Contacts of the helix formed by residues 141 - 151 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140J ALA* 1.3 94.1 - - + +
142J GLY* 1.3 57.9 + - - +
144J GLU* 4.2 0.5 + - - +
145J GLY* 2.7 48.1 + - - -
146J VAL* 4.3 5.8 - - + -
149J MET* 3.7 27.8 - - + -
272J ALA* 5.6 2.0 - - - -
275J GLY* 3.3 32.5 - - - -
276J LEU 3.7 7.9 - - - -
277J ALA* 3.7 29.6 - - + -
311J ASP* 2.8 14.8 + - - +
360J LYS* 4.0 13.6 + - - +
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Residues in contact with GLY 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J PRO* 3.7 10.3 - - - +
141J PHE* 1.3 76.6 - - - +
143J ILE* 1.3 66.3 + - - -
144J GLU 3.3 1.1 - - - -
146J VAL* 2.9 22.1 + - - +
311J ASP* 2.7 26.7 + - - -
360J LYS* 4.4 6.1 - - - -
361J ALA 3.0 17.3 - - - -
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Residues in contact with ILE 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J GLY* 1.3 71.4 - - - -
144J GLU* 1.3 66.2 + - - +
146J VAL* 3.0 2.9 + - - +
147J ARG* 2.9 39.3 + - + +
338J ARG* 3.7 28.3 - - + -
361J ALA* 3.1 21.3 + - + +
362J ALA 3.5 32.3 - - - +
363J PHE* 3.7 35.4 - - + +
385J ASP* 4.2 20.0 - - + +
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Residues in contact with GLU 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141J PHE 4.7 1.6 - - - +
142J GLY 3.3 0.4 - - - -
143J ILE* 1.3 79.2 - - - +
145J GLY* 1.3 63.4 + - - +
147J ARG* 4.1 5.0 - - - +
148J LYS* 3.1 26.6 + - - +
360J LYS* 5.3 8.5 - - - +
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Residues in contact with GLY 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141J PHE* 2.7 47.4 + - - -
144J GLU* 1.3 76.0 - - - +
146J VAL* 1.3 60.5 + - - +
148J LYS* 3.9 7.1 - - - +
149J MET* 3.3 21.7 + - - +
360J LYS* 5.7 0.4 - - - +
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Residues in contact with VAL 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141J PHE* 4.3 11.4 - - + -
142J GLY 2.9 21.9 + - - +
143J ILE 3.8 2.2 - - - +
145J GLY* 1.3 76.8 - - - +
147J ARG* 1.3 66.3 + - - +
148J LYS 3.2 0.2 - - - -
149J MET* 3.2 8.7 + - - +
150J LEU* 3.0 43.6 + - + +
157J ILE* 5.2 2.5 - - + -
251J HIS* 4.4 8.5 - - + +
277J ALA* 4.6 7.2 - - + -
311J ASP* 4.6 2.9 - - + -
312J GLN* 3.3 35.9 - - + +
363J PHE* 4.0 19.1 - - + -
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Residues in contact with ARG 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J ILE* 2.9 24.8 + - + +
144J GLU* 4.1 4.7 - - - +
146J VAL* 1.3 75.7 - - - +
148J LYS* 1.3 53.3 + - - +
150J LEU* 3.3 2.4 + - - +
151J GLU* 2.6 32.2 + - - -
152J ILE* 2.6 49.4 + - - +
153J LYS* 3.2 26.0 + - - +
154J ASP 3.5 5.9 + - - -
155J ARG 2.9 24.4 + - - -
156J PRO* 4.5 0.4 - - - +
157J ILE* 4.2 5.9 - - + +
363J PHE* 3.9 21.4 - - + -
384J THR 2.9 21.8 + - - -
385J ASP* 2.7 34.7 + - - +
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Residues in contact with LYS 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144J GLU 3.1 17.2 + - - +
145J GLY* 3.9 8.1 - - - +
147J ARG* 1.3 80.0 - - - +
149J MET* 1.3 63.0 + - - +
151J GLU* 3.3 20.5 + - - +
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Residues in contact with MET 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141J PHE* 3.7 35.2 - - + -
145J GLY 3.3 8.8 + - - +
146J VAL* 3.2 10.0 + - - +
148J LYS* 1.3 80.5 - - - +
150J LEU* 1.3 67.7 + - + +
151J GLU* 4.7 0.3 - - - +
223J LYS* 3.7 21.8 - - - +
250J LYS* 3.6 46.3 + - + +
251J HIS* 3.9 17.5 - - + -
275J GLY 5.6 0.4 - - - +
277J ALA* 4.1 16.6 - - + -
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Residues in contact with LEU 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146J VAL* 3.0 35.5 + - + +
147J ARG* 4.2 1.3 - - - +
149J MET* 1.3 90.1 - - + +
151J GLU* 1.3 71.7 + - - +
152J ILE* 3.1 23.8 + - + +
157J ILE* 4.1 27.8 - - + -
186J ASP* 5.0 3.8 - - + +
223J LYS* 3.7 35.4 + - + +
224J LYS* 4.3 4.3 - - - +
225J THR* 4.0 35.9 - - + -
227J PHE* 6.2 1.1 - - + -
250J LYS* 4.8 0.9 - - - +
251J HIS* 5.0 1.8 - - + -
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Residues in contact with GLU 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147J ARG 2.6 15.0 + - - -
148J LYS* 3.3 14.1 + - - +
149J MET 4.7 0.4 - - - +
150J LEU* 1.3 76.0 - - - +
152J ILE* 1.3 57.8 + - - +
153J LYS 3.9 2.2 + - - -
221J GLY 4.9 6.8 - - - +
223J LYS* 3.7 34.4 + - + +
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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