Contacts of the helix formed by residues 113 - 145 (chain F) in PDB entry 5KHU
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 SER 113 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112F ASP* 3.7 30.3 - - - +
114F ALA* 3.8 28.7 - - - +
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Residues in contact with ALA 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F SER* 3.8 23.8 - - - +
115F CYS* 3.8 29.2 - - - +
117F THR* 4.3 18.4 - - - +
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Residues in contact with CYS 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F ALA* 3.8 26.0 - - - +
116F PHE* 3.7 29.4 - - - +
141F SER* 4.1 26.5 - - - +
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Residues in contact with PHE 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F CYS* 3.7 29.8 - - - +
117F THR* 3.8 25.1 - - - +
119F SER* 4.3 17.5 - - - +
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Residues in contact with THR 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F ALA* 4.3 19.3 - - - +
116F PHE* 3.8 26.0 - - - +
118F LEU* 3.7 29.2 - - - +
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Residues in contact with LEU 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F THR* 3.7 29.6 - - - +
119F SER* 3.8 24.7 - - - +
121F LEU* 4.2 20.9 - - - +
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Residues in contact with SER 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F PHE* 4.3 19.3 - - - +
118F LEU* 3.8 25.4 - - - +
120F LEU* 3.7 29.8 - - - +
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Residues in contact with LEU 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F SER* 3.7 30.3 - - - +
121F LEU* 3.8 25.8 - - - +
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Residues in contact with LEU 121 (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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118F LEU* 4.2 18.2 - - - +
120F LEU* 3.8 24.0 - - - +
122F GLY* 3.7 29.8 - - - +
124F VAL* 4.3 15.7 - - - +
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Residues in contact with GLY 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F LEU* 3.7 29.4 - - - +
123F HIS* 3.8 26.7 - - - +
134F GLY* 4.3 24.0 - - - +
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Residues in contact with HIS 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F GLY* 3.8 24.2 - - - +
124F VAL* 3.8 29.8 - - - +
126F CYS* 4.3 15.9 - - - +
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Residues in contact with VAL 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F LEU* 4.3 18.6 - - - +
123F HIS* 3.8 26.5 - - - +
125F TYR* 3.7 29.4 - - - +
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Residues in contact with TYR 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F VAL* 3.7 29.2 - - - +
126F CYS* 3.7 24.7 - - - +
128F THR* 4.3 18.4 - - - +
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Residues in contact with CYS 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F HIS* 4.3 19.1 - - - +
125F TYR* 3.7 29.4 - - - +
127F LYS* 3.8 25.6 - - - +
----------------------------------------------------------
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Residues in contact with LYS 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F CYS* 3.8 24.7 - - - +
128F THR* 3.8 29.4 - - - +
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Residues in contact with THR 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F TYR* 4.3 19.1 - - - +
127F LYS* 3.8 28.9 - - - +
129F ASP* 3.8 29.6 - - - +
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Residues in contact with ASP 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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128F THR* 3.8 29.2 - - - +
130F ARG* 3.8 27.6 - - - +
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Residues in contact with ARG 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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129F ASP* 3.8 28.3 - - - +
131F LEU* 3.8 29.6 - - - +
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Residues in contact with LEU 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F ARG* 3.8 29.2 - - - +
132F ALA* 3.8 27.8 - - - +
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Residues in contact with ALA 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F LEU* 3.8 26.7 - - - +
133F LYS* 3.8 28.9 - - - +
135F SER* 4.5 15.9 - - - +
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Residues in contact with LYS 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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132F ALA* 3.8 25.4 - - - +
134F GLY* 3.8 29.4 - - - +
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Residues in contact with GLY 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F GLY* 4.3 24.2 - - - +
133F LYS* 3.8 29.6 - - - +
135F SER* 3.8 26.5 - - - +
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Residues in contact with SER 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F ALA* 4.5 15.7 - - - +
134F GLY* 3.8 27.1 - - - +
136F GLU* 3.8 29.2 - - - +
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Residues in contact with GLU 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135F SER* 3.8 28.9 - - - +
137F CYS* 3.8 26.7 - - - +
----------------------------------------------------------
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Residues in contact with CYS 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F GLU* 3.8 25.1 - - - +
138F TYR* 3.8 29.8 - - - +
140F LYS* 4.3 17.5 - - - +
----------------------------------------------------------
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Residues in contact with TYR 138 (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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137F CYS* 3.8 26.2 - - - +
139F GLN* 3.8 29.4 - - - +
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Residues in contact with GLN 139 (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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138F TYR* 3.8 29.4 - - - +
140F LYS* 3.8 25.4 - - - +
142F LEU* 4.4 17.0 - - - +
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Residues in contact with LYS 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F CYS* 4.3 17.7 - - - +
139F GLN* 3.8 25.4 - - - +
141F SER* 3.7 29.4 - - - +
----------------------------------------------------------
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Residues in contact with SER 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F CYS* 4.1 26.5 - - - +
140F LYS* 3.7 29.8 - - - +
142F LEU* 3.8 26.5 - - - +
----------------------------------------------------------
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Residues in contact with LEU 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F GLN* 4.4 15.5 - - - +
141F SER* 3.8 25.4 - - - +
143F SER* 3.8 29.4 - - - +
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Residues in contact with SER 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142F LEU* 3.8 26.5 - - - +
144F LEU* 3.7 29.2 - - - +
----------------------------------------------------------
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Residues in contact with LEU 144 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F SER* 3.7 29.4 - - - +
145F ASN* 3.8 25.8 - - - +
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Residues in contact with ASN 145 (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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144F LEU* 3.8 29.4 - - - +
146F PRO* 3.8 28.9 - - - -
----------------------------------------------------------
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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