Contacts of the helix formed by residues 134 - 162 (chain Y) 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 134 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133Y PRO* 3.8 28.7 - - - -
135Y GLU* 3.8 29.4 - - - +
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Residues in contact with GLU 135 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134Y SER* 3.8 25.6 - - - +
136Y ILE* 3.8 29.2 - - - +
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Residues in contact with ILE 136 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135Y GLU* 3.8 29.2 - - - +
137Y GLU* 3.8 25.8 - - - +
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Residues in contact with GLU 137 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136Y ILE* 3.8 25.4 - - - +
138Y VAL* 3.8 29.6 - - - +
140Y TYR* 4.6 14.1 - - - +
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Residues in contact with VAL 138 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137Y GLU* 3.8 29.4 - - - +
139Y LYS* 3.8 26.0 - - - +
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Residues in contact with LYS 139 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138Y VAL* 3.8 29.4 - - - +
140Y TYR* 3.8 24.7 - - - +
142Y MET* 4.4 16.4 - - - +
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Residues in contact with TYR 140 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137Y GLU* 4.6 16.8 - - - +
139Y LYS* 3.8 25.4 - - - +
141Y LYS* 3.8 28.7 - - - +
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Residues in contact with LYS 141 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140Y TYR* 3.8 29.6 - - - +
142Y MET* 3.8 25.8 - - - +
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Residues in contact with MET 142 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139Y LYS* 4.4 19.3 - - - +
141Y LYS* 3.8 25.4 - - - +
143Y ALA* 3.8 29.6 - - - +
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Residues in contact with ALA 143 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142Y MET* 3.8 28.9 - - - +
144Y GLU* 3.8 26.2 - - - +
155Y ALA* 4.0 27.4 - - - +
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Residues in contact with GLU 144 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143Y ALA* 3.8 25.4 - - - +
145Y CYS* 3.8 28.7 - - - +
147Y THR* 4.5 14.8 - - - +
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Residues in contact with CYS 145 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144Y GLU* 3.8 29.2 - - - +
146Y TYR* 3.8 25.8 - - - +
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Residues in contact with TYR 146 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145Y CYS* 3.8 29.4 - - - +
147Y THR* 3.8 24.0 - - - +
149Y LEU* 4.5 16.8 - - - +
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Residues in contact with THR 147 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144Y GLU* 4.5 18.4 - - - +
146Y TYR* 3.8 26.7 - - - +
148Y MET* 3.8 28.9 - - - +
150Y LYS* 4.6 12.3 - - - +
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Residues in contact with MET 148 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147Y THR* 3.8 29.4 - - - +
149Y LEU* 3.8 26.2 - - - +
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Residues in contact with LEU 149 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146Y TYR* 4.5 15.7 - - - +
148Y MET* 3.8 28.7 - - - +
150Y LYS* 3.8 23.8 - - - +
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Residues in contact with LYS 150 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147Y THR* 4.6 15.3 - - - +
149Y LEU* 3.8 27.1 - - - +
151Y GLN* 3.8 28.9 - - - +
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Residues in contact with GLN 151 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150Y LYS* 3.8 28.5 - - - +
152Y ASP* 3.8 29.4 - - - +
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Residues in contact with ASP 152 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151Y GLN* 3.8 29.4 - - - +
153Y LYS* 3.8 27.4 - - - +
155Y ALA* 4.4 17.9 - - - +
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Residues in contact with LYS 153 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152Y ASP* 3.8 24.0 - - - +
154Y ASP* 3.8 29.4 - - - +
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Residues in contact with ASP 154 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153Y LYS* 3.8 29.4 - - - +
155Y ALA* 3.8 25.6 - - - +
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Residues in contact with ALA 155 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143Y ALA* 4.0 27.4 - - - +
152Y ASP* 4.4 14.8 - - - +
154Y ASP* 3.8 29.6 - - - +
156Y ILE* 3.8 26.2 - - - +
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Residues in contact with ILE 156 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155Y ALA* 3.8 28.7 - - - +
157Y ALA* 3.8 26.5 - - - +
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Residues in contact with ALA 157 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156Y ILE* 3.8 25.1 - - - +
158Y ILE* 3.8 29.2 - - - +
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Residues in contact with ILE 158 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157Y ALA* 3.8 27.4 - - - +
159Y LEU* 3.8 29.8 - - - +
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Residues in contact with LEU 159 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158Y ILE* 3.8 29.4 - - - +
160Y ASP* 3.8 28.7 - - - +
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Residues in contact with ASP 160 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159Y LEU* 3.8 28.7 - - - +
161Y GLY* 3.8 25.1 - - - +
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Residues in contact with GLY 161 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160Y ASP* 3.8 28.9 - - - +
162Y ILE* 3.8 25.6 - - - +
----------------------------------------------------------
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Residues in contact with ILE 162 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161Y GLY* 3.8 29.4 - - - +
163Y PRO* 3.8 28.5 - - - -
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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
------------------------------------------------------------
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