Contacts of the helix formed by residues 149 - 161 (chain B) in PDB entry 5FDK
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 ALA 149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B MET* 5.8 0.7 - - + -
128B LYS* 3.6 25.4 - - + -
134B CYS* 3.3 33.7 + - + +
135B PHE* 4.4 3.6 - - - +
147B LEU 4.4 1.1 - - - -
148B GLU* 1.3 80.1 - - - +
150B ASP* 1.3 58.6 + - - +
152B LEU* 3.3 11.0 - - + +
153B PHE* 2.9 41.9 + - + -
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Residues in contact with ASP 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LYS* 4.9 11.7 - - + +
148B GLU* 3.2 22.4 - - - +
149B ALA* 1.3 72.6 - - - +
151B LYS* 1.3 67.1 + - - +
153B PHE* 3.3 23.0 - - + +
154B TYR* 2.8 27.0 + - - +
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Residues in contact with LYS 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LEU* 3.9 13.2 - - + -
148B GLU* 3.5 25.3 + - + +
149B ALA 3.4 0.4 - - - -
150B ASP* 1.3 79.9 + - - +
152B LEU* 1.3 57.3 + - - +
154B TYR* 2.7 30.3 + - + +
155B PHE* 2.9 20.6 + - + -
174B GLU* 5.5 2.4 + - - +
175B THR* 3.0 40.7 + - - +
177B TYR* 5.8 3.8 - - - -
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B GLU* 6.4 0.2 - - + -
113B LEU* 4.3 17.9 - - + -
116B PHE* 4.0 31.2 - - + -
121B ILE* 3.8 28.7 - - + -
136B VAL* 4.2 13.2 - - + +
147B LEU* 4.1 18.2 - - + +
148B GLU 3.2 10.3 + - - +
149B ALA* 3.3 14.6 - - - +
151B LYS* 1.3 78.0 - - - +
153B PHE* 1.3 69.5 + - + +
155B PHE* 3.1 9.5 + - - +
156B TRP* 2.8 24.7 + - + +
167B ILE* 4.7 2.0 - - + -
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Residues in contact with PHE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE* 3.9 24.5 - - + -
124B MET* 4.1 11.7 - - + -
125B LYS* 3.7 55.0 - - + +
128B LYS* 4.4 16.2 - - + -
149B ALA* 2.9 34.0 + - + -
150B ASP* 3.3 25.8 - - + +
151B LYS 3.1 0.2 - - - -
152B LEU* 1.3 79.7 - - + +
154B TYR* 1.3 65.8 + - - +
156B TRP* 3.0 6.4 + - - +
157B ASP* 2.9 25.8 + - - +
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Residues in contact with TYR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ASP 2.8 13.0 + - - +
151B LYS* 2.7 17.1 + - + +
153B PHE* 1.3 77.3 - - - +
155B PHE* 1.3 76.4 + + - -
157B ASP* 3.6 4.0 + - - +
158B ARG* 3.0 38.0 + - + +
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Residues in contact with PHE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU* 3.8 9.4 - - + +
147B LEU* 4.9 4.5 - - + -
151B LYS* 2.9 34.5 + - + -
152B LEU* 3.5 6.7 - - - +
154B TYR* 1.3 89.9 - + - +
156B TRP* 1.3 65.2 + - - +
158B ARG* 3.2 43.2 + - - +
159B LYS* 3.0 22.5 + - - +
167B ILE* 3.3 47.3 - - + -
171B GLU* 4.3 15.0 - - + -
172B LEU* 5.9 0.4 - - + -
175B THR* 3.8 30.5 - - - -
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Residues in contact with TRP 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU* 3.6 30.3 - - + +
116B PHE* 3.2 39.5 - + + -
117B HIS 4.4 0.7 - - - -
118B ASP* 3.2 37.1 + - - -
121B ILE* 3.5 39.7 - - + +
125B LYS* 5.7 6.7 - - - -
152B LEU* 2.8 15.9 + - + +
153B PHE* 3.6 10.3 - - - +
155B PHE* 1.3 73.5 - - - +
157B ASP* 1.3 63.9 + - - +
159B LYS* 3.2 9.9 + - + +
160B GLU* 2.9 31.3 + - + +
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Residues in contact with ASP 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LYS* 6.1 3.1 - - - +
153B PHE 2.9 15.7 + - - +
154B TYR* 4.1 4.5 - - + +
156B TRP* 1.3 76.9 - - + +
158B ARG* 1.3 57.9 + - - +
160B GLU* 2.5 32.2 + - - +
161B LYS* 2.7 28.3 + - - +
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Residues in contact with ARG 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU* 5.8 0.2 - - - +
154B TYR* 3.0 26.9 + - + +
155B PHE* 3.2 46.8 + - - +
157B ASP* 1.3 80.2 + - - +
159B LYS* 1.3 62.5 + - - +
160B GLU 3.3 0.2 + - - -
161B LYS* 3.5 10.6 + - - +
163B GLY* 3.2 18.1 + - - -
164B ARG* 4.4 29.3 + - - +
166B SER 3.3 23.2 + - - -
167B ILE* 4.2 4.9 - - - +
168B ARG 4.8 3.6 - - - +
171B GLU* 5.1 4.0 - - - +
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Residues in contact with LYS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU* 4.3 12.1 - - + -
155B PHE 3.0 13.4 + - - +
156B TRP* 3.6 10.5 - - + +
158B ARG* 1.3 75.7 - - - +
160B GLU* 1.3 60.6 + - - +
162B ASN* 3.8 3.1 + - - -
163B GLY 3.6 22.3 + - - +
164B ARG 3.5 18.2 - - - +
165B LYS* 4.4 7.6 - - - +
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Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B TRP* 2.9 24.1 + - + +
157B ASP* 2.5 27.5 + - - +
159B LYS* 1.3 71.5 - - - +
161B LYS* 1.3 49.6 + - - +
162B ASN* 2.6 18.5 + - - +
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Residues in contact with LYS 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ASP* 2.7 28.0 + - - +
158B ARG* 3.6 5.9 - - - +
160B GLU* 1.3 66.5 - - - +
162B ASN* 1.3 67.0 + - - +
163B GLY* 3.3 4.0 + - - -
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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