Contacts of the helix formed by residues 162 - 167 (chain B) in PDB entry 1XAH
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 162 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B HIS* 2.8 29.0 + - - +
19B GLY* 2.7 30.7 + - - -
46B PHE* 5.2 2.6 - - - -
49B LYS* 4.6 15.3 + - - +
160B ASP* 2.8 13.9 + - - +
161B LEU* 1.3 75.1 - - - +
163B PHE* 1.3 63.9 + - - +
164B LEU 3.1 1.8 + - - -
165B LYS* 3.2 39.8 + - + +
166B THR* 5.9 0.3 - - - +
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Residues in contact with PHE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 4.3 15.5 - - + -
46B PHE* 3.7 43.3 - + + -
49B LYS* 5.1 8.5 - - + -
50B PHE* 3.7 28.9 - + - -
97B VAL* 5.3 0.2 - - + -
122B VAL* 4.0 16.4 - - + -
123B PRO 3.6 8.3 - - - -
124B THR* 3.5 45.8 - - + +
160B ASP* 3.0 39.8 + - + +
162B ASP* 1.3 79.4 - - - +
164B LEU* 1.3 57.7 + - + +
165B LYS 3.3 0.2 - - - -
166B THR* 3.4 9.8 + - - -
401B NAD 2.5 26.0 + - - -
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B THR 3.5 11.4 - - - +
125B THR* 3.4 34.5 - - - +
126B ILE* 3.6 11.4 - - + +
159B TYR* 4.0 6.3 - - + +
161B LEU* 3.5 33.2 - - + +
162B ASP 3.1 1.0 - - - -
163B PHE* 1.3 77.4 - - + +
165B LYS* 1.3 63.4 + - - +
166B THR 3.2 0.4 - - - -
167B LEU* 3.1 30.2 + - + +
207B LEU* 3.8 21.7 - - + +
210B MET* 5.1 4.9 - - + -
211B ASP* 5.7 2.2 - - - +
214B ILE* 3.6 30.5 - - + -
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Residues in contact with LYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B HIS* 4.0 14.1 + - + -
161B LEU 4.4 1.8 + - - +
162B ASP* 3.2 41.4 + - + +
164B LEU* 1.3 76.3 - - - +
166B THR* 1.3 63.0 + - + +
167B LEU 3.4 2.7 + - - +
207B LEU* 4.9 6.3 - - - +
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Residues in contact with THR 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B TYR* 3.4 41.4 + - + -
46B PHE* 3.1 24.0 - - + -
162B ASP 5.9 0.2 - - - +
163B PHE 3.4 1.9 + - - -
164B LEU 3.1 0.4 + - - -
165B LYS* 1.3 80.8 - - + +
167B LEU* 1.3 60.7 + - - +
168B PRO* 3.4 3.1 - - - +
401B NAD 2.7 34.0 + - - -
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B THR 4.1 0.2 - - - +
125B THR* 3.8 15.0 - - + -
126B ILE* 3.7 45.8 - - + +
164B LEU* 3.1 32.1 + - + +
165B LYS 3.4 2.7 - - - +
166B THR* 1.3 76.8 - - - +
168B PRO* 1.3 75.6 - - - +
169B PHE 3.6 0.2 + - - -
171B GLN* 4.0 18.6 - - + +
172B ILE* 3.6 20.2 - - + +
207B LEU* 5.6 0.2 - - + -
401B NAD 3.5 36.8 - - + +
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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