Contacts of the helix formed by residues 173 - 178 (chain B) in PDB entry 1I0H
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 TYR 173 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ASP* 5.8 1.6 - - - -
22B THR* 5.4 1.6 - - - -
168B VAL* 3.4 13.9 + - - -
169B TRP 3.4 21.5 - - - -
170B GLU* 3.0 25.1 + - + +
172B ALA* 1.3 78.0 - - - +
174B PHE* 1.3 59.5 + - - +
175B LEU 3.5 2.0 - - - -
176B LYS 4.3 1.1 - - - -
177B PHE* 2.8 46.7 + - + +
178B GLN 3.3 28.5 + - - -
179B ASN* 4.4 8.9 + - - -
181B ARG* 3.0 57.5 + - + +
184B TYR* 3.4 40.6 - + + -
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Residues in contact with PHE 174 (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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22A THR* 5.3 2.5 - - + -
25A ILE* 4.2 25.4 - - + -
30A HIS* 3.8 16.2 - + - -
171A HIS* 3.8 43.1 - - + -
174A PHE* 3.8 30.5 - + + -
175A LEU* 3.4 36.8 - - + -
22B THR* 5.4 0.2 + - - -
170B GLU* 2.9 22.2 + - + +
171B HIS* 4.2 2.2 + - - -
172B ALA 3.9 0.6 - - - -
173B TYR* 1.3 77.9 - - - +
175B LEU* 1.3 68.3 + - - +
178B GLN* 2.8 43.9 + - - +
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Residues in contact with LEU 175 (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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174A PHE* 3.6 21.0 - - + -
175A LEU* 3.7 29.8 - - + -
19B ASP* 3.8 5.4 - - - +
21B GLN* 3.7 42.8 - - + +
22B THR* 3.5 23.8 + - - +
25B ILE* 4.2 11.9 - - + -
171B HIS 5.4 0.2 + - - -
173B TYR 3.5 0.6 - - - -
174B PHE* 1.3 80.2 - - - +
176B LYS* 1.3 60.0 + - - +
178B GLN* 5.1 3.8 - - - +
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Residues in contact with LYS 176 (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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15B GLU* 5.0 2.6 + - - -
16B PRO 2.6 30.5 + - - -
17B HIS* 3.0 16.6 + - - +
18B PHE 5.0 0.2 - - - -
19B ASP* 3.5 35.4 + - + +
173B TYR 3.6 1.8 + - - -
174B PHE 3.2 0.2 - - - -
175B LEU* 1.3 80.5 - - - +
177B PHE* 1.3 95.3 + - + +
178B GLN* 3.7 1.9 - - - +
180B ARG* 3.2 15.1 + - - -
187B GLU* 4.9 5.7 + - - -
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Residues in contact with PHE 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B HIS 3.7 12.8 - - - -
18B PHE* 5.0 2.7 - + - -
19B ASP* 4.9 4.0 - - - -
173B TYR* 2.8 38.9 + - + +
176B LYS* 1.3 115.3 - - + +
178B GLN* 1.3 72.1 + - - +
179B ASN 3.0 0.5 + - - -
180B ARG* 2.8 50.3 + - - +
183B ASP* 3.9 18.2 - - + -
184B TYR* 3.6 42.2 - + + -
187B GLU* 3.9 15.5 - - + -
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Residues in contact with GLN 178 (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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21A GLN* 4.8 1.4 + - - -
25A ILE* 3.1 48.2 - - + +
29A LYS* 4.2 23.8 + - + +
30A HIS* 4.7 1.7 + - + -
170B GLU* 6.1 0.2 - - - +
173B TYR* 3.3 26.8 + - - +
174B PHE* 2.8 43.2 + - + +
175B LEU 5.1 4.0 - - - +
176B LYS 5.1 1.1 - - - +
177B PHE* 1.3 77.4 - - - +
179B ASN* 1.3 62.4 + - + +
180B ARG* 5.1 9.7 + - + +
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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