Contacts of the helix formed by residues 147 - 155 (chain A) in PDB entry 3U78
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 THR 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A SER 3.7 21.3 - - - +
145A GLN* 2.9 5.9 + - - +
146A LEU* 1.3 79.0 - - - +
148A GLN* 1.3 65.0 + - - +
149A ARG* 3.5 10.2 + - - +
150A TYR* 3.1 23.8 + - - +
151A LEU* 3.2 22.3 + - - +
244A ILE* 3.9 7.9 - - - -
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Residues in contact with GLN 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A THR* 1.3 71.8 - - - +
149A ARG* 1.3 65.1 + - - +
151A LEU* 3.1 7.2 + - - +
152A GLU* 3.0 45.0 + - + +
244A ILE* 3.7 12.6 - - + +
247A LYS* 3.9 43.7 + - + +
248A LEU* 4.3 23.8 - - + +
253A ASN* 5.4 2.0 - - - +
373A LEU* 5.8 0.2 - - - +
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Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A THR* 3.2 9.8 + - - +
148A GLN* 1.3 79.0 - - - +
150A TYR* 1.3 68.7 + - - +
152A GLU* 3.4 15.8 + - - +
153A LYS* 3.3 17.5 + - - +
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Residues in contact with TYR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ILE* 3.5 28.2 - - + +
141A MET* 3.6 28.9 - - + +
145A GLN* 3.5 18.4 - - + +
146A LEU* 5.2 1.1 - - + -
147A THR* 3.1 20.2 + - - +
149A ARG* 1.3 79.1 - - - +
151A LEU* 1.3 80.5 + - + +
153A LYS* 2.9 19.5 + - - -
154A HIS* 2.9 67.1 + + + +
155A GLY 4.4 3.8 - - - -
160A ILE* 4.6 2.2 - - + -
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 4.3 7.4 - - + -
147A THR 3.5 14.1 - - - +
148A GLN* 3.1 7.3 + - - +
150A TYR* 1.3 93.4 - - + +
152A GLU* 1.3 55.3 - - - +
155A GLY* 2.7 45.7 + - - +
156A PHE* 3.9 15.8 + - + -
160A ILE* 3.6 30.1 - - + -
244A ILE* 3.9 15.3 - - + -
248A LEU* 3.7 29.8 - - + -
373A LEU* 3.7 21.3 - - + +
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Residues in contact with GLU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLN* 3.0 42.6 + - + +
149A ARG* 3.8 16.1 - - - +
151A LEU* 1.3 77.3 - - - +
153A LYS* 1.3 59.9 + - - +
155A GLY 4.3 0.2 - - - -
373A LEU* 4.0 15.7 - - + -
425A GLN* 3.4 35.5 + - - +
427A TYR* 3.4 34.8 + - + +
705A EDO 4.5 8.5 - - - -
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Residues in contact with LYS 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ARG 3.3 8.0 + - - +
150A TYR* 2.9 9.0 + - - +
152A GLU* 1.3 81.8 - - - +
154A HIS* 1.3 74.9 + - + +
155A GLY 3.4 0.2 - - - -
425A GLN* 5.1 2.7 - - - +
705A EDO 3.7 14.2 + - - -
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Residues in contact with HIS 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ILE* 6.1 0.9 - - + -
150A TYR* 2.9 63.1 + + + +
153A LYS* 1.3 87.1 - - + +
155A GLY* 1.3 63.1 + - - +
157A ASP* 3.9 9.5 - - - +
705A EDO 4.0 10.0 + - - -
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Residues in contact with GLY 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ILE* 6.0 1.7 - - - +
150A TYR* 4.4 3.3 - - - -
151A LEU* 2.7 33.7 + - - +
153A LYS 3.4 1.8 - - - -
154A HIS* 1.3 86.1 - - - +
156A PHE* 1.3 59.8 + - - -
157A ASP* 3.6 11.7 + - - +
158A VAL* 6.1 0.5 - - - +
160A ILE* 5.5 0.7 - - - +
373A LEU* 5.6 1.6 - - - -
705A EDO 3.9 15.1 - - - -
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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