Contacts of the helix formed by residues 134 - 157 (chain F) in PDB entry 5WUA
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 LYS 134 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F PHE* 2.7 15.7 + - + +
133F PRO* 1.3 76.9 - - - +
135F LEU* 1.3 64.3 + - + +
137F ILE* 4.4 0.3 - - - +
138F ALA* 3.8 13.3 + - - +
192F VAL* 5.0 10.9 - - - +
193F ARG* 6.1 0.2 - - - -
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Residues in contact with LEU 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F PHE 4.6 0.8 + - - -
134F LYS* 1.3 78.6 - - + +
136F LEU* 1.3 69.3 + - - +
138F ALA* 3.0 17.9 + - - +
139F LEU* 3.0 14.1 + - - +
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Residues in contact with LEU 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127F ILE* 3.8 28.7 - - + -
132F PHE 5.3 5.8 + - - +
133F PRO* 5.5 1.6 - - + -
134F LYS 3.6 1.0 - - - +
135F LEU* 1.3 78.1 - - - +
137F ILE* 1.3 63.5 + - - +
139F LEU* 3.2 9.1 + - - +
140F LEU* 3.0 22.8 + - - +
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Residues in contact with ILE 137 (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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127F ILE* 5.3 1.6 - - - +
133F PRO* 3.6 33.2 + - + +
134F LYS 4.2 0.8 + - - +
135F LEU 3.3 0.2 - - - -
136F LEU* 1.3 77.9 - - - +
138F ALA* 1.3 64.2 + - - +
140F LEU* 3.1 9.1 + - - +
141F ILE* 2.9 20.9 + - - +
186F GLU* 6.2 4.0 - - + -
192F VAL* 4.6 9.9 - - + -
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Residues in contact with ALA 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F LYS 3.8 8.7 + - - +
135F LEU* 3.0 15.9 + - - +
137F ILE* 1.3 75.8 - - - +
139F LEU* 1.3 54.7 + - - +
141F ILE* 2.6 32.2 + - - +
142F TYR* 2.9 9.9 + - - +
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Residues in contact with LEU 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F PHE* 6.1 5.4 - - + -
135F LEU 3.0 11.5 + - - +
136F LEU* 3.6 10.5 - - - +
138F ALA* 1.3 74.8 - - - +
140F LEU* 1.3 59.2 + - - +
142F TYR* 2.8 27.8 + - - +
143F TRP* 3.0 12.6 + - - +
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Residues in contact with LEU 140 (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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136F LEU 3.0 12.6 + - - +
137F ILE* 3.4 12.1 - - - +
139F LEU* 1.3 76.2 - - - +
141F ILE* 1.3 61.5 + - - +
143F TRP* 3.3 7.2 + - - +
144F THR* 3.0 25.3 + - - -
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Residues in contact with ILE 141 (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 ILE 2.9 9.9 + - - +
138F ALA* 2.6 23.2 + - - +
140F LEU* 1.3 71.2 - - - +
142F TYR* 1.3 60.0 + - - +
144F THR* 3.5 6.8 + - - -
145F LEU* 2.9 24.1 + - - +
183F LEU* 5.1 13.4 - - + +
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Residues in contact with TYR 142 (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 ALA 2.9 7.7 + - - +
139F LEU* 2.8 18.1 + - - +
141F ILE* 1.3 76.7 - - - +
143F TRP* 1.3 64.1 + - - +
145F LEU* 2.9 10.2 + - - +
146F ALA* 2.9 22.0 + - - +
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Residues in contact with TRP 143 (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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37F VAL* 5.5 3.3 - - - +
41F PHE* 3.5 33.4 - - + -
139F LEU 3.0 10.5 + - - +
140F LEU* 3.9 8.7 - - - +
142F TYR* 1.3 73.4 - - - +
144F THR* 1.3 65.3 + - - +
146F ALA* 3.0 17.8 + - - +
147F PHE* 3.0 12.3 + - - +
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Residues in contact with THR 144 (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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140F LEU 3.0 17.7 + - - -
141F ILE* 3.7 7.4 - - - -
143F TRP* 1.3 76.1 - - - +
145F LEU* 1.3 65.3 + - - +
147F PHE* 3.3 16.3 - - - +
148F ILE* 4.0 2.9 + - - +
176F VAL 5.3 4.7 - - - +
179F TYR* 5.6 1.3 - - - -
180F GLY* 4.3 24.4 - - - -
183F LEU* 5.2 6.7 - - - -
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Residues in contact with LEU 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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141F ILE 2.9 14.2 + - - +
142F TYR* 2.9 11.8 + - - +
144F THR* 1.3 71.9 - - - +
146F ALA* 1.3 52.8 + - - +
147F PHE 2.7 4.2 + - - -
148F ILE* 2.5 41.4 + - - +
149F THR 4.0 0.9 + - - -
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Residues in contact with ALA 146 (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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37F VAL* 3.5 33.0 - - + +
142F TYR 2.9 16.8 + - - +
143F TRP* 3.0 6.2 + - - +
145F LEU* 1.3 72.0 - - - +
147F PHE* 1.3 61.5 + - - +
148F ILE 3.3 0.2 - - - -
149F THR* 3.8 16.3 + - - +
150F LYS* 4.0 3.3 + - - +
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Residues in contact with PHE 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F VAL* 4.5 3.3 - - - +
143F TRP 3.0 9.6 + - - +
144F THR* 3.3 16.4 - - - +
145F LEU 2.7 4.9 + - - -
146F ALA* 1.3 73.4 - - - +
148F ILE* 1.3 55.4 + - - +
150F LYS* 2.6 33.7 + - - +
151F THR* 3.0 10.6 + - - -
176F VAL* 4.6 21.5 - - + -
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Residues in contact with ILE 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F THR 4.0 2.8 + - - +
145F LEU* 2.5 21.4 + - - +
147F PHE* 1.3 73.4 - - - +
149F THR* 1.3 54.9 + - - +
151F THR* 3.3 11.3 + - - -
152F ILE* 2.9 26.7 + - - +
177F ILE* 6.4 3.4 - - + -
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Residues in contact with THR 149 (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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145F LEU 4.0 1.2 + - - -
146F ALA* 3.8 13.1 + - - -
147F PHE 3.1 0.6 - - - -
148F ILE* 1.3 78.9 - - - +
150F LYS* 1.3 62.2 + - - +
152F ILE* 3.0 11.1 + - - +
153F LYS* 2.9 19.8 + - - +
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Residues in contact with LYS 150 (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 VAL 5.4 1.3 - - - +
34F VAL* 3.6 37.3 - - + +
37F VAL* 6.0 1.3 - - + -
146F ALA 4.0 3.9 + - - +
147F PHE* 2.6 19.2 + - - +
149F THR* 1.3 73.7 - - - +
151F THR* 1.3 62.1 + - - +
153F LYS* 2.8 21.9 + - - +
154F PHE* 3.1 9.9 + - - +
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Residues in contact with THR 151 (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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147F PHE 3.0 7.6 + - - -
148F ILE* 3.4 15.3 - - - -
150F LYS* 1.3 76.9 - - - +
152F ILE* 1.3 63.4 + - - +
154F PHE* 2.9 20.6 + - - +
155F VAL* 2.9 10.0 + - - +
172F THR 5.5 0.7 - - - -
173F GLY* 4.1 27.6 - - - -
176F VAL* 6.1 3.4 - - - -
177F ILE* 6.4 0.4 - - - -
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Residues in contact with ILE 152 (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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148F ILE 2.9 14.0 + - - +
149F THR* 3.0 13.7 + - - +
151F THR* 1.3 74.7 - - - +
153F LYS* 1.3 55.7 + - - +
155F VAL* 2.4 33.6 + - + +
156F LYS* 2.9 12.0 + - - +
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Residues in contact with LYS 153 (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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30F ALA* 4.3 32.9 - - + +
33F VAL* 6.3 0.7 - - + -
34F VAL* 5.9 2.0 - - + +
149F THR 2.9 11.1 + - - +
150F LYS* 2.8 17.7 + - - +
152F ILE* 1.3 74.8 - - - +
154F PHE* 1.3 61.1 + - - +
156F LYS* 3.5 6.5 + - - +
157F PHE* 3.0 20.7 + - - +
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Residues in contact with PHE 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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150F LYS 3.1 6.8 + - - +
151F THR* 2.9 17.9 + - - +
153F LYS* 1.3 77.5 - - - +
155F VAL* 1.3 56.4 + - - +
157F PHE* 2.9 25.7 + - + +
158F TYR* 3.0 12.0 + - - +
169F PHE* 4.8 20.4 - - + -
170F CYS* 4.8 14.6 - - + +
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Residues in contact with VAL 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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151F THR 2.9 6.5 + - - +
152F ILE* 2.4 37.5 + - + +
154F PHE* 1.3 68.9 - - - +
156F LYS* 1.3 54.2 + - - -
158F TYR* 3.0 24.4 - - - +
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Residues in contact with LYS 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152F ILE 2.9 9.4 + - - +
153F LYS* 4.1 7.6 - - - +
155F VAL* 1.3 72.7 - - - +
157F PHE* 1.3 58.5 + - - +
158F TYR* 2.9 9.9 + - - +
159F ASP* 4.0 9.4 + - - +
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Residues in contact with PHE 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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153F LYS 3.0 15.3 + - - +
154F PHE* 2.9 17.6 + - + +
156F LYS* 1.3 75.5 - - - +
158F TYR* 1.3 55.4 + - - +
159F ASP* 3.1 9.5 + - - +
160F HIS* 4.1 7.8 + - - +
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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) + - + + + + + -
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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