Contacts of the helix formed by residues 141 - 151 (chain F) in PDB entry 3KDO
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 PHE 141 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F ALA* 1.3 90.6 - - + +
142F GLY* 1.3 63.9 + - - +
144F GLU* 3.3 10.4 + - - +
145F GLY* 2.9 46.7 + - - -
146F VAL* 4.3 5.6 - - + -
149F MET* 3.6 26.2 - - + -
272F ALA* 6.1 1.1 - - - -
275F GLY* 3.6 25.6 - - - -
276F LEU 3.7 8.1 - - - -
277F ALA* 3.6 31.0 - - + -
311F ASP* 2.9 14.6 + - - +
360F LYS* 3.8 7.6 - - - +
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Residues in contact with GLY 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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139F PRO* 3.7 11.7 - - - +
141F PHE* 1.3 80.0 - - - +
143F ILE* 1.3 66.6 + - - -
144F GLU 4.4 0.4 - - - -
146F VAL* 3.0 23.2 + - - +
311F ASP* 3.0 20.5 + - - -
360F LYS* 4.5 5.8 - - - -
361F ALA 3.0 17.7 - - - -
363F PHE* 5.0 0.2 - - - -
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Residues in contact with ILE 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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142F GLY* 1.3 71.4 - - - +
144F GLU* 1.3 64.0 + - - +
146F VAL* 3.9 0.2 - - - -
147F ARG* 3.0 36.1 + - - +
338F ARG* 3.8 28.3 - - + -
361F ALA* 3.2 21.8 + - + +
362F ALA 3.7 17.3 - - - +
363F PHE* 3.7 45.6 - - + +
364F PRO* 4.2 4.0 - - + -
385F ASP* 4.0 23.8 - - + +
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Residues in contact with GLU 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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141F PHE 3.3 9.9 - - - +
142F GLY 3.3 0.4 - - - -
143F ILE* 1.3 80.9 - - - +
145F GLY* 1.3 71.1 + - - +
147F ARG* 4.1 4.7 - - - +
148F LYS* 3.0 38.0 + - + +
360F LYS* 4.1 19.1 + - + +
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Residues in contact with GLY 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 PHE* 2.9 45.5 + - - -
144F GLU* 1.3 87.0 + - - +
146F VAL* 1.3 57.6 + - - +
148F LYS* 3.8 4.4 - - - +
149F MET* 3.0 27.0 + - - +
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Residues in contact with VAL 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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141F PHE* 4.3 12.1 - - + -
142F GLY 3.0 17.7 + - - +
145F GLY* 1.3 75.6 - - - +
147F ARG* 1.3 66.8 + - - +
148F LYS 3.1 1.1 - - - -
149F MET* 3.0 7.1 + - + +
150F LEU* 2.9 42.9 + - + +
157F ILE* 5.2 3.4 - - + -
251F HIS* 4.4 9.4 - - + +
277F ALA* 4.6 5.4 - - + -
311F ASP* 4.7 2.2 - - + -
312F GLN* 3.4 36.6 - - + +
363F PHE* 3.9 22.0 - - + -
387F VAL* 6.0 0.4 - - + -
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Residues in contact with ARG 147 (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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143F ILE* 3.0 26.4 + - - +
144F GLU* 4.1 4.3 - - - +
146F VAL* 1.3 77.1 - - - +
148F LYS* 1.3 53.7 + - - +
150F LEU* 5.0 2.2 - - - -
151F GLU* 2.6 33.1 + - - -
152F ILE* 2.6 52.9 + - - +
153F LYS* 3.3 26.9 + - - +
154F ASP 3.0 17.3 + - - -
155F ARG 2.9 20.4 + - - -
156F PRO* 4.3 0.4 - - - +
157F ILE* 4.1 6.6 - - + +
363F PHE* 3.8 22.9 - - + -
384F THR 3.0 15.6 + - - -
385F ASP* 2.7 33.1 + - - +
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Residues in contact with LYS 148 (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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144F GLU* 3.0 30.6 + - + +
145F GLY* 3.8 5.8 - - - +
147F ARG* 1.3 73.8 - - - +
149F MET* 1.3 66.8 + - - +
150F LEU 3.5 0.2 + - - -
151F GLU* 3.6 16.5 + - - +
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Residues in contact with MET 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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141F PHE* 3.6 36.3 - - + -
145F GLY 3.0 17.0 + - - +
146F VAL* 3.0 8.3 + - - +
148F LYS* 1.3 81.9 - - - +
150F LEU* 1.3 67.3 + - + +
151F GLU* 3.8 1.2 + - - +
223F LYS* 3.7 18.5 - - - +
250F LYS* 3.7 48.3 + - + +
251F HIS* 3.5 27.8 - - - -
275F GLY 5.5 0.4 - - - +
277F ALA* 4.2 7.9 - - + -
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Residues in contact with LEU 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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146F VAL* 2.9 35.6 + - + +
147F ARG* 4.2 1.3 - - - +
149F MET* 1.3 89.0 - - + +
151F GLU* 1.3 72.9 - - - +
152F ILE* 3.4 22.8 + - + +
157F ILE* 4.0 27.6 - - + -
186F ASP* 4.9 5.2 - - + +
187F TYR* 5.7 0.4 - - + -
223F LYS* 3.5 33.3 + - + +
224F LYS 4.4 8.1 - - - +
225F THR* 4.0 35.2 - - + -
227F PHE* 6.2 1.1 - - + -
250F LYS* 5.2 1.1 - - - +
251F HIS* 5.1 1.1 - - + -
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Residues in contact with GLU 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 ARG 2.6 16.8 + - - -
148F LYS* 3.6 14.3 + - - +
149F MET 3.4 1.1 - - - +
150F LEU* 1.3 78.0 - - - +
152F ILE* 1.3 58.8 + - - +
153F LYS 4.0 2.0 + - - -
221F GLY 5.1 5.5 - - - +
223F LYS* 3.9 30.5 + - + +
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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
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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