Contacts of the helix formed by residues 134 - 145 (chain C) in PDB entry 2BME
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 134 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131C ARG* 4.0 9.9 - - - +
132C GLU 5.8 1.1 - - - +
133C VAL* 1.3 76.2 - - - +
135C PHE* 1.3 65.7 + - - +
136C LEU* 3.7 6.6 + - - +
137C GLU* 2.8 43.2 + - - +
138C ALA* 3.2 23.9 + - - +
151C GLU* 4.7 0.4 - - - +
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Residues in contact with PHE 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ARG* 3.7 10.4 - - - +
134C THR* 1.3 74.3 - - - +
136C LEU* 1.3 75.3 + - + +
138C ALA 3.5 0.2 + - - -
139C SER* 2.8 46.4 + - - -
149C PHE* 3.4 35.3 - + - -
151C GLU* 3.9 26.2 - - - +
1179C TRS 3.6 45.3 - - - -
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Residues in contact with LEU 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C THR* 3.3 6.4 + - - +
135C PHE* 1.3 97.9 - - + +
137C GLU* 1.3 58.4 + - - +
139C SER* 3.2 9.1 + - - -
140C ARG* 3.0 28.4 + - - +
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Residues in contact with GLU 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ARG* 2.6 45.5 + - - -
98C TYR* 3.2 17.3 + - - +
132C GLU 4.1 0.5 - - - +
133C VAL* 3.4 6.6 - - + -
134C THR* 2.8 48.3 + - - +
136C LEU* 1.3 76.1 - - - +
138C ALA* 1.3 66.0 + - - +
140C ARG* 3.2 9.1 + - - +
141C PHE* 3.0 17.8 + - - +
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Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C TYR* 3.2 28.7 - - + +
98C TYR* 3.6 23.1 - - + -
120C LEU* 4.3 4.2 - - + +
133C VAL* 4.1 1.3 - - + -
134C THR 3.2 12.6 + - - +
137C GLU* 1.3 80.5 - - - +
139C SER* 1.3 61.5 + - - +
141C PHE* 3.3 2.3 + - - +
142C ALA* 2.8 29.8 + - - +
149C PHE* 3.6 17.0 - - + -
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Residues in contact with SER 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C PHE* 2.8 43.3 + - - -
136C LEU* 3.4 13.5 - - - -
138C ALA* 1.3 75.5 - - - +
140C ARG* 1.3 56.9 + - - +
142C ALA* 3.4 3.0 + - - +
143C GLN* 2.9 30.5 + - - +
149C PHE* 3.4 21.1 - - - -
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Residues in contact with ARG 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C LEU 3.0 13.3 + - - +
137C GLU* 3.5 11.1 - - - +
138C ALA 3.2 0.2 - - - -
139C SER* 1.3 74.9 - - - +
141C PHE* 1.3 60.3 + - - +
143C GLN* 3.3 11.3 + - - +
144C GLU* 2.9 58.2 + - + +
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Residues in contact with PHE 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C LEU* 5.5 0.2 - - + -
98C TYR* 3.5 26.9 - + - +
101C LEU* 3.8 41.5 - - + -
102C THR* 3.5 35.4 - - + -
105C LEU* 4.5 5.2 - - + -
120C LEU* 4.2 10.3 - - + -
137C GLU 3.0 6.6 + - - +
138C ALA* 3.6 5.2 - - - +
140C ARG* 1.3 77.7 - - - +
142C ALA* 1.3 63.6 + - - +
144C GLU* 3.4 9.3 + - - -
145C ASN* 2.9 55.7 + - - +
147C LEU* 4.0 19.7 - - + -
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Residues in contact with ALA 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C LEU* 4.1 8.3 - - + -
138C ALA 2.8 19.7 + - - +
139C SER 3.6 4.3 - - - +
141C PHE* 1.3 78.0 - - - +
143C GLN* 1.3 62.1 + - - +
145C ASN 3.1 1.9 + - - -
146C GLU 3.0 5.2 + - - -
147C LEU* 2.9 50.0 + - + +
149C PHE* 3.6 24.7 - - + -
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Residues in contact with GLN 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C SER 2.9 16.4 + - - +
140C ARG* 3.8 11.4 + - - +
142C ALA* 1.3 75.1 - - - +
144C GLU* 1.3 69.4 + - - +
145C ASN 3.1 1.0 + - - -
146C GLU* 3.2 16.1 + - - +
147C LEU 4.8 2.2 - - - -
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Residues in contact with GLU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C ARG* 2.9 48.2 + - + +
141C PHE* 3.8 10.2 - - - +
143C GLN* 1.3 82.1 - - + +
145C ASN* 1.3 69.1 + - - +
146C GLU* 3.9 4.5 + - - +
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Residues in contact with ASN 145 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C THR* 5.9 1.0 - - - +
105C LEU* 3.7 28.3 - - + +
109C ARG* 3.0 28.8 + - - +
141C PHE* 2.9 51.1 + - - +
144C GLU* 1.3 85.9 + - - +
146C GLU* 1.3 69.1 + - - +
147C LEU* 3.3 11.9 + - + +
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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