Contacts of the helix formed by residues 134 - 162 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133X PRO* 3.8 29.4 - - - -
135X GLU* 3.8 28.7 - - - +
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Residues in contact with GLU 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134X SER* 3.8 26.7 - - - +
136X ILE* 3.8 29.2 - - - +
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Residues in contact with ILE 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135X GLU* 3.8 28.9 - - - +
137X GLU* 3.8 28.7 - - - +
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Residues in contact with GLU 137 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136X ILE* 3.8 25.1 - - - +
138X VAL* 3.8 28.9 - - - +
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Residues in contact with VAL 138 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X GLU* 3.8 29.4 - - - +
139X LYS* 3.8 26.0 - - - +
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Residues in contact with LYS 139 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138X VAL* 3.8 29.2 - - - +
140X TYR* 3.8 24.9 - - - +
142X MET* 4.5 14.8 - - - +
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Residues in contact with TYR 140 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139X LYS* 3.8 26.7 - - - +
141X LYS* 3.8 29.6 - - - +
143X ALA* 4.7 13.5 - - - +
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Residues in contact with LYS 141 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140X TYR* 3.8 24.5 - - - +
142X MET* 3.8 28.7 - - - +
144X GLU* 4.3 16.2 - - - +
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Residues in contact with MET 142 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139X LYS* 4.5 16.2 - - - +
141X LYS* 3.8 29.4 - - - +
143X ALA* 3.8 25.8 - - - +
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Residues in contact with ALA 143 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140X TYR* 4.7 12.6 - - - +
142X MET* 3.8 29.8 - - - +
144X GLU* 3.8 24.7 - - - +
155X ALA* 4.4 22.4 - - - +
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Residues in contact with GLU 144 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141X LYS* 4.3 18.6 - - - +
143X ALA* 3.8 25.4 - - - +
145X CYS* 3.8 29.4 - - - +
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Residues in contact with CYS 145 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144X GLU* 3.8 29.8 - - - +
146X TYR* 3.8 26.5 - - - +
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Residues in contact with TYR 146 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145X CYS* 3.8 25.1 - - - +
147X THR* 3.7 30.3 - - - +
149X LEU* 4.0 20.0 - - - +
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Residues in contact with THR 147 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146X TYR* 3.7 29.2 - - - +
148X MET* 3.8 25.8 - - - +
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Residues in contact with MET 148 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147X THR* 3.8 25.1 - - - +
149X LEU* 3.8 29.8 - - - +
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Residues in contact with LEU 149 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146X TYR* 4.0 19.7 - - - +
148X MET* 3.8 28.9 - - - +
150X LYS* 3.8 25.6 - - - +
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Residues in contact with LYS 150 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149X LEU* 3.8 29.6 - - - +
151X GLN* 3.8 25.4 - - - +
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Residues in contact with GLN 151 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150X LYS* 3.8 29.8 - - - +
152X ASP* 3.8 29.8 - - - +
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Residues in contact with ASP 152 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151X GLN* 3.8 29.2 - - - +
153X LYS* 3.8 29.4 - - - +
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Residues in contact with LYS 153 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152X ASP* 3.8 24.7 - - - +
154X ASP* 3.8 29.6 - - - +
156X ILE* 4.7 14.8 - - - +
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Residues in contact with ASP 154 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153X LYS* 3.8 28.9 - - - +
155X ALA* 3.8 28.5 - - - +
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Residues in contact with ALA 155 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143X ALA* 4.4 21.8 - - - +
154X ASP* 3.8 25.1 - - - +
156X ILE* 3.8 28.9 - - - +
158X ILE* 4.4 17.0 - - - +
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Residues in contact with ILE 156 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153X LYS* 4.7 15.9 - - - +
155X ALA* 3.8 28.9 - - - +
157X ALA* 3.8 26.5 - - - +
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Residues in contact with ALA 157 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156X ILE* 3.8 28.7 - - - +
158X ILE* 3.8 25.6 - - - +
160X ASP* 4.3 18.2 - - - +
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Residues in contact with ILE 158 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155X ALA* 4.4 17.9 - - - +
157X ALA* 3.8 25.1 - - - +
159X LEU* 3.8 29.8 - - - +
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Residues in contact with LEU 159 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158X ILE* 3.8 26.0 - - - +
160X ASP* 3.8 29.8 - - - +
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Residues in contact with ASP 160 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157X ALA* 4.3 18.2 - - - +
159X LEU* 3.8 30.5 - - - +
161X GLY* 3.8 23.8 - - - +
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Residues in contact with GLY 161 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160X ASP* 3.8 29.2 - - - +
162X ILE* 3.8 24.9 - - - +
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Residues in contact with ILE 162 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161X GLY* 3.8 28.9 - - - +
163X PRO* 3.8 28.7 - - - -
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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