Contacts of the helix formed by residues 188 - 193 (chain A) in PDB entry 2XB2
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 GLU 188 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LYS* 5.7 1.6 - - - -
114A PRO* 3.7 19.1 - - + -
118A LEU* 3.7 22.9 - - + -
187A ASP* 1.3 80.0 + - - +
189A ALA* 1.3 60.1 + - - +
190A ASP* 3.4 4.5 - - - -
191A GLU* 3.0 20.2 + - - +
192A MET* 3.0 9.5 + - - +
217A ILE 2.9 10.6 + - - -
218A SER* 4.3 10.2 - - - -
219A ALA 5.7 0.2 + - - -
339A ARG* 3.0 38.4 - - + +
340A GLY 3.9 4.1 + - - -
363A HIS* 3.5 17.2 - - - -
1412A MG 2.7 26.3 - - - -
1413A ANP 3.2 8.8 + - - -
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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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186A LEU* 3.5 18.8 - - - +
187A ASP 3.1 1.0 - - - -
188A GLU* 1.3 71.0 - - - +
190A ASP* 1.3 56.9 + - - +
191A GLU 2.9 5.6 - - - -
192A MET* 2.9 9.5 + - - -
193A LEU* 2.8 37.8 + - + +
216A LEU* 3.6 36.8 - - + -
217A ILE 3.1 11.4 + - - +
218A SER* 3.8 2.6 - - - -
221A LEU* 4.8 4.9 - - + -
225A ILE* 5.8 0.2 - - + -
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Residues in contact with ASP 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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188A GLU 3.9 1.6 - - - +
189A ALA* 1.3 77.7 - - - +
191A GLU* 1.3 58.2 + - - +
193A LEU 4.0 0.2 - - - -
194A ASN* 3.4 23.7 + - - +
218A SER* 2.9 14.3 + - - -
220A THR* 2.8 40.6 + - - +
221A LEU* 4.1 6.1 - - + +
222A PRO* 3.7 23.0 - - + +
225A ILE* 4.2 20.9 - - + +
339A ARG* 2.7 33.7 + - - -
359A GLU* 3.9 5.5 - - - +
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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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114A PRO* 3.7 29.1 - - + +
188A GLU* 3.0 10.0 + - + +
189A ALA 2.9 0.4 - - - -
190A ASP* 1.3 78.8 + - - +
192A MET* 1.3 59.0 + - - +
193A LEU 3.0 8.8 + - - -
194A ASN* 3.3 22.8 + - - +
197A PHE* 3.6 26.1 - - + +
339A ARG* 3.5 41.2 + - - +
3E U 5.5 2.4 - - - +
4E U 5.2 5.0 + - - -
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Residues in contact with MET 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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112A LEU* 3.4 15.9 - - + +
113A ALA 3.4 31.6 - - - +
114A PRO* 3.2 31.6 - - - -
164A PRO* 3.5 22.9 - - + -
186A LEU* 4.5 11.9 - - + -
187A ASP 3.3 23.6 - - - +
188A GLU 3.4 3.1 - - - +
189A ALA* 2.9 11.1 + - - +
191A GLU* 1.3 74.5 - - - +
193A LEU* 1.3 59.8 + - - +
194A ASN 3.7 0.2 - - - -
197A PHE* 3.7 21.8 - - - +
198A LYS 3.8 0.2 + - - -
201A ILE* 3.1 34.3 - - + +
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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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186A LEU* 4.1 16.4 - - + -
189A ALA 2.8 16.5 + - - +
190A ASP 4.2 0.2 - - - -
192A MET* 1.3 85.9 - - - +
194A ASN* 1.3 63.9 + - - +
195A LYS* 3.7 0.7 + - - +
198A LYS* 3.4 28.8 - - + +
201A ILE* 4.7 1.1 - - + -
216A LEU* 4.1 16.6 - - + -
225A ILE* 3.8 36.3 - - + +
228A MET* 4.2 15.1 - - + +
232A PHE* 3.5 41.1 - - + -
218T TRP* 4.4 15.3 - - + -
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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