - -
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Residues in contact with PHE 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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166A ASN* 3.2 22.7 - - + +
180A ASP 3.4 4.9 - - - +
181A GLU* 1.3 82.8 - - + +
183A LEU* 1.3 75.9 + - + +
185A THR* 3.2 7.2 + - - -
186A VAL* 3.0 41.9 + - + +
114B GLN 4.7 0.7 - - - -
115B LEU* 3.2 31.4 - - - -
116B SER 3.7 20.9 - - - +
117B ARG* 3.9 2.2 - - - -
118B THR 3.7 5.6 - - - -
119B PRO* 3.3 43.1 - - + -
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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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166A ASN* 5.7 2.5 - - - +
180A ASP* 3.9 23.5 + - - +
181A GLU 3.4 0.6 - - - -
182A PHE* 1.3 90.1 - - + +
184A ASP* 1.3 57.0 + - - +
186A VAL* 3.3 3.2 + - + -
187A SER* 2.9 26.3 + - - -
208A VAL* 3.4 39.1 - - + +
209A ARG* 4.6 5.2 - - - -
210A GLY* 4.5 4.9 - - - +
211A HIS* 3.1 41.5 - - - +
213A ASP* 4.8 14.1 - - - +
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Residues in contact with ASP 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 ASP 3.7 14.0 + - - +
181A GLU* 4.1 5.1 - - - +
182A PHE 3.3 0.6 - - - -
183A LEU* 1.3 77.6 - - - +
185A THR* 1.3 67.5 + - - +
187A SER* 3.2 2.9 + - - -
188A THR* 3.1 29.8 + - - +
209A ARG* 3.1 46.5 + - + +
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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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181A GLU 2.8 15.8 + - - -
182A PHE* 3.2 10.0 + - - -
184A ASP* 1.3 82.2 + - - +
186A VAL* 1.3 57.8 + - - +
188A THR* 3.2 7.1 + - - +
189A ALA* 2.9 30.4 + - - +
119B PRO* 3.5 24.9 - - + -
120B TRP* 3.6 32.9 + - + -
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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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182A PHE* 3.0 46.3 + - + +
183A LEU* 3.5 8.7 - - + +
185A THR* 1.3 74.1 - - - +
187A SER* 1.3 61.0 + - - +
189A ALA* 3.2 0.7 + - - +
190A TRP* 2.8 65.6 + - + +
208A VAL* 3.7 16.6 - - + -
119B PRO* 3.8 20.4 - - + +
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Residues in contact with SER 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 2.9 14.0 + - - -
184A ASP 3.5 8.5 - - - -
186A VAL* 1.3 77.7 - - - +
188A THR* 1.3 61.3 + - - +
190A TRP* 3.5 3.3 + - - +
191A GLU* 3.1 27.7 + - - +
205A ALA 3.2 21.3 + - - +
206A ASP* 3.6 13.5 + - - -
208A VAL* 3.8 14.6 - - - +
209A ARG* 3.2 30.4 + - - -
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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 ASP* 3.1 18.2 + - - +
185A THR* 3.2 11.6 + - - +
187A SER* 1.3 75.1 - - - +
189A ALA* 1.3 65.9 + - - +
191A GLU* 3.0 25.1 + - - +
192A GLY* 3.3 7.6 + - - -
209A ARG* 2.9 30.3 - - - +
120B TRP* 6.1 0.5 - - - -
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Residues in contact with ALA 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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185A THR 2.9 19.1 + - - +
186A VAL 3.6 3.6 - - - +
188A THR* 1.3 77.9 + - - +
190A TRP* 1.3 63.5 + - + +
192A GLY* 3.1 14.4 + - - -
193A LEU* 3.9 6.2 + - - +
119B PRO 3.8 15.0 - - - +
120B TRP* 3.3 38.4 - - + +
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Residues in contact with TRP 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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186A VAL* 2.8 41.1 + - + +
187A SER* 3.8 4.3 - - - +
189A ALA* 1.3 71.7 - - + +
191A GLU* 1.3 57.9 + - - +
192A GLY 2.8 5.6 - - - -
193A LEU* 2.8 35.4 + - + +
201A THR* 3.4 24.6 - - + +
202A ARG* 3.9 5.7 - - - -
204A VAL 5.9 0.9 - - - -
205A ALA* 4.4 13.4 - - + +
208A VAL* 3.8 26.2 - - + -
119B PRO 4.3 11.8 + - - -
120B TRP* 6.3 0.2 - - - -
121B GLY 4.8 1.7 + - - -
124B ALA* 4.2 9.8 - - + +
125B PRO* 3.9 41.4 - - + +
128B PHE* 3.6 46.4 - + + -
146B PHE* 4.7 3.1 - + - -
153B MSE 6.4 0.2 - - - -
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Residues in contact with GLU 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 SER* 3.1 17.8 + - - +
188A THR* 3.0 19.3 + - - +
190A TRP* 1.3 74.2 - - - +
192A GLY* 1.3 56.4 + - - +
193A LEU 3.4 0.4 - - - -
202A ARG* 2.9 45.9 + - - +
205A ALA* 3.5 15.5 - - + -
206A ASP* 3.7 26.9 - - - +
209A ARG* 3.6 20.8 + - - -
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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