Contacts of the helix formed by residues 124 - 135 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A CYS* 1.3 76.4 - - - +
125A ALA* 1.3 60.4 + - - +
126A ASP* 3.8 8.4 + - - +
127A THR* 3.0 23.2 + - - -
128A MET* 2.9 29.1 + - - +
179A GLU* 2.8 28.0 + - - -
1201A CL 3.7 16.8 - - - -
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Residues in contact with ALA 125 (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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123A CYS 3.9 0.6 + - - -
124A SER* 1.3 73.6 - - - +
126A ASP* 1.3 59.2 + - - +
128A MET* 4.3 0.7 - - - -
129A THR* 2.6 40.7 + - - +
153A LEU* 3.7 16.5 - - + +
157A TYR* 3.4 23.6 + - + +
1201A CL 3.5 14.2 - - + +
141F PRO* 4.6 7.0 - - + -
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Residues in contact with ASP 126 (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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124A SER* 3.2 9.1 - - - +
125A ALA* 1.3 83.3 - - - +
127A THR* 1.3 56.8 + - - +
129A THR* 3.7 5.5 - - - -
130A ASN* 3.1 28.9 + - - +
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Residues in contact with THR 127 (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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123A CYS* 3.6 11.9 - - - -
124A SER* 3.0 15.2 + - - -
126A ASP* 1.3 77.6 - - - +
128A MET* 1.3 65.2 + - - +
130A ASN* 3.4 5.0 + - - +
131A ARG* 3.0 53.3 + - + +
179A GLU* 2.6 30.6 + - - +
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Residues in contact with MET 128 (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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19A GLY* 3.7 24.2 - - - +
20A PRO 3.5 24.5 - - - +
21A GLY 4.5 5.8 - - - -
22A SER 4.8 0.4 - - - -
123A CYS* 3.6 40.4 - - + +
124A SER 2.9 16.3 + - - +
125A ALA* 3.9 2.9 - - - +
127A THR* 1.3 75.4 - - - +
129A THR* 1.3 62.9 + - - +
131A ARG* 3.4 4.9 + - - +
132A LEU* 3.0 31.6 + - - +
153A LEU* 3.8 20.9 - - + -
156A TYR* 4.7 6.7 - - + -
157A TYR* 3.3 34.1 - - + +
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Residues in contact with THR 129 (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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125A ALA* 2.6 24.7 + - - +
126A ASP* 3.7 7.2 - - - +
128A MET* 1.3 77.5 - - - +
130A ASN* 1.3 57.2 + - - +
132A LEU* 3.4 1.7 + - - +
133A LEU* 2.9 42.5 + - + +
146A THR* 4.0 27.1 - - + -
149A ILE* 4.0 19.2 - - + +
150A ALA* 5.6 1.2 + - - -
153A LEU* 3.6 13.9 - - - +
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Residues in contact with ASN 130 (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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126A ASP 3.1 19.0 + - - +
127A THR* 3.8 5.8 - - - +
128A MET 3.4 0.2 - - - -
129A THR* 1.3 76.0 - - - +
131A ARG* 1.3 60.5 + - - +
133A LEU* 3.3 12.4 + - - +
134A GLN* 2.8 50.4 + - - +
165E ALA* 2.8 34.5 + - - +
168E GLU* 3.8 14.1 + - - +
169E THR* 3.2 19.7 - - - +
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Residues in contact with ARG 131 (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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21A GLY* 3.0 32.8 + - - +
22A SER 3.5 11.9 + - - -
123A CYS* 3.7 8.7 - - - -
127A THR* 3.0 36.2 + - + +
128A MET 3.8 3.4 - - - +
130A ASN* 1.3 80.7 - - - +
132A LEU* 1.3 63.3 + - - +
134A GLN* 3.1 15.0 + - - +
135A MET* 3.1 30.9 + - - +
178A ALA 3.0 29.5 + - - -
179A GLU* 3.5 21.4 + - - +
180A GLY 3.7 8.5 + - - -
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Residues in contact with LEU 132 (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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20A PRO* 3.6 33.0 - - + +
21A GLY* 3.8 20.9 - - - +
128A MET 3.0 20.4 + - - +
129A THR 3.8 3.6 - - - +
131A ARG* 1.3 75.3 - - - +
133A LEU* 1.3 57.8 + - - +
135A MET* 3.2 23.8 + - + +
136A SER* 3.0 26.5 + - - -
149A ILE* 3.9 32.2 - - + +
152A ARG* 3.8 32.3 - - + +
153A LEU* 4.6 3.6 - - + -
1199A SO4 5.3 0.7 - - - +
55B GLU* 4.5 3.2 - - - +
58B LYS* 5.5 0.5 + - - -
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Residues in contact with LEU 133 (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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129A THR* 2.9 31.0 + - + +
130A ASN* 3.6 11.4 - - - +
132A LEU* 1.3 77.5 - - - +
134A GLN* 1.3 60.9 + - - +
136A SER* 3.1 18.2 + - - -
142A VAL* 4.1 11.0 - - + -
145A THR* 3.9 10.8 - - + -
146A THR* 3.7 24.0 - - + +
149A ILE* 3.5 20.9 - - + -
161E ILE* 3.9 21.2 - - + +
162E PRO* 3.3 16.7 - - - +
165E ALA* 3.6 17.3 - - + -
168E GLU* 5.7 4.0 - - - +
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Residues in contact with GLN 134 (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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130A ASN* 2.8 40.5 + - - +
131A ARG* 3.1 17.6 + - - +
133A LEU* 1.3 76.3 - - - +
135A MET* 1.3 60.5 + - + +
102E VAL* 4.2 14.1 - - + +
162E PRO* 3.5 24.5 - - - +
165E ALA* 3.7 17.6 + - + -
166E TYR* 3.5 36.1 - - + +
169E THR* 4.3 7.5 + - - +
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Residues in contact with MET 135 (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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21A GLY* 5.3 4.9 - - - -
131A ARG* 3.1 25.3 + - - +
132A LEU* 3.2 25.1 + - + +
133A LEU 3.1 0.2 - - - -
134A GLN* 1.3 78.1 - - + +
136A SER* 1.3 63.7 + - - +
137A ARG* 3.7 4.3 + - - +
1199A SO4 5.2 12.3 - - - +
58B LYS* 3.1 22.6 + - - +
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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