Contacts of the helix formed by residues 125 - 135 (chain F) in PDB entry 5ITZ
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 HIS 125 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B ASP* 2.9 42.8 + - - +
181B VAL* 3.5 18.3 - - + +
88F ALA 2.9 25.8 - - - -
89F LEU 2.6 22.7 + - - -
90F ILE 3.5 1.2 - - - -
91F GLY* 3.3 22.3 + - - -
120F ALA* 2.8 12.3 + - - +
123F MET* 3.4 18.0 - - + +
124F GLY* 1.3 72.8 - - - +
126F LEU* 1.3 60.0 + - - +
127F GLU 3.4 2.2 - - - -
128F ILE* 3.1 20.7 + - + -
129F VAL* 2.8 28.2 + - - +
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Residues in contact with LEU 126 (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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176B LYS* 5.8 12.1 - - + -
121F ALA* 5.2 4.0 - - - +
124F GLY* 3.1 26.6 + - - +
125F HIS* 1.3 70.5 - - - +
127F GLU* 1.3 66.7 + - - +
129F VAL* 3.3 18.2 + - + +
130F GLU* 3.0 29.7 + - + +
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Residues in contact with GLU 127 (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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93F LEU* 4.0 29.1 - - + +
125F HIS 3.4 0.4 - - - -
126F LEU* 1.3 77.0 - - - +
128F ILE* 1.3 58.0 + - + +
130F GLU* 3.3 9.2 + - - +
131F VAL* 3.0 31.8 + - + +
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Residues in contact with ILE 128 (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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87F ALA 4.3 1.1 - - - +
88F ALA* 4.3 5.4 - - - +
91F GLY* 3.3 44.2 - - - +
92F HIS 3.7 3.8 - - - +
93F LEU* 3.8 28.9 - - + +
96F VAL* 4.1 20.2 - - + -
120F ALA* 3.7 19.1 - - + -
125F HIS* 3.1 17.7 + - + +
127F GLU* 1.3 75.3 - - + +
129F VAL* 1.3 65.9 + - - +
131F VAL* 3.0 7.7 + - - +
132F LEU* 2.9 36.6 + - + +
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Residues in contact with VAL 129 (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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117F LEU* 3.5 23.8 - - + +
120F ALA* 3.7 7.0 - - + +
121F ALA* 3.6 39.3 - - + +
125F HIS 2.8 17.6 + - - +
126F LEU* 3.3 18.1 + - + +
128F ILE* 1.3 77.3 - - - +
130F GLU* 1.3 76.8 + - - +
132F LEU 3.4 0.3 + - - -
133F LEU* 3.0 30.8 + - + +
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Residues in contact with GLU 130 (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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126F LEU* 3.0 18.2 + - + +
127F GLU* 3.5 9.9 - - - +
128F ILE 3.1 0.2 - - - -
129F VAL* 1.3 86.9 - - - +
131F VAL* 1.3 59.6 + - + +
133F LEU* 3.1 21.6 + - - +
134F LYS* 2.8 45.9 + - + +
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Residues in contact with VAL 131 (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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93F LEU* 3.5 20.9 - - + -
96F VAL* 4.0 8.1 - - + -
97F GLU* 3.9 28.7 - - + +
100F LEU* 3.7 23.6 - - + -
127F GLU 3.0 18.9 + - - +
128F ILE* 3.0 9.6 + - - +
130F GLU* 1.3 74.1 - - + +
132F LEU* 1.3 63.3 + - - +
134F LYS* 3.1 13.7 + - - +
135F HIS* 2.8 31.9 + - + +
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Residues in contact with LEU 132 (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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84F LEU* 4.1 16.6 - - + -
88F ALA* 4.4 1.6 - - + -
96F VAL* 4.1 9.4 - - + -
100F LEU* 4.0 20.6 - - + -
106F VAL* 4.0 17.1 - - + +
116F PRO* 3.8 8.7 - - + +
117F LEU* 3.5 38.1 - - + +
120F ALA* 4.4 1.6 - - + -
128F ILE* 2.9 35.9 + - + +
129F VAL 3.8 3.4 - - - +
131F VAL* 1.3 77.4 - - - +
133F LEU* 1.3 61.5 + - - +
135F HIS* 2.9 14.6 + - - +
136F GLY 3.3 0.5 + - - -
137F ALA* 3.0 30.6 + - + +
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Residues in contact with LEU 133 (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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117F LEU* 4.3 14.8 - - + -
129F VAL* 3.0 25.8 + - + +
130F GLU* 3.1 33.0 + - - +
132F LEU* 1.3 76.2 - - - +
134F LYS* 1.3 61.5 + - + +
135F HIS 3.3 0.3 + - - -
136F GLY* 3.4 10.0 + - - -
137F ALA* 4.1 18.7 + - + +
138F ASP 5.5 1.1 - - - +
139F VAL* 5.5 10.3 - - + -
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Residues in contact with LYS 134 (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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130F GLU* 2.8 30.1 + - + +
131F VAL* 3.1 12.3 + - - +
133F LEU* 1.3 77.2 - - + +
135F HIS* 1.3 68.6 + - + +
136F GLY 3.4 2.0 + - - -
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Residues in contact with HIS 135 (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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97F GLU* 5.3 7.3 + - + -
100F LEU* 3.7 44.4 - - + +
101F LYS* 5.7 0.8 + - - -
106F VAL* 3.6 15.5 - - + +
131F VAL* 2.8 34.1 + - + +
132F LEU 2.9 10.3 + - - +
134F LYS* 1.3 85.6 - - + +
136F GLY* 1.3 59.5 + - - +
137F ALA 3.5 0.3 + - - -
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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