Contacts of the helix formed by residues 125 - 137 (chain A) in PDB entry 2EE5
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 ASP 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A ILE* 3.6 3.3 - - + +
124A PRO* 1.3 84.9 - - - +
126A LYS* 1.3 67.1 + - - +
127A THR* 3.2 3.1 - - - +
128A GLU* 3.1 31.9 + - + +
129A ARG* 2.9 23.6 + - - +
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Residues in contact with LYS 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 PRO 3.0 9.0 + - - +
125A ASP* 1.3 71.4 - - - +
127A THR* 1.3 67.5 + - - +
129A ARG* 3.2 50.4 + - - +
130A LEU* 3.3 21.3 + - + +
207A GLN* 6.2 1.6 - - - -
217A ILE* 4.1 30.1 - - + -
218A VAL 4.6 3.4 - - - -
219A GLU* 3.8 23.2 + - - -
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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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125A ASP* 3.2 2.6 - - - -
126A LYS* 1.3 78.6 - - - +
128A GLU* 1.3 69.5 + - - +
130A LEU* 2.7 22.8 + - - +
131A HIS* 3.0 43.9 - - + +
210A PHE* 5.2 3.6 - - + -
217A ILE* 4.4 16.4 - - + +
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Residues in contact with GLU 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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123A ILE* 3.9 15.5 - - + -
125A ASP* 3.1 31.9 + - + +
127A THR* 1.3 80.4 - - - +
129A ARG* 1.3 64.9 + - - +
131A HIS* 2.9 22.0 + - - +
132A ALA* 2.8 26.9 + - + +
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Residues in contact with ARG 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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120A ALA 2.9 27.0 - - - +
121A ALA* 3.3 28.9 + - - +
123A ILE* 3.8 21.6 + - + +
124A PRO 5.1 2.6 + - - -
125A ASP 2.9 11.8 + - - +
126A LYS* 3.2 45.6 - - - +
127A THR 3.0 0.2 + - - -
128A GLU* 1.3 75.2 - - - +
130A LEU* 1.3 62.5 + - - +
132A ALA* 4.0 0.2 - - - +
133A LEU* 2.9 41.6 + - + +
199A SER* 4.8 8.9 + - - -
203A THR* 3.9 23.9 + - - +
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Residues in contact with LEU 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 LYS* 3.3 23.3 - - + +
127A THR* 2.7 15.1 + - - +
129A ARG* 1.3 76.1 - - + +
131A HIS* 1.3 59.0 + - - +
133A LEU* 3.3 4.0 + - - -
134A LYS* 2.9 28.8 + - - +
203A THR* 3.8 24.2 - - + -
207A GLN* 3.2 49.6 - - + +
210A PHE* 3.5 24.5 - - + -
211A PHE* 3.6 8.9 - - + -
217A ILE* 4.3 21.8 - - + -
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Residues in contact with HIS 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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127A THR* 3.0 51.0 + - + +
128A GLU* 2.9 23.9 + - - +
130A LEU* 1.3 73.7 - - - +
132A ALA* 1.3 59.5 + - - +
134A LYS* 2.7 29.2 + - + +
135A GLU* 2.9 18.6 + - - +
210A PHE* 3.5 26.6 - + - -
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Residues in contact with ALA 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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120A ALA* 3.4 24.2 - - + -
123A ILE* 3.8 13.0 - - + -
128A GLU 2.8 19.7 + - - +
129A ARG 4.0 0.7 - - - +
131A HIS* 1.3 72.7 - - - +
133A LEU* 1.3 57.8 + - - +
135A GLU* 3.2 17.0 + - - +
136A ILE* 2.8 39.9 + - + +
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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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117A LEU* 3.6 31.6 - - + +
120A ALA* 3.9 14.4 - - + +
121A ALA* 4.5 3.6 - - + +
129A ARG* 2.9 36.2 + - + +
130A LEU* 3.7 5.8 - - - +
131A HIS 3.1 0.4 - - - -
132A ALA* 1.3 75.9 - - - +
134A LYS* 1.3 57.3 + - - +
136A ILE* 3.9 4.7 - - + -
137A VAL* 3.2 29.1 + - - +
200A VAL* 4.2 4.5 - - + +
203A THR* 3.8 31.4 - - + -
204A PHE* 3.6 36.4 - - + -
211A PHE* 4.7 6.3 - - + -
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Residues in contact with LYS 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 LEU 2.9 13.5 + - - +
131A HIS* 2.7 16.0 + - + +
133A LEU* 1.3 79.2 - - - +
135A GLU* 1.3 57.3 + - + +
137A VAL* 3.1 21.2 - - - +
138A LYS* 3.4 29.3 - - - +
210A PHE* 4.6 10.8 - - + +
211A PHE* 3.1 53.1 + - + +
212A PHE* 5.1 7.5 - - - +
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Residues in contact with GLU 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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131A HIS* 2.9 9.7 + - - +
132A ALA* 3.2 25.4 + - - +
134A LYS* 1.3 78.9 - - + +
136A ILE* 1.3 70.4 + - + +
137A VAL 3.3 0.4 - - - -
138A LYS* 3.1 36.6 - - + +
139A LYS* 4.2 8.3 + - - +
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Residues in contact with ILE 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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113A LEU* 4.6 5.8 - - + +
116A GLU* 3.0 56.1 - - + +
117A LEU* 4.6 18.8 - - + -
119A GLU* 5.2 2.2 - - - +
120A ALA* 3.4 18.8 - - + -
132A ALA* 2.8 28.3 + - + +
133A LEU* 4.3 5.6 - - + +
135A GLU* 1.3 82.2 - - + +
137A VAL* 1.3 58.8 + - - +
138A LYS 2.9 11.1 + - - -
139A LYS* 3.0 37.0 + - + +
140A PHE* 3.8 8.1 - - + -
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Residues in contact with VAL 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 LEU 3.2 15.0 + - - +
134A LYS* 3.1 24.9 - - - +
136A ILE* 1.3 77.4 - - - +
138A LYS* 1.3 60.8 + - + +
139A LYS 3.3 0.4 - - - -
140A PHE* 3.3 30.0 - - + +
145A TYR* 3.1 34.5 - - + +
148A PHE* 4.3 13.7 - - + -
149A ARG* 5.5 5.8 - - + -
204A PHE* 3.8 23.3 - - + -
211A PHE* 6.1 4.5 - - + -
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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