Contacts of the helix formed by residues 125 - 136 (chain A) in PDB entry 1EG4
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 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 LEU 3.7 4.6 + - - -
124A LEU* 1.3 78.1 - - - +
126A LEU* 1.3 66.1 + - - +
127A SER* 3.5 9.8 + - - -
128A ALA* 2.9 27.8 + - - +
129A ALA* 3.0 19.4 + - - +
160A ARG* 5.3 0.2 + - - -
207A CYS* 4.4 1.3 - - - -
208A LYS* 3.9 22.6 - - - +
209A ALA* 4.8 1.6 - - - +
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Residues in contact with LEU 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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125A SER* 1.3 73.1 - - - +
127A SER* 1.3 57.7 + - - +
129A ALA* 3.3 2.7 + - - +
130A CYS* 2.9 46.5 + - - +
204A ILE* 4.0 31.9 - - + -
207A CYS* 4.2 7.2 - - - -
209A ALA* 3.6 23.1 - - + +
213A ASP* 3.8 37.5 - - + +
217A TYR* 4.0 17.0 - - + -
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Residues in contact with SER 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 SER* 3.2 9.3 - - - -
126A LEU* 1.3 80.2 - - - +
128A ALA* 1.3 62.7 + - - +
130A CYS* 3.3 6.0 + - - +
131A ASP* 3.0 32.8 + - - +
160A ARG* 5.3 2.1 + - - -
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Residues in contact with ALA 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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124A LEU* 4.0 15.5 - - + +
125A SER* 2.9 21.8 + - - +
127A SER* 1.3 76.9 - - - +
129A ALA* 1.3 62.9 + - - +
131A ASP* 3.3 3.0 + - - +
132A ALA* 3.2 21.3 + - - +
157A ILE* 5.1 0.7 - - - +
160A ARG* 3.5 43.1 + - - +
161A LEU* 6.0 1.6 - - + -
164A GLU* 5.8 0.9 - - - +
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Residues in contact with ALA 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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124A LEU* 3.9 26.3 - - + +
125A SER 3.0 17.8 + - - +
126A LEU* 3.3 7.2 + - - +
128A ALA* 1.3 73.5 - - - +
130A CYS* 1.3 62.5 + - - +
132A ALA* 3.2 8.2 + - - +
133A LEU* 2.9 29.3 + - + +
157A ILE* 5.1 3.4 - - + +
203A ILE* 4.3 13.7 - - + -
204A ILE* 4.7 14.6 - - + -
207A CYS* 5.3 2.9 - - + -
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Residues in contact with CYS 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 LEU* 2.9 34.7 + - - +
127A SER* 3.7 6.5 - - - +
129A ALA* 1.3 77.5 - - - +
131A ASP* 1.3 57.6 + - - +
133A LEU* 3.7 8.5 - - - +
134A ASP* 2.8 39.2 + - - +
217A TYR* 3.5 36.6 - - - -
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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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127A SER* 3.0 29.2 + - - +
128A ALA 3.3 2.2 + - - +
130A CYS* 1.3 76.8 - - - +
132A ALA* 1.3 57.8 + - - +
134A ASP* 3.6 5.4 - - - +
135A GLN* 3.0 36.3 + - + +
160A ARG* 2.6 39.0 + - - +
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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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128A ALA 3.2 8.1 + - - +
129A ALA 3.5 7.2 - - - +
131A ASP* 1.3 80.7 - - - +
133A LEU* 1.3 61.2 + - - +
135A GLN* 3.4 1.2 + - - +
136A HIS* 3.2 29.3 + - - +
153A CYS* 4.1 7.9 - - - -
156A THR* 4.0 24.0 - - + -
157A ILE* 3.5 36.1 - - + -
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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 ALA* 2.9 28.7 + - + +
130A CYS* 3.7 9.9 - - - +
132A ALA* 1.3 71.5 - - + +
134A ASP* 1.3 62.0 + - - +
136A HIS 3.4 1.0 + - - -
137A ASN 3.3 2.9 + - - -
138A LEU* 3.0 49.1 + - + +
153A CYS* 4.4 1.6 - - - -
157A ILE* 6.2 1.3 - - + -
199A PHE* 3.6 37.0 - - + -
200A LYS* 3.9 19.1 - - + -
203A ILE* 6.0 2.9 - - + -
204A ILE* 3.8 22.2 - - + -
217A TYR* 3.4 24.2 - - + +
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Residues in contact with ASP 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 CYS* 2.8 25.6 + - - +
131A ASP* 3.6 7.2 - - - +
133A LEU* 1.3 79.1 - - - +
135A GLN* 1.3 67.3 + - - +
137A ASN* 3.0 27.4 + - - +
139A LYS* 6.1 0.5 - - - +
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Residues in contact with GLN 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 ASP* 3.0 17.5 + - + +
132A ALA* 3.9 6.1 - - - +
134A ASP* 1.3 88.3 + - - +
136A HIS* 1.3 67.9 + - + +
137A ASN* 3.3 10.5 + - - +
156A THR* 5.4 4.9 - - + -
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Residues in contact with HIS 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 ALA 3.2 24.8 + - - +
133A LEU 3.4 0.2 + - - -
134A ASP 3.1 1.0 - - - -
135A GLN* 1.3 79.3 - - + +
137A ASN* 1.3 71.5 + - - +
138A LEU* 3.3 30.4 + - + +
149A GLN* 4.9 5.9 + - + -
152A ASN* 3.4 37.7 + - + +
153A CYS* 3.6 12.7 - - + -
156A THR* 2.8 36.3 - - + -
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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