Contacts of the helix formed by residues 153 - 161 (chain F) in PDB entry 1H4O
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 LEU 153 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50F THR* 4.0 24.7 - - + +
51F HIS* 3.6 25.6 - - + +
55F PHE* 4.0 1.8 - - - -
129F SER* 5.0 0.2 + - - -
149F LEU* 3.6 48.2 - - + +
150F THR* 3.3 15.2 + - - +
151F CYS 3.4 0.2 - - - -
152F SER* 1.3 84.9 - - - +
154F ALA* 1.3 67.5 + - - +
155F PRO* 3.3 13.5 - - + -
156F ASN* 3.1 14.5 + - - +
157F ILE* 3.6 7.1 + - - +
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Residues in contact with ALA 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F HIS* 5.1 0.6 + - - -
54F GLY* 3.7 30.6 - - - +
55F PHE* 3.5 35.9 - - + -
58F GLN* 3.8 13.5 - - + -
62F LEU* 5.2 1.1 - - + -
153F LEU* 1.3 72.4 - - - +
155F PRO* 1.3 70.4 - - + +
157F ILE* 3.1 14.7 + - + +
158F ILE* 3.2 15.5 + - - +
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Residues in contact with PRO 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F GLY* 5.9 2.0 - - - -
58F GLN* 3.9 19.3 - - - +
153F LEU* 3.4 16.2 - - + -
154F ALA* 1.3 93.1 - - + +
156F ASN* 1.3 60.8 + - - +
158F ILE* 3.3 18.3 + - + +
159F SER* 3.3 12.8 + - - -
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Residues in contact with ASN 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F ASN* 3.4 17.8 + - - -
150F THR 4.7 3.1 - - - +
151F CYS* 2.9 44.3 + - - +
153F LEU* 3.1 7.1 + - - +
155F PRO* 1.3 78.6 - - - +
157F ILE* 1.3 63.2 + - - +
159F SER* 2.8 28.9 + - - -
160F GLN* 3.4 19.6 + - - +
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Residues in contact with ILE 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F VAL* 4.1 11.2 - - + -
55F PHE* 4.0 14.6 - - + -
62F LEU* 3.7 24.2 - - + -
129F SER* 3.6 28.3 - - - +
130F MET 3.8 20.2 - - - +
131F VAL* 3.5 30.3 - - + +
141F ASN* 4.1 5.3 - - - +
153F LEU 3.6 6.1 + - - +
154F ALA 3.1 12.5 + - - +
156F ASN* 1.3 77.6 - - - +
158F ILE* 1.3 60.4 + - - +
160F GLN* 2.7 34.0 + - - +
161F LEU* 3.1 16.7 + - + +
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Residues in contact with ILE 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F GLN* 4.8 11.9 - - + +
61F ALA* 3.8 26.2 - - + +
62F LEU* 3.1 41.3 - - + +
65F LYS* 3.9 25.7 + - + -
154F ALA 3.2 16.1 + - - +
155F PRO* 3.5 10.5 - - + +
157F ILE* 1.3 76.0 - - - +
159F SER* 1.3 62.1 + - - +
160F GLN 3.2 1.0 + - - -
161F LEU* 3.2 22.3 + - + +
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Residues in contact with SER 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F PRO 3.3 7.9 + - - -
156F ASN* 2.8 30.3 + - - -
157F ILE 3.1 0.8 - - - -
158F ILE* 1.3 80.9 - - - +
160F GLN* 1.3 59.0 + - - +
161F LEU* 3.5 3.6 - - - +
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Residues in contact with GLN 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F VAL* 5.0 4.1 - - + +
139F ALA* 3.9 26.2 - - + +
140F LEU 5.6 0.2 - - - +
141F ASN* 2.8 44.9 + - - -
156F ASN* 3.4 21.5 + - - +
157F ILE* 2.7 26.8 + - + +
159F SER* 1.3 72.9 - - - +
161F LEU* 1.3 62.6 + - - +
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Residues in contact with LEU 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LYS* 3.9 31.6 + - + +
35F VAL* 5.1 1.6 - - + -
62F LEU* 3.8 22.0 - - + -
65F LYS* 3.9 36.3 + - + +
67F VAL* 3.6 33.9 - - + -
131F VAL* 3.7 32.8 - - + -
157F ILE* 3.1 16.8 + - + +
158F ILE* 3.2 16.3 + - - +
159F SER 4.4 3.6 - - - +
160F GLN* 1.3 82.6 - - - +
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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