Contacts of the helix formed by residues 128 - 145 (chain A) in PDB entry 5EJC
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 GLU 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A PHE* 4.7 14.2 - - + -
126A PRO 4.5 7.4 - - - +
127A LEU* 1.3 77.0 - - - +
129A PRO* 1.3 79.1 - - + +
130A ASP* 3.3 4.0 - - + +
131A ASP* 2.9 30.4 + - - +
132A GLU* 3.3 8.6 + - - +
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Residues in contact with PRO 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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127A LEU 4.7 0.7 - - - +
128A GLU* 1.3 88.1 - - + +
130A ASP* 1.3 66.8 + - - +
132A GLU* 3.2 24.7 + - - +
133A VAL* 3.3 18.3 + - - +
209A ARG* 5.5 0.3 + - - -
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Residues in contact with ASP 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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128A GLU* 3.1 4.1 + - + +
129A PRO* 1.3 83.2 - - - +
131A ASP* 1.3 65.5 + - - +
133A VAL* 3.3 12.4 + - - +
134A PHE* 3.2 19.8 + - - +
208A LYS* 5.3 9.2 + - - +
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Residues in contact with ASP 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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109A LEU* 4.2 24.3 - - + +
112A TYR* 6.0 1.7 - - - -
113A GLN* 3.3 29.9 + - - +
118A LYS* 6.2 0.3 - - - -
126A PRO 5.1 0.2 - - - +
127A LEU* 4.2 13.6 - - + +
128A GLU* 2.9 36.9 + - - +
130A ASP* 1.3 80.1 - - - +
132A GLU* 1.3 58.5 + - - +
134A PHE* 3.4 6.0 + - - +
135A LEU* 3.0 27.1 + - - +
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Residues in contact with GLU 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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127A LEU* 4.0 31.0 - - + +
128A GLU 3.7 8.7 - - - +
129A PRO* 3.2 20.7 + - - +
131A ASP* 1.3 74.9 - - - +
133A VAL* 1.3 63.2 + - - +
135A LEU* 3.8 10.9 - - + +
136A ALA* 3.2 22.5 + - - +
209A ARG* 3.8 22.3 + - - +
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Residues in contact with VAL 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 PRO 3.3 14.6 + - - +
130A ASP* 3.4 14.1 - - - +
131A ASP 3.2 0.4 - - - -
132A GLU* 1.3 75.1 - - - +
134A PHE* 1.3 67.3 + - - +
136A ALA* 3.2 5.2 + - - +
137A ILE* 3.1 30.2 + - + +
159A VAL* 6.0 3.4 - - + -
162A LEU* 5.6 1.3 - - + -
204A ASP* 6.3 1.1 - - + -
208A LYS* 3.4 47.3 - - + +
209A ARG* 4.0 26.0 - - + +
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Residues in contact with PHE 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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108A TYR* 3.6 15.7 - - + -
109A LEU* 3.4 44.0 - - + -
112A TYR* 3.4 53.4 - + + -
130A ASP 3.2 8.8 + - - +
131A ASP* 3.5 9.2 - - - +
133A VAL* 1.3 80.2 - - - +
135A LEU* 1.3 54.1 + - - +
137A ILE* 3.2 6.7 + - - +
138A ALA* 2.8 43.2 + - + -
152A TYR* 4.9 4.7 - + - -
155A THR* 3.9 23.7 - - + +
156A ARG* 4.8 2.0 - - - -
159A VAL* 4.0 26.2 - - + +
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Residues in contact with LEU 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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105A ALA* 3.3 37.0 - - + +
106A GLU* 3.7 16.6 - - + +
109A LEU* 4.1 14.8 - - + -
127A LEU* 4.0 23.6 - - + -
131A ASP 3.0 15.5 + - - +
132A GLU* 3.8 9.4 - - + +
133A VAL 3.2 0.2 - - - -
134A PHE* 1.3 78.4 - - - +
136A ALA* 1.3 62.5 + - - +
138A ALA* 3.6 3.1 + - - +
139A LYS* 3.1 53.5 + - - +
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Residues in contact with ALA 136 (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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132A GLU 3.2 13.8 + - - +
133A VAL 3.2 9.5 + - - +
135A LEU* 1.3 78.3 - - - +
137A ILE* 1.3 59.6 + - - +
139A LYS* 3.5 11.8 + - - +
140A ALA* 3.3 16.1 + - - +
209A ARG* 3.9 30.3 - - - +
212A ALA* 3.7 22.7 - - + +
213A GLY* 5.1 1.0 + - - -
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Residues in contact with ILE 137 (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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133A VAL* 3.1 20.9 + - + +
134A PHE 3.7 5.6 - - - +
136A ALA* 1.3 72.6 - - - +
138A ALA* 1.3 61.0 + - - +
140A ALA* 3.0 3.5 + - - +
141A MSE 2.8 35.5 + - + +
155A THR* 4.2 10.1 - - + -
158A PHE* 3.9 20.9 - - + -
159A VAL* 4.1 18.8 - - + -
162A LEU* 4.3 10.8 - - + -
208A LYS 4.0 20.4 - - - +
209A ARG* 3.8 21.5 - - - +
212A ALA* 4.0 8.7 - - + -
224A TRP* 3.8 17.0 - - + -
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Residues in contact with ALA 138 (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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105A ALA* 4.1 19.7 - - + +
108A TYR* 4.4 9.1 - - + -
134A PHE* 2.8 40.8 + - + +
135A LEU 3.8 4.9 - - - +
137A ILE* 1.3 72.4 - - - +
139A LYS* 1.3 57.3 + - - +
141A MSE 3.6 1.9 + - - +
142A GLU* 3.1 32.8 + - - +
151A CYS* 4.5 2.8 - - - -
155A THR* 3.8 15.7 - - + +
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Residues in contact with LYS 139 (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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103A PRO* 6.4 2.0 - - - -
105A ALA* 3.7 17.9 - - + -
135A LEU* 3.1 46.6 + - - +
136A ALA* 3.6 9.4 - - - +
137A ILE 3.1 0.2 - - - -
138A ALA* 1.3 74.8 - - - +
140A ALA* 1.3 64.6 + - - +
142A GLU* 3.4 23.0 - - - +
143A GLU* 3.8 12.8 + - - +
217A GLU* 4.9 0.4 - - - +
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Residues in contact with ALA 140 (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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136A ALA 3.3 10.3 + - - +
137A ILE 3.0 8.4 + - - +
139A LYS* 1.3 76.4 - - - +
141A MSE 1.3 65.0 + - - +
143A GLU 3.1 10.7 + - - -
144A MSE 3.5 15.7 + - + +
212A ALA* 4.1 9.4 - - + -
213A GLY 5.3 0.7 - - - +
217A GLU* 3.4 34.4 - - - +
220A LEU* 4.4 3.4 - - + -
224A TRP* 3.8 21.3 - - + -
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Residues in contact with MSE 141 (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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60A TRP* 3.8 18.2 - - + -
137A ILE* 2.8 28.4 + - + +
138A ALA 3.8 2.0 - - - +
140A ALA* 1.3 72.5 - - - +
142A GLU* 1.3 55.9 + - - +
144A MSE 2.9 7.5 + - + +
145A VAL* 2.8 69.7 + - + +
151A CYS* 3.7 9.9 - - - +
154A ILE* 3.6 33.9 - - + -
155A THR* 3.4 27.8 - - - +
158A PHE* 5.4 4.7 - - + -
224A TRP* 3.8 23.8 - - + -
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Residues in contact with GLU 142 (chain A).
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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104A GLN* 3.4 28.2 + - + +
105A ALA* 3.8 25.2 + - - +
108A TYR* 4.5 8.1 - - + +
138A ALA 3.1 13.0 + - - +
139A LYS* 3.4 17.1 - - - +
140A ALA 3.1 0.4 - - - -
141A MSE 1.3 76.5 - - - +
143A GLU* 1.3 66.2 + - - +
145A VAL 3.1 16.4 - - - +
146A GLU* 4.6 2.9 + - - -
151A CYS* 3.6 15.9 - - - -
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Residues in contact with GLU 143 (chain A).
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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139A LYS 3.8 13.3 - - - +
140A ALA 3.1 5.9 + - - +
142A GLU* 1.3 85.6 - - - +
144A MSE 1.3 63.2 - - - +
145A VAL 3.6 0.7 - - - -
217A GLU* 3.8 32.1 - - + +
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Residues in contact with MSE 144 (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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56A ARG* 5.7 2.0 - - - -
60A TRP* 4.0 13.2 - - + -
140A ALA* 3.6 9.9 - - + +
141A MSE 2.9 14.5 + - + +
143A GLU* 1.3 80.7 - - - +
145A VAL* 1.3 62.2 + - + +
146A GLU 4.2 1.1 + - - -
217A GLU* 3.7 35.7 - - + +
220A LEU* 3.8 24.7 - - + -
221A GLN* 3.8 38.7 - - + +
224A TRP* 3.7 39.9 - - + -
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Residues in contact with VAL 145 (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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56A ARG* 6.6 0.2 - - + -
57A ALA* 4.9 14.1 - - + -
60A TRP* 5.2 4.5 - - + -
141A MSE 2.8 42.8 + - + +
142A GLU* 3.1 17.1 - - - +
143A GLU 5.0 0.4 - - - -
144A MSE 1.3 78.1 - - + +
146A GLU* 1.3 63.1 + - - +
147A ASP* 3.6 9.0 - - + +
150A ASP* 3.6 15.3 - - + +
151A CYS* 3.4 37.4 - - - +
154A ILE* 3.8 14.1 - - + -
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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