Contacts of the helix formed by residues 148 - 161 (chain C) 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 GLU 148 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134C CYS 4.0 11.5 + - - +
135C PHE* 5.2 1.1 - - - +
146C PHE* 3.7 24.3 + - + -
147C LEU* 1.3 86.0 - - - +
149C ALA* 1.3 93.5 + - - +
150C ASP* 3.7 15.6 + - + +
151C LYS* 3.8 27.1 + - + +
152C LEU* 3.4 14.0 + - - +
175C THR 4.8 3.4 + - - +
177C TYR* 5.3 10.7 - - + -
196C LEU* 5.5 5.9 - - - +
197C TYR* 3.3 24.3 + - - -
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Residues in contact with ALA 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C MET* 4.6 4.9 - - + -
128C LYS* 5.2 6.1 - - + -
134C CYS* 3.4 33.3 + - + +
135C PHE 5.6 0.2 - - - -
136C VAL* 5.7 0.2 - - - -
147C LEU 4.4 0.7 - - - -
148C GLU* 1.3 84.7 + - - +
150C ASP* 1.3 60.7 + - - +
151C LYS 3.1 1.6 - - - -
152C LEU* 2.8 27.4 + - - +
153C PHE* 2.9 35.9 + - + -
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Residues in contact with ASP 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C GLU* 3.7 12.0 - - + +
149C ALA* 1.3 77.0 - - - +
151C LYS* 1.3 63.0 + - + +
153C PHE* 3.2 21.9 - - - +
154C TYR* 2.9 27.8 + - - +
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Residues in contact with LYS 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C LEU* 4.1 14.1 - - + -
148C GLU* 3.9 30.7 - - + +
149C ALA 3.1 0.2 - - - -
150C ASP* 1.3 76.9 - - + +
152C LEU* 1.3 64.3 + - - +
154C TYR* 3.1 9.0 - - - +
155C PHE* 2.8 37.5 + - + -
174C GLU 5.2 3.2 + - - -
175C THR* 3.9 28.1 + - - +
177C TYR* 6.5 0.7 - - - -
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Residues in contact with LEU 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LEU* 3.7 16.4 - - + -
116C PHE* 3.4 38.4 - - + -
121C ILE* 4.1 17.0 - - + -
124C MET* 3.7 16.4 - - + -
136C VAL* 3.5 27.6 - - + -
147C LEU* 3.6 25.4 - - + +
148C GLU 3.4 6.2 + - - +
149C ALA* 2.8 13.2 + - - +
151C LYS* 1.3 71.5 - - - +
153C PHE* 1.3 68.1 + - + +
155C PHE* 3.3 6.0 + - + +
156C TRP* 2.9 22.7 + - + +
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Residues in contact with PHE 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ILE* 4.0 33.9 - - + -
124C MET* 3.4 39.5 - - + -
125C LYS* 4.0 11.2 - - + -
128C LYS* 4.9 7.6 - - + -
149C ALA* 2.9 36.3 + - + -
150C ASP* 3.2 26.5 - - - +
152C LEU* 1.3 74.6 - - + +
154C TYR* 1.3 58.6 + - - +
156C TRP* 2.9 10.4 + - - +
157C ASP* 2.8 30.4 + - - +
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Residues in contact with TYR 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ASP 2.9 13.7 + - - +
151C LYS* 3.1 11.9 - - - +
153C PHE* 1.3 73.9 - - - +
155C PHE* 1.3 90.4 + + - +
157C ASP* 2.8 27.2 + - + +
158C ARG* 2.9 53.9 + - + +
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Residues in contact with PHE 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LEU* 3.5 19.8 - - + +
147C LEU* 4.7 9.0 - - + -
151C LYS* 2.8 40.3 + - + -
152C LEU* 3.7 9.2 - - + +
154C TYR* 1.3 93.4 - + - +
156C TRP* 1.3 56.7 + - - +
158C ARG* 3.8 16.3 + - - +
159C LYS* 3.0 29.8 + - - +
164C ARG 4.4 2.6 - - - +
166C SER 4.6 2.5 - - - +
167C ILE* 3.5 43.1 - - + -
171C GLU* 3.9 25.1 - - + -
172C LEU* 4.5 1.6 - - + -
175C THR* 3.7 32.1 - - - -
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Residues in contact with TRP 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LEU* 3.1 59.9 - - + +
114C GLN* 5.7 0.2 - - - -
116C PHE* 2.9 28.0 - + + -
117C HIS* 3.9 9.6 - - - -
118C ASP* 3.0 29.6 + - - +
121C ILE* 4.0 39.6 - - + +
152C LEU* 2.9 14.7 + - + +
153C PHE* 3.3 12.8 - - - +
155C PHE* 1.3 77.8 - - - +
157C ASP* 1.3 57.2 + - - +
159C LYS* 3.6 25.7 - - + +
160C GLU* 2.9 31.7 + - + +
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Residues in contact with ASP 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C PHE 2.8 11.2 + - - +
154C TYR* 2.8 15.6 + - + +
156C TRP* 1.3 76.3 - - - +
158C ARG* 1.3 60.2 + - - +
159C LYS 3.1 0.7 - - - -
160C GLU* 2.7 26.1 + - - +
161C LYS* 3.0 13.9 + - - +
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Residues in contact with ARG 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C TYR* 2.9 49.5 + - + +
155C PHE* 3.8 11.8 + - - +
157C ASP* 1.3 76.4 + - - +
159C LYS* 1.3 57.5 + - - +
161C LYS* 2.9 26.1 + - - +
163C GLY* 3.2 16.3 + - - -
164C ARG* 3.7 36.3 + - - +
166C SER 3.8 5.9 + - - -
171C GLU* 2.5 43.8 + - - -
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Residues in contact with LYS 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LEU* 3.7 22.4 - - + -
118C ASP* 4.9 2.8 + - - -
155C PHE 3.0 18.7 + - - +
156C TRP* 3.6 37.6 - - + +
158C ARG* 1.3 80.3 - - - +
160C GLU* 1.3 69.0 + - - +
162C ASN* 3.3 12.5 + - - -
163C GLY 3.5 8.7 + - - +
164C ARG 3.4 11.6 + - - +
165C LYS* 3.4 33.2 - - + -
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Residues in contact with GLU 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C TRP* 2.9 22.6 + - + +
157C ASP* 2.7 17.7 + - - +
159C LYS* 1.3 77.4 - - - +
161C LYS* 1.3 56.1 + - - +
162C ASN 3.1 9.6 + - - -
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Residues in contact with LYS 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ASP* 3.0 10.0 + - - +
158C ARG* 2.9 14.7 + - - +
160C GLU* 1.3 75.3 - - - +
162C ASN* 1.3 64.4 + - - +
163C GLY* 3.1 5.9 + - - -
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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
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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