Contacts of the helix formed by residues 141 - 151 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140B ALA* 1.3 93.0 - - + +
142B GLY* 1.3 70.1 + - - +
144B GLU* 4.4 1.6 + - - +
145B GLY* 2.9 38.7 + - - -
146B VAL* 4.4 2.7 - - + +
149B MET* 5.4 10.3 - - + -
250B LYS 5.4 0.4 - - - -
272B ALA* 5.4 1.3 - - - -
275B GLY* 3.1 33.2 - - - -
276B LEU 3.4 24.0 - - - -
277B ALA* 3.8 24.5 - - + -
311B ASP* 3.0 10.6 + - - +
360B LYS* 3.8 14.1 + - - +
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Residues in contact with GLY 142 (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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139B PRO* 3.6 14.2 - - - +
141B PHE* 1.3 75.4 - - - +
143B ILE* 1.3 68.0 + - - -
144B GLU 3.4 0.7 - - - -
146B VAL* 2.9 26.6 + - - +
311B ASP* 2.9 20.5 + - - -
360B LYS* 4.6 4.7 - - - -
361B ALA 3.3 15.0 - - - -
363B PHE* 5.1 0.2 - - - -
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Residues in contact with ILE 143 (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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142B GLY* 1.3 68.9 - - - -
144B GLU* 1.3 68.4 + - - +
146B VAL* 2.9 4.5 + - - +
147B ARG* 2.9 29.9 + - - +
338B ARG* 3.7 29.6 - - + -
361B ALA* 3.1 21.0 + - + +
362B ALA 3.4 28.0 - - - +
363B PHE* 3.7 41.6 - - + +
385B ASP* 4.1 25.8 - - + +
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Residues in contact with GLU 144 (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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141B PHE 4.8 1.1 - - - +
142B GLY 3.4 0.6 - - - -
143B ILE* 1.3 81.6 - - - +
145B GLY* 1.3 63.7 + - - +
147B ARG* 3.3 6.7 + - - +
148B LYS* 3.0 24.8 + - - +
360B LYS* 5.7 7.4 - - + +
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Residues in contact with GLY 145 (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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141B PHE* 2.9 40.4 + - - -
144B GLU* 1.3 78.2 - - - +
146B VAL* 1.3 58.2 + - - +
148B LYS* 3.4 8.6 + - - +
149B MET* 3.0 27.0 + - - +
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Residues in contact with VAL 146 (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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141B PHE* 4.4 11.0 - - + -
142B GLY 2.9 22.3 + - - +
143B ILE 3.6 3.6 - - - +
145B GLY* 1.3 73.4 - - - +
147B ARG* 1.3 66.4 + - - +
149B MET* 3.3 7.7 + - - +
150B LEU* 3.0 42.0 + - + +
157B ILE* 5.0 5.4 - - + -
251B HIS* 4.2 10.1 - - + +
277B ALA* 4.6 5.4 - - + -
311B ASP* 4.7 2.9 - - + -
312B GLN* 3.4 34.3 - - + +
363B PHE* 4.1 19.5 - - + -
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Residues in contact with ARG 147 (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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143B ILE* 2.9 22.6 + - - +
144B GLU* 3.7 7.2 - - - +
146B VAL* 1.3 76.9 - - - +
148B LYS* 1.3 52.7 + - - +
150B LEU* 5.1 1.1 - - - -
151B GLU* 2.8 29.3 + - - -
152B ILE* 3.0 44.3 + - - +
153B LYS* 3.4 14.4 + - - -
154B ASP* 3.1 22.6 + - - +
155B ARG 2.8 29.5 + - - -
156B PRO* 4.3 0.4 - - - +
157B ILE* 4.1 6.1 - - + +
363B PHE* 4.1 20.6 - - + -
384B THR 3.4 11.3 + - - -
385B ASP* 2.8 33.1 + - - +
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Residues in contact with LYS 148 (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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144B GLU 3.0 17.7 + - - +
145B GLY* 3.6 8.5 - - - +
146B VAL 3.2 0.2 - - - -
147B ARG* 1.3 76.7 - - - +
149B MET* 1.3 64.1 + - - +
150B LEU 3.4 0.5 + - - -
151B GLU* 3.4 17.5 + - - +
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Residues in contact with MET 149 (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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141B PHE* 5.4 10.8 - - + -
145B GLY 3.0 17.9 + - - +
146B VAL* 3.3 6.7 + - - +
148B LYS* 1.3 77.6 - - - +
150B LEU* 1.3 65.8 + - + +
223B LYS* 3.4 22.7 - - - +
225B THR* 3.1 25.6 - - - +
250B LYS* 2.8 58.0 + - + +
251B HIS* 3.1 26.7 - - + +
277B ALA* 5.0 4.7 - - - -
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Residues in contact with LEU 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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146B VAL* 3.0 33.3 + - + +
147B ARG* 5.1 0.2 - - - -
149B MET* 1.3 102.0 - - + +
151B GLU* 1.3 71.7 + - - +
152B ILE* 3.0 24.8 + - + +
157B ILE* 4.2 23.8 - - + -
186B ASP* 4.9 5.2 - - + +
223B LYS* 3.4 33.6 + - + +
224B LYS* 4.1 10.8 - - - +
225B THR* 3.9 25.6 - - + -
227B PHE* 6.2 0.4 - - + -
250B LYS* 4.5 0.7 - - - +
251B HIS* 4.9 0.9 - - + -
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Residues in contact with GLU 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 ARG 2.8 11.4 + - - -
148B LYS* 3.4 13.4 + - - +
149B MET 3.4 0.4 - - - -
150B LEU* 1.3 82.2 - - - +
152B ILE* 1.3 59.1 + - - +
153B LYS* 4.0 1.8 + - - +
221B GLY 5.4 3.5 - - - +
223B LYS* 2.8 36.3 + - + +
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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