Contacts of the helix formed by residues 141 - 151 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140E ALA* 1.3 94.0 - - + +
142E GLY* 1.3 64.0 + - - +
144E GLU* 4.1 2.3 + - - +
145E GLY* 2.8 43.0 + - - -
146E VAL* 4.3 4.9 - - + +
149E MET* 3.6 28.0 - - + -
272E ALA* 5.7 2.0 - - - -
275E GLY* 3.5 30.3 - - - -
276E LEU 3.8 19.7 - - - -
277E ALA* 4.0 15.5 - - + -
311E ASP* 3.0 13.5 + - - +
360E LYS* 3.8 12.6 + - - +
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Residues in contact with GLY 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E PRO* 3.6 13.9 - - - +
141E PHE* 1.3 77.3 - - - +
143E ILE* 1.3 66.3 + - - -
144E GLU 3.3 0.2 - - - -
146E VAL* 3.0 22.0 + - - +
311E ASP* 2.9 24.3 + - - -
360E LYS* 4.4 6.1 - - - -
361E ALA 3.1 15.5 - - - -
363E PHE* 5.0 0.2 - - - -
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Residues in contact with ILE 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E GLY* 1.3 71.4 - - - +
144E GLU* 1.3 64.0 + - - +
146E VAL* 3.8 0.5 - - - -
147E ARG* 2.9 31.9 + - + +
338E ARG* 3.7 29.4 - - + -
361E ALA* 2.9 24.5 + - + +
362E ALA 3.4 32.1 - - - +
363E PHE* 3.7 36.6 - - + +
364E PRO* 4.3 0.9 - - + -
385E ASP* 4.1 26.5 - - + +
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Residues in contact with GLU 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E PHE 4.1 2.7 + - - +
142E GLY 3.3 0.2 - - - -
143E ILE* 1.3 79.8 - - - +
145E GLY* 1.3 61.9 + - - +
147E ARG* 3.5 5.6 + - - +
148E LYS* 3.0 26.8 + - - +
360E LYS* 6.1 3.1 - - + +
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Residues in contact with GLY 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E PHE* 2.8 46.3 + - - -
144E GLU* 1.3 75.5 - - - +
146E VAL* 1.3 55.8 + - - +
148E LYS* 3.5 7.0 + - - +
149E MET* 3.0 27.9 + - - +
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Residues in contact with VAL 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E PHE* 4.4 10.3 - - + -
142E GLY 3.0 19.0 + - - +
143E ILE 3.9 3.1 - - - +
145E GLY* 1.3 73.9 - - - +
147E ARG* 1.3 60.7 + - - +
148E LYS 3.1 1.6 - - - -
149E MET* 3.1 8.1 + - + +
150E LEU* 2.9 49.5 + - + +
157E ILE* 5.1 4.0 - - + -
251E HIS* 4.5 5.2 - - + +
277E ALA* 4.5 11.2 - - + -
311E ASP* 4.7 3.4 - - + -
312E GLN* 3.4 35.0 - - + +
363E PHE* 4.0 18.8 - - + -
387E VAL* 5.8 0.4 - - + -
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Residues in contact with ARG 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E ILE* 2.9 25.2 + - - +
144E GLU* 4.0 5.6 - - - +
146E VAL* 1.3 76.4 - - - +
148E LYS* 1.3 53.3 + - - +
150E LEU* 5.0 1.6 - - - -
151E GLU* 2.8 27.7 + - - -
152E ILE* 2.7 61.3 + - - +
153E LYS* 3.3 20.2 + - - +
154E ASP* 3.2 9.7 + - - -
155E ARG 2.6 30.0 + - - -
156E PRO* 3.9 3.2 - - - +
157E ILE* 4.1 6.5 - - + +
363E PHE* 4.0 20.0 - - + -
384E THR 3.1 23.6 + - - -
385E ASP* 3.2 26.6 + - - +
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Residues in contact with LYS 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E GLU 3.0 19.3 + - - +
145E GLY* 3.7 6.7 - - - +
147E ARG* 1.3 76.5 - - - +
149E MET* 1.3 63.9 + - - +
151E GLU* 3.4 17.8 + - - +
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Residues in contact with MET 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E PHE* 3.6 36.6 - - + -
145E GLY 3.0 15.0 + - - +
146E VAL* 3.1 7.8 + - - +
148E LYS* 1.3 80.0 - - - +
150E LEU* 1.3 64.0 + - + +
151E GLU* 4.7 0.7 - - - +
223E LYS* 3.7 19.4 - - - +
250E LYS* 3.7 41.3 + - + +
251E HIS* 3.6 26.7 - - + -
275E GLY 5.5 0.7 - - - +
277E ALA* 4.0 17.0 - - + -
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Residues in contact with LEU 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E VAL* 2.9 34.8 + - + +
147E ARG* 4.5 0.7 - - - +
149E MET* 1.3 90.7 - - + +
151E GLU* 1.3 71.5 + - - +
152E ILE* 3.2 22.7 + - + +
157E ILE* 4.1 27.8 - - + -
186E ASP* 5.0 4.5 - - + +
187E TYR* 5.9 0.2 - - + -
223E LYS* 3.4 26.9 + - + +
224E LYS* 4.2 13.5 - - - +
225E THR* 4.0 37.2 - - + -
227E PHE* 6.2 0.7 - - + -
250E LYS* 4.6 1.1 - - - +
251E HIS* 4.9 1.6 - - + -
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Residues in contact with GLU 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E ARG 2.8 10.9 + - - -
148E LYS* 3.4 13.7 + - - +
149E MET 3.4 1.3 - - - +
150E LEU* 1.3 81.7 - - - +
152E ILE* 1.3 57.6 + - - +
153E LYS* 4.0 10.4 + - - +
221E GLY 4.8 8.0 - - - +
223E LYS* 3.8 33.0 + - + +
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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