Contacts of the helix formed by residues 126 - 141 (chain N) in PDB entry 1G3I
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 GLY 126 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1N THR 3.1 5.1 + - - -
2N THR* 3.2 29.8 - - - +
125N SER* 1.3 81.3 + - - +
127N GLY* 1.3 68.5 + - - +
129N TYR* 3.3 24.9 + - - +
130N ALA 3.3 8.7 + - - -
156N ALA* 4.9 0.4 - - - -
160N CYS* 4.0 9.6 - - - -
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Residues in contact with GLY 127 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2N THR* 4.2 2.4 - - - +
122N ALA* 4.1 17.7 - - - +
123N ILE* 4.1 14.1 - - - -
124N GLY 3.2 11.7 + - - -
125N SER 2.9 9.9 + - - -
126N GLY* 1.3 79.0 - - - +
128N ASN* 1.3 55.3 + - - -
129N TYR 2.5 15.5 + - - -
130N ALA* 2.7 12.6 + - - +
131N LEU 3.0 7.7 + - - -
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Residues in contact with ASN 128 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H TYR* 3.5 24.9 + - + -
159H ILE* 3.8 16.8 - - + +
25M THR* 3.7 33.3 + - - +
26M VAL 5.2 3.1 - - - +
27M MET* 6.1 0.2 - - - -
122N ALA* 4.9 0.2 - - - +
125N SER 5.1 5.3 + - - -
127N GLY* 1.3 72.7 - - - +
129N TYR* 1.3 57.9 + - + +
131N LEU* 3.6 20.1 - - - +
132N SER* 2.7 34.9 + - - -
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Residues in contact with TYR 129 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H ASN* 3.5 23.4 + - + -
129H TYR* 3.5 31.6 + + - -
132H SER* 3.6 22.7 - - - +
25I THR* 3.2 25.3 - - + +
125N SER 4.7 5.6 - - - -
126N GLY* 3.4 25.3 - - - +
127N GLY 2.5 6.1 + - - -
128N ASN* 1.3 76.1 - - + +
130N ALA* 1.3 64.8 + - - +
132N SER* 3.0 9.8 + - - -
133N ALA* 3.0 10.9 + - - +
155N ILE* 5.0 0.9 - - - -
156N ALA* 4.0 14.1 - - + -
159N ILE* 3.6 29.4 - - + -
160N CYS* 4.3 15.9 - - + -
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Residues in contact with ALA 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2N THR* 3.8 22.9 - - + -
4N VAL* 3.9 26.7 - - + -
122N ALA* 4.8 0.9 - - + -
127N GLY 2.7 12.4 + - - +
129N TYR* 1.3 75.9 - - - +
131N LEU* 1.3 50.8 + - - +
133N ALA* 3.2 4.6 + - - +
134N ALA* 2.7 34.0 + - - +
152N SER* 3.5 28.1 + - - +
153N LEU* 4.7 0.2 - - + -
156N ALA* 3.8 2.1 - - + +
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Residues in contact with LEU 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H ILE* 4.1 14.4 - - + -
26M VAL 5.2 4.7 - - - +
27M MET* 6.0 1.3 - - - +
4N VAL* 4.9 1.3 - - - -
120N ILE* 4.2 22.9 - - + +
122N ALA* 4.1 19.6 - - + +
127N GLY 3.0 5.9 + - - +
128N ASN* 3.4 26.0 - - - +
130N ALA* 1.3 77.5 - - - +
132N SER* 1.3 64.4 + - - +
134N ALA* 3.0 5.1 + - - +
135N ARG* 2.9 76.2 + - + +
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Residues in contact with SER 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H TYR* 3.7 31.7 - - - +
132H SER* 4.0 4.0 - - - -
133H ALA* 4.1 3.6 - - - -
155H ILE* 3.7 26.0 - - - +
159H ILE* 3.0 20.4 - - - +
128N ASN 2.7 25.6 + - - -
129N TYR 3.5 3.8 - - - -
131N LEU* 1.3 73.0 - - - +
133N ALA* 1.3 57.3 + - - +
135N ARG* 4.6 1.1 - - - -
136N ALA* 3.0 28.6 + - - +
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Residues in contact with ALA 133 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H SER* 4.3 5.3 - - - +
136H ALA* 4.3 7.6 - - + -
129N TYR 3.0 11.0 + - - +
130N ALA* 3.3 9.0 - - - +
132N SER* 1.3 74.9 - - - +
134N ALA* 1.3 71.6 + - - +
136N ALA* 3.0 8.6 + - - +
137N LEU* 2.8 23.7 + - + +
152N SER* 3.5 22.2 - - - +
155N ILE* 4.1 25.4 - - + -
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Residues in contact with ALA 134 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4N VAL* 4.5 3.1 - - + -
6N VAL* 4.1 11.9 - - + -
120N ILE* 3.4 33.2 - - + -
130N ALA 2.7 17.1 + - - +
131N LEU* 3.4 7.6 - - - +
133N ALA* 1.3 68.6 - - - +
135N ARG* 1.3 57.1 + - - +
137N LEU* 2.5 26.7 + - - -
138N VAL* 2.8 13.1 + - - -
148N ILE* 4.0 6.5 - - - -
152N SER* 2.9 15.2 + - - +
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Residues in contact with ARG 135 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155H ILE* 4.5 14.2 + - + +
158H ASP* 4.5 16.8 + - - +
159H ILE* 3.7 27.6 - - - +
26M VAL 4.6 10.3 + - - -
27M MET 4.7 8.9 + - - -
28M LYS* 5.9 1.0 - - - +
116N GLU* 6.1 2.4 - - - +
118N ASP* 4.2 18.5 + - - +
120N ILE* 3.4 19.7 + - + +
131N LEU* 2.9 55.7 + - + +
132N SER* 4.0 3.6 - - - +
134N ALA* 1.3 75.7 - - - +
136N ALA* 1.3 63.4 + - - +
138N VAL* 4.6 0.2 - - - -
139N GLU* 3.0 47.4 + - - +
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Residues in contact with ALA 136 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H ALA* 4.0 9.9 - - - -
136H ALA* 4.1 2.0 - - + -
137H LEU* 3.2 28.0 - - + +
155H ILE* 3.5 20.1 - - + +
132N SER 3.0 17.5 + - - +
133N ALA* 3.0 13.9 - - - +
135N ARG* 1.3 78.5 - - - +
137N LEU* 1.3 61.3 - - - +
140N ASN* 3.2 27.4 + - - +
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Residues in contact with LEU 137 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136H ALA* 3.7 31.2 - - + +
137H LEU* 4.5 3.1 - - + -
140H ASN* 3.8 21.1 - - + +
141H THR* 6.4 0.4 - - + -
133N ALA* 2.8 11.0 + - + +
134N ALA 2.5 12.2 + - - +
136N ALA* 1.3 68.4 - - - +
138N VAL* 1.3 69.7 + - - +
139N GLU 2.8 3.8 + - - -
140N ASN* 2.8 13.7 + - - -
141N THR* 2.8 29.9 - - + +
143N LEU* 4.1 9.2 - - + -
148N ILE* 3.6 29.2 - - + -
151N LYS* 4.0 27.6 - - + -
152N SER* 4.1 7.2 - - - +
155N ILE* 6.4 0.4 - - + -
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Residues in contact with VAL 138 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N VAL* 3.5 25.1 - - + -
8N ARG* 3.9 28.7 + - + +
118N ASP* 4.7 14.4 - - + +
120N ILE* 3.7 25.6 - - + -
134N ALA 2.8 13.4 + - - +
135N ARG 4.2 0.9 - - - +
137N LEU* 1.3 73.7 - - - +
139N GLU* 1.3 65.9 + - + +
141N THR 3.6 10.0 - - - +
148N ILE* 3.2 27.1 - - + +
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Residues in contact with GLU 139 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155H ILE* 5.0 10.0 - - - +
118N ASP* 4.7 12.2 - - + +
135N ARG* 3.0 40.2 + - - +
137N LEU 2.8 4.0 + - - -
138N VAL* 1.3 81.8 - - + +
140N ASN* 1.3 70.3 + - - +
141N THR 3.7 0.4 - - - -
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Residues in contact with ASN 140 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137H LEU* 4.3 16.9 - - + +
141H THR* 5.3 9.8 - - + +
143H LEU* 4.5 25.3 - - + +
151H LYS* 4.6 12.1 - - - +
155H ILE* 5.7 1.4 - - - +
136N ALA* 3.2 24.2 + - - +
137N LEU* 2.8 6.6 + - - -
139N GLU* 1.3 88.4 + - - +
141N THR* 1.3 62.3 + - - +
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Residues in contact with THR 141 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140H ASN 4.7 12.8 + - - -
141H THR* 6.1 1.1 - - - -
8N ARG* 2.7 26.5 + - - -
137N LEU* 2.8 43.7 + - + +
138N VAL 3.6 6.1 - - - +
139N GLU 3.7 1.4 - - - -
140N ASN* 1.3 80.6 - - - +
142N GLU* 1.3 69.7 + - - +
143N LEU* 3.2 39.8 - - + +
148N ILE* 4.7 0.2 - - + -
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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