Contacts of the helix formed by residues 124 - 136 (chain E) in PDB entry 2BWJ
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 SER 124 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123E CYS* 1.3 78.0 - - - +
125E ALA* 1.3 65.0 + - - +
126E ASP* 3.6 9.4 + - - +
127E THR* 2.8 31.2 + - - -
128E MET* 3.1 23.3 + - - +
179E GLU* 2.7 18.8 + - - -
1199E CL 3.9 16.2 - - - -
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Residues in contact with ALA 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A PRO* 4.5 8.3 - - + -
124E SER* 1.3 73.0 - - - +
126E ASP* 1.3 55.4 + - - +
128E MET* 3.5 1.2 + - - -
129E THR* 2.7 39.0 + - - +
153E LEU* 3.7 16.0 - - + +
157E TYR* 3.5 23.4 + - + +
1199E CL 3.7 13.8 - - + +
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Residues in contact with ASP 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E SER* 3.2 9.1 - - - +
125E ALA* 1.3 79.0 - - - +
127E THR* 1.3 59.8 + - - +
129E THR* 3.4 4.7 + - - -
130E ASN* 2.9 53.2 + - - +
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Residues in contact with THR 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E CYS* 3.5 21.8 - - - -
124E SER* 2.8 17.4 + - - -
126E ASP* 1.3 78.1 - - - +
128E MET* 1.3 62.2 + - - +
130E ASN* 3.3 5.2 + - - +
131E ARG* 3.0 56.6 + - + +
179E GLU* 2.4 33.2 + - - +
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Residues in contact with MET 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E GLY* 3.7 24.7 - - - +
20E PRO 3.4 24.2 - - - +
21E GLY 4.7 2.0 - - - -
22E SER 4.3 5.2 - - - +
123E CYS* 3.6 36.1 - - + +
124E SER 3.1 10.8 + - - +
125E ALA* 4.0 1.3 - - - +
127E THR* 1.3 75.7 - - - +
129E THR* 1.3 59.1 + - - +
131E ARG* 3.7 5.4 - - - +
132E LEU* 2.9 37.6 + - - +
153E LEU* 3.8 22.4 - - + -
156E TYR* 4.5 8.7 - - + -
157E TYR* 3.3 34.5 - - + +
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Residues in contact with THR 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E ALA* 2.7 25.4 + - - +
126E ASP* 3.7 6.3 - - - -
128E MET* 1.3 77.5 - - - +
130E ASN* 1.3 60.1 + - - +
132E LEU* 3.7 1.9 - - - +
133E LEU* 2.9 45.2 + - + +
146E THR* 6.0 5.2 - - + -
149E ILE* 4.0 22.5 - - + +
150E ALA* 5.9 0.5 - - - -
153E LEU* 3.4 16.1 - - - +
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Residues in contact with ASN 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E ASP* 2.9 37.7 + - - +
127E THR* 3.9 4.8 - - - +
129E THR* 1.3 78.5 - - - +
131E ARG* 1.3 61.4 + - + +
133E LEU* 3.5 13.5 + - - +
134E GLN* 2.8 30.7 + - - +
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Residues in contact with ARG 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E GLY* 2.9 30.7 + - - +
22E SER 3.2 14.1 + - - -
23E GLY* 5.0 0.6 - - - -
123E CYS* 3.7 10.3 - - - -
127E THR* 3.0 37.0 + - + +
128E MET 3.7 3.4 - - - +
130E ASN* 1.3 75.9 - - + +
132E LEU* 1.3 60.3 + - - +
134E GLN* 3.1 7.8 + - - +
135E MET* 2.9 42.1 + - + +
178E ALA 3.0 28.5 + - - -
179E GLU 3.7 16.4 + - - -
180E GLY 3.9 7.5 + - - -
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Residues in contact with LEU 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D GLU* 4.3 5.4 - - - +
58D LYS* 5.6 0.6 + - + -
20E PRO* 3.6 31.2 - - + +
21E GLY* 4.0 13.5 - - - +
128E MET 2.9 26.0 + - - +
129E THR 3.7 3.1 - - - +
131E ARG* 1.3 76.4 - - - +
133E LEU* 1.3 62.8 + - - +
135E MET* 3.4 26.1 + - + +
136E SER* 3.1 21.3 + - - -
149E ILE* 3.8 34.3 - - + +
152E ARG* 3.5 28.5 - - - +
153E LEU* 4.4 3.8 - - + -
1198E SO4 5.5 0.7 - - - +
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Residues in contact with LEU 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E THR* 2.9 32.2 + - + +
130E ASN* 3.6 14.4 - - - +
132E LEU* 1.3 76.8 - - - +
134E GLN* 1.3 62.3 + - - +
136E SER* 3.0 22.8 + - - +
142E VAL* 5.6 6.3 - - + -
145E THR* 4.0 18.2 - - + -
146E THR* 4.4 20.6 - - + -
149E ILE* 3.7 19.7 - - + +
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Residues in contact with GLN 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E ASN 2.8 22.3 + - - +
131E ARG* 3.1 8.5 + - - +
133E LEU* 1.3 73.5 - - - +
135E MET* 1.3 57.3 + - - +
136E SER 4.2 1.7 - - - +
137E ARG* 3.5 16.5 + - - -
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Residues in contact with MET 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D LYS* 4.6 6.6 + - - -
21E GLY* 4.0 16.2 - - - -
131E ARG* 2.9 31.8 + - + +
132E LEU* 3.8 32.8 - - + +
134E GLN* 1.3 74.5 - - - +
136E SER* 1.3 65.9 + - - +
137E ARG* 3.5 21.6 + - - +
1198E SO4 5.2 6.3 - - - +
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Residues in contact with SER 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D GLU* 3.9 10.3 + - - -
58D LYS* 4.2 9.6 + - - +
132E LEU 3.1 12.6 + - - -
133E LEU* 3.0 24.5 + - - +
134E GLN 4.2 1.4 - - - +
135E MET* 1.3 77.6 - - - +
137E ARG* 1.3 73.0 + - - +
138E SER* 3.3 20.8 + - - -
145E THR* 3.9 14.9 - - - +
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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