Contacts of the helix formed by residues 141 - 151 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140G ALA* 1.3 94.5 - - + +
142G GLY* 1.3 59.5 + - - +
144G GLU* 4.1 1.6 + - - +
145G GLY* 2.7 53.0 + - - -
146G VAL* 4.2 6.1 - - + -
149G MET* 5.1 14.1 - - + -
250G LYS 5.4 0.7 - - - -
272G ALA* 5.8 0.9 - - - -
275G GLY* 3.3 29.4 - - - -
276G LEU 3.7 20.2 - - - -
277G ALA* 3.7 23.8 - - + -
311G ASP* 3.0 12.7 + - - +
360G LYS* 3.9 11.4 - - - +
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Residues in contact with GLY 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G PRO* 3.7 13.0 - - - +
141G PHE* 1.3 81.9 - - - +
143G ILE* 1.3 65.2 + - - -
144G GLU 3.3 0.4 - - - -
146G VAL* 3.0 22.1 + - - +
311G ASP* 3.1 20.3 + - - -
360G LYS* 4.4 7.0 - - - -
361G ALA 3.0 16.6 - - - -
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Residues in contact with ILE 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142G GLY* 1.3 71.5 - - - +
144G GLU* 1.3 63.2 + - - +
147G ARG* 3.0 35.3 + - - +
338G ARG* 3.5 39.7 - - + -
361G ALA* 3.0 24.6 + - + +
362G ALA 3.5 18.4 - - - +
363G PHE* 3.7 39.5 - - + +
364G PRO* 4.2 3.4 - - + -
385G ASP* 4.1 20.0 - - + +
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Residues in contact with GLU 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G PHE 4.8 1.6 - - - +
142G GLY 3.3 0.4 - - - -
143G ILE* 1.3 81.0 - - - +
145G GLY* 1.3 58.1 + - - +
147G ARG* 4.0 5.5 - - - +
148G LYS* 3.0 30.3 + - - +
360G LYS* 6.5 0.9 - - + -
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Residues in contact with GLY 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G PHE* 2.7 45.6 + - - -
144G GLU* 1.3 76.0 - - - +
146G VAL* 1.3 57.4 + - - +
148G LYS* 3.6 7.8 + - - +
149G MET* 3.1 27.0 + - - +
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Residues in contact with VAL 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G PHE* 4.2 12.6 - - + -
142G GLY 3.0 21.0 + - - +
145G GLY* 1.3 74.1 - - - +
147G ARG* 1.3 62.1 + - - +
149G MET* 3.3 7.6 + - - +
150G LEU* 3.0 46.6 + - + +
157G ILE* 5.2 4.9 - - + -
251G HIS* 4.3 11.7 - - + +
277G ALA* 4.6 4.9 - - + -
311G ASP* 4.7 3.4 - - + +
312G GLN* 3.4 37.5 - - + +
363G PHE* 4.1 19.7 - - + -
387G VAL* 5.9 0.2 - - + -
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Residues in contact with ARG 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143G ILE* 3.0 26.1 + - - +
144G GLU* 4.0 5.4 - - - +
146G VAL* 1.3 76.2 - - - +
148G LYS* 1.3 55.0 + - - +
150G LEU* 5.0 1.6 - - - -
151G GLU* 2.7 30.3 + - - -
152G ILE* 2.8 42.9 + - - +
153G LYS* 3.3 23.5 + - - +
154G ASP* 3.1 10.4 + - - -
155G ARG 2.9 29.7 + - - -
156G PRO* 4.4 0.2 - - - +
157G ILE* 4.1 5.1 - - + +
363G PHE* 3.9 22.6 - - + -
384G THR 3.2 11.5 + - - -
385G ASP* 2.9 33.7 + - - +
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Residues in contact with LYS 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G GLU 3.0 19.7 + - - +
145G GLY* 3.7 7.2 - - - +
147G ARG* 1.3 77.7 - - - +
149G MET* 1.3 61.4 + - - +
151G GLU* 3.3 18.7 + - - +
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Residues in contact with MET 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G PHE* 5.1 13.0 - - + -
145G GLY 3.1 17.9 + - - +
146G VAL* 3.6 7.6 - - - +
148G LYS* 1.3 79.1 - - - +
150G LEU* 1.3 67.5 + - + +
151G GLU* 4.4 0.3 - - - +
223G LYS* 3.6 22.2 - - - +
225G THR* 3.4 15.3 - - - +
250G LYS* 3.0 55.4 + - + +
251G HIS* 3.1 36.1 - - + +
277G ALA* 5.0 5.4 - - - -
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Residues in contact with LEU 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G VAL* 3.0 31.2 + - + +
147G ARG* 4.4 1.1 - - - +
149G MET* 1.3 103.1 - - + +
151G GLU* 1.3 73.4 + - - +
152G ILE* 3.4 22.9 + - + +
157G ILE* 4.0 27.6 - - + -
186G ASP* 4.9 4.9 - - + +
187G TYR* 5.7 0.2 - - + -
223G LYS* 3.4 32.2 + - + +
224G LYS* 4.2 9.2 - - - +
225G THR* 4.0 25.4 - - + -
227G PHE* 6.1 1.6 - - + -
250G LYS* 4.7 0.7 - - - +
251G HIS* 5.0 1.3 - - + -
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Residues in contact with GLU 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147G ARG 2.7 16.9 + - - -
148G LYS* 3.3 14.7 + - - +
149G MET 4.4 0.7 - - - +
150G LEU* 1.3 78.2 - - - +
152G ILE* 1.3 59.0 + - - +
153G LYS* 4.0 1.5 + - - -
221G GLY 4.8 8.1 - - - +
222G GLU* 5.9 0.2 - - - -
223G LYS* 4.0 30.2 + - + +
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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