Contacts of the helix formed by residues 133 - 141 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B THR* 3.2 31.6 + - - +
77B THR 5.7 0.4 + - - -
131B GLU* 2.9 38.6 + - + +
132B PHE* 1.3 73.5 - - - +
134B PRO* 1.3 74.8 - - + +
135B TRP* 3.3 34.9 - - + +
136B GLU* 3.2 20.7 + - + +
137B VAL* 2.9 20.6 + - - +
96S GLU* 2.9 31.1 + - - +
99S ARG* 5.2 0.6 - - - +
100S GLU* 3.0 27.5 + - - -
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Residues in contact with PRO 134 (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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132B PHE 3.3 3.7 - - - +
133B ARG* 1.3 85.5 - - + +
135B TRP* 1.3 76.4 + - + +
137B VAL* 3.2 3.7 + - + +
138B THR* 2.8 33.6 + - - +
188B SER* 3.6 18.8 - - - +
49S ARG 5.9 0.7 - - - +
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Residues in contact with TRP 135 (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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133B ARG* 3.5 34.2 - - + +
134B PRO* 1.3 93.3 - - + +
136B GLU* 1.3 99.5 + - + +
138B THR* 2.7 20.1 + - - -
139B ASP* 2.8 27.8 + - - +
45S GLU* 5.5 2.2 - - - -
48S LYS 5.0 4.0 - - - +
49S ARG* 3.5 75.9 - - + +
93S TYR* 3.9 26.7 - + - -
96S GLU* 5.6 1.8 - - + -
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Residues in contact with GLU 136 (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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75B LEU* 3.3 29.3 - - + +
76B THR* 2.8 60.0 + - - +
82B SER* 4.1 7.0 - - - -
133B ARG* 3.2 22.8 + - + +
135B TRP* 1.3 101.6 + - + +
137B VAL* 1.3 60.8 + - - +
139B ASP* 3.6 8.8 + - - +
140B LEU* 3.2 24.4 + - - +
100S GLU* 4.8 2.3 - - - +
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Residues in contact with VAL 137 (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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68B LEU* 4.6 5.3 - - + +
75B LEU* 4.3 11.7 - - + -
132B PHE* 3.6 31.0 - - + +
133B ARG 2.9 16.7 + - - +
134B PRO* 3.3 8.7 - - + +
136B GLU* 1.3 75.4 - - - +
138B THR* 1.3 65.6 + - - +
140B LEU* 3.8 6.2 - - - +
141B GLN* 3.2 40.9 + - + +
186B ILE 5.0 0.7 - - - +
187B THR* 4.9 1.6 - - - -
188B SER* 3.7 17.3 - - - +
191B LEU* 4.2 20.6 - - + -
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Residues in contact with THR 138 (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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134B PRO* 2.8 19.4 + - - +
135B TRP* 2.7 16.7 + - - -
137B VAL* 1.3 75.1 - - - +
139B ASP* 1.3 65.3 + - - +
140B LEU 3.3 1.0 + - - -
141B GLN* 3.6 11.6 + - - +
142B PRO* 3.3 15.4 - - - +
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Residues in contact with ASP 139 (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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135B TRP* 2.8 30.6 + - - +
136B GLU* 3.9 8.2 + - - +
138B THR* 1.3 80.6 - - - +
140B LEU* 1.3 56.5 + - - +
142B PRO* 3.1 20.7 - - - +
143B GLN* 5.7 0.2 - - - +
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Residues in contact with LEU 140 (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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68B LEU* 4.0 15.9 - - + +
71B LEU* 3.8 15.7 - - + +
72B ALA* 3.5 36.3 - - + +
74B PRO* 6.0 1.1 - - + -
75B LEU* 3.6 22.4 - - + -
136B GLU 3.2 16.3 + - - +
137B VAL* 3.8 6.3 - - - +
138B THR 3.2 0.2 - - - -
139B ASP* 1.3 73.8 - - - +
141B GLN* 1.3 59.3 + - - +
142B PRO* 3.1 4.3 - - - -
143B GLN* 2.7 53.7 + - + +
144B LEU 4.2 0.2 + - - -
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Residues in contact with GLN 141 (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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68B LEU* 3.9 28.2 - - + +
137B VAL* 3.2 25.8 + - - +
138B THR* 4.0 10.1 + - - +
140B LEU* 1.3 77.0 - - - +
142B PRO* 1.3 63.8 - - + +
143B GLN 2.7 6.9 + - - -
144B LEU* 2.8 25.5 + - + +
183B ILE* 3.7 5.7 - - - +
184B GLY* 2.8 50.1 + - - +
186B ILE* 3.1 39.1 + - - +
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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