Contacts of the helix formed by residues 133 - 141 (chain O) in PDB entry 3L73
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 ARG 133 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F GLU* 2.9 31.4 + - - +
100F GLU* 3.0 26.9 + - - -
76O THR* 3.2 33.8 + - - +
77O THR 5.8 0.2 + - - -
131O GLU* 2.8 40.7 + - + +
132O PHE* 1.3 70.0 - - - +
134O PRO* 1.3 75.1 - - + +
135O TRP* 3.3 38.7 - - + +
136O GLU* 3.0 21.1 + - + +
137O VAL* 2.8 21.0 + - - +
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Residues in contact with PRO 134 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ARG 5.9 0.7 - - - +
131O GLU 5.4 0.2 - - - +
132O PHE 3.2 4.6 - - - +
133O ARG* 1.3 83.1 - - + +
135O TRP* 1.3 68.6 + - + +
137O VAL* 3.3 3.6 + - + +
138O THR* 2.7 40.7 + - - +
188O SER* 3.6 20.6 - - - +
189O GLU* 6.2 0.4 - - - +
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Residues in contact with TRP 135 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F GLU* 5.5 2.0 - - - -
48F LYS 4.9 3.8 - - - +
49F ARG* 3.4 72.0 - - + +
93F TYR* 3.8 28.3 - + - -
96F GLU* 5.7 1.6 - - + -
100F GLU* 5.3 0.2 + - - -
133O ARG* 3.5 40.1 - - + +
134O PRO* 1.3 92.2 - - + +
136O GLU* 1.3 96.7 + - + +
138O THR* 2.8 7.8 + - - -
139O ASP* 2.8 37.8 + - - +
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Residues in contact with GLU 136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F GLU* 5.0 1.9 - - - +
75O LEU* 3.3 28.5 - - + +
76O THR* 2.8 60.0 + - - +
82O SER* 4.0 7.3 - - - -
133O ARG* 3.0 23.0 + - + +
135O TRP* 1.3 100.3 + - + +
137O VAL* 1.3 62.2 + - - +
139O ASP* 3.5 8.3 + - - +
140O LEU* 3.1 24.1 + - - +
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Residues in contact with VAL 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68O LEU* 4.5 7.1 - - + +
75O LEU* 4.4 11.2 - - + -
132O PHE* 3.5 31.6 - - + +
133O ARG 2.8 15.6 + - - +
134O PRO* 3.4 9.2 - - + +
136O GLU* 1.3 74.9 - - - +
138O THR* 1.3 65.9 + - - +
140O LEU* 3.3 6.3 + - - +
141O GLN* 3.2 39.2 + - - +
186O ILE 4.9 0.2 - - - +
187O THR* 4.9 1.6 - - - -
188O SER* 3.6 17.5 - - - +
191O LEU* 4.1 20.9 - - + -
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Residues in contact with THR 138 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134O PRO* 2.7 28.4 + - - +
135O TRP* 2.8 8.7 + - - -
137O VAL* 1.3 76.0 - - - +
139O ASP* 1.3 67.6 + - - +
140O LEU 3.3 0.5 + - - -
141O GLN* 3.6 10.6 + - - +
142O PRO* 3.3 15.4 - - - +
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Residues in contact with ASP 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135O TRP* 2.8 32.4 + - - +
136O GLU* 3.9 7.3 + - - +
138O THR* 1.3 81.0 - - - +
140O LEU* 1.3 57.4 + - - +
142O PRO* 3.1 20.6 - - - +
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Residues in contact with LEU 140 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68O LEU* 4.1 17.0 - - + +
71O LEU* 4.0 16.8 - - + +
72O ALA* 3.6 24.7 - - + +
74O PRO* 6.0 2.2 - - + -
75O LEU* 3.5 35.2 - - + -
136O GLU 3.1 15.8 + - - +
137O VAL* 3.7 5.8 - - - +
138O THR 3.1 0.6 - - - -
139O ASP* 1.3 75.0 - - - +
141O GLN* 1.3 53.1 + - - +
142O PRO* 3.1 3.6 - - - -
143O GLN* 2.7 56.5 + - + +
144O LEU 4.2 0.2 + - - -
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Residues in contact with GLN 141 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68O LEU* 3.9 24.5 - - + -
137O VAL* 3.2 26.0 + - - +
138O THR* 4.1 8.7 + - - +
140O LEU* 1.3 76.7 - - - +
142O PRO* 1.3 64.2 - - + +
143O GLN 2.7 6.6 + - - -
144O LEU* 2.8 23.0 + - + +
183O ILE* 3.7 6.6 - - - +
184O GLY* 2.8 51.4 + - - +
186O ILE* 2.9 47.2 + - - +
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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