Contacts of the helix formed by residues 126 - 141 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1P THR 3.2 5.3 + - - -
2P THR* 3.2 30.4 + - - +
125P SER* 1.3 81.3 + - - +
127P GLY* 1.3 68.9 + - - +
129P TYR* 3.3 24.9 + - - +
130P ALA 3.3 8.1 + - - -
156P ALA* 3.8 0.6 - - - +
160P CYS* 3.9 10.0 - - - -
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Residues in contact with GLY 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2P THR* 4.1 2.8 - - - +
122P ALA* 4.2 17.0 - - - +
123P ILE* 4.2 13.9 - - - -
124P GLY 3.1 13.0 + - - -
125P SER 2.9 8.9 + - - -
126P GLY* 1.3 79.4 - - - +
128P ASN* 1.3 55.1 + - - -
129P TYR 2.4 16.7 + - - -
130P ALA* 2.6 12.0 + - - +
131P LEU 3.0 7.4 + - - -
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Residues in contact with ASN 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J TYR* 3.4 25.5 + - + -
159J ILE* 3.9 17.2 - - + +
25O THR* 3.7 32.1 + - - +
26O VAL 5.2 3.3 - - - +
122P ALA 5.6 0.4 + - - -
124P GLY 5.7 1.0 + - - -
125P SER 5.0 5.9 + - - -
127P GLY* 1.3 69.3 - - - +
129P TYR* 1.3 55.1 + - + +
131P LEU* 3.5 21.2 - - - +
132P SER* 2.7 38.9 + - - -
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Residues in contact with TYR 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J ASN* 3.3 29.5 + - + -
129J TYR* 3.6 26.8 + + - -
132J SER* 3.6 23.2 - - - +
25K THR* 3.3 22.6 - - + +
125P SER 4.7 4.7 - - - -
126P GLY* 3.4 27.1 - - - +
127P GLY 2.4 11.1 + - - -
128P ASN* 1.3 72.0 - - + +
130P ALA* 1.3 64.3 + - - +
132P SER* 3.0 2.9 + - - -
133P ALA* 3.0 17.7 + - - +
155P ILE* 4.9 1.1 - - - -
156P ALA* 4.0 14.6 - - + -
159P ILE* 3.6 29.6 - - + -
160P CYS* 4.3 15.0 - - + -
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Residues in contact with ALA 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2P THR* 3.8 23.3 - - + -
4P VAL* 3.9 27.1 - - + -
122P ALA* 4.9 1.6 - - + -
126P GLY 3.3 1.0 + - - -
127P GLY 2.6 11.7 + - - +
129P TYR* 1.3 74.9 - - - +
131P LEU* 1.3 55.7 + - - +
133P ALA* 3.1 4.5 + - - +
134P ALA* 2.7 30.8 + - - +
152P SER* 3.5 26.2 + - - +
153P LEU* 4.7 0.2 - - + -
156P ALA* 3.8 2.1 - - + +
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Residues in contact with LEU 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159J ILE* 4.0 14.4 - - + -
26O VAL 5.3 4.3 - - - +
27O MET* 6.5 0.2 - - - -
4P VAL* 4.9 0.7 - - - -
120P ILE* 4.2 22.4 - - + +
122P ALA* 4.0 19.8 - - + +
127P GLY 3.0 6.5 + - - +
128P ASN* 3.5 24.7 - - - +
130P ALA* 1.3 75.8 - - - +
132P SER* 1.3 64.8 + - - +
134P ALA* 3.1 5.3 + - - -
135P ARG* 2.9 76.8 + - + +
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Residues in contact with SER 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J TYR* 3.7 19.0 - - - +
132J SER* 3.9 15.0 - - - -
133J ALA* 4.0 3.3 - - - -
155J ILE* 3.6 27.2 - - - +
159J ILE* 3.1 19.2 - - - +
128P ASN 2.7 27.7 + - - -
129P TYR 3.5 4.0 - - - -
131P LEU* 1.3 74.2 - - - +
133P ALA* 1.3 57.6 + - - +
135P ARG* 4.6 0.9 - - - -
136P ALA* 3.0 28.6 + - - +
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Residues in contact with ALA 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J SER* 4.3 4.9 - - - +
136J ALA* 4.2 8.3 - - + -
129P TYR 3.0 11.9 + - - +
130P ALA 3.2 9.2 - - - +
132P SER* 1.3 74.0 - - - +
134P ALA* 1.3 71.5 + - - +
136P ALA* 3.0 10.2 - - - +
137P LEU* 2.8 22.8 + - + +
152P SER* 3.4 22.7 - - - +
155P ILE* 4.1 24.7 - - + -
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Residues in contact with ALA 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4P VAL* 4.5 3.1 - - + -
6P VAL* 4.0 13.5 - - + -
120P ILE* 3.5 33.2 - - + -
130P ALA 2.7 16.5 + - - +
131P LEU* 3.4 8.1 - - - +
133P ALA* 1.3 68.0 - - - +
135P ARG* 1.3 56.0 + - - +
137P LEU* 2.5 26.4 + - - +
138P VAL* 2.8 13.4 + - - -
148P ILE* 4.0 6.5 - - - -
152P SER* 2.9 15.8 + - - +
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Residues in contact with ARG 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155J ILE* 4.5 16.9 + - + +
158J ASP* 4.5 16.6 + - - +
159J ILE* 3.7 22.2 - - - +
26O VAL 4.7 10.3 + - - -
27O MET 5.0 6.9 + - - -
28O LYS* 6.1 0.6 - - - +
118P ASP* 4.2 17.8 + - - +
120P ILE* 3.5 19.1 + - + +
131P LEU* 2.9 56.8 + - + +
132P SER* 4.0 3.8 - - - +
134P ALA* 1.3 74.9 - - - +
136P ALA* 1.3 64.7 + - - +
138P VAL* 4.6 0.2 - - - -
139P GLU* 3.0 47.1 + - - +
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Residues in contact with ALA 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J ALA* 3.9 4.5 - - - -
136J ALA* 3.9 8.5 - - + -
137J LEU* 3.2 28.3 - - + +
155J ILE* 3.6 19.6 - - + +
132P SER 3.0 17.5 + - - +
133P ALA 3.0 14.5 + - - +
134P ALA 2.8 0.4 + - - -
135P ARG* 1.3 78.4 - - - +
137P LEU* 1.3 61.1 + - - +
139P GLU* 5.3 0.2 - - - -
140P ASN* 3.2 26.8 + - - +
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Residues in contact with LEU 137 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J ALA* 3.6 31.6 - - + +
137J LEU* 4.6 2.0 - - + -
140J ASN* 3.8 20.6 - - + +
141J THR* 6.1 0.9 - - + -
133P ALA* 2.8 6.5 + - + +
134P ALA 2.5 12.0 + - - +
136P ALA* 1.3 68.6 - - - +
138P VAL* 1.3 68.5 + - - +
139P GLU 3.0 1.6 - - - -
140P ASN 2.7 17.0 + - - -
141P THR* 2.9 29.4 + - + +
143P LEU* 4.1 8.3 - - + -
148P ILE* 3.6 22.9 - - + -
151P LYS* 3.9 28.3 - - + -
152P SER* 4.1 17.3 - - - +
155P ILE* 6.4 0.7 - - + -
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Residues in contact with VAL 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6P VAL* 3.5 25.4 - - + -
8P ARG* 3.9 29.1 + - + +
118P ASP* 4.7 14.4 - - + +
120P ILE* 3.7 26.5 - - + -
134P ALA 2.8 13.9 + - - +
135P ARG 4.2 0.9 - - - +
137P LEU* 1.3 73.3 - - - +
139P GLU* 1.3 63.5 + - + +
141P THR 3.6 10.7 - - - +
148P ILE* 3.1 27.5 - - + +
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Residues in contact with GLU 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155J ILE* 5.0 10.0 - - - +
118P ASP* 4.7 11.6 - - + +
135P ARG* 3.0 40.0 + - - +
137P LEU 2.7 5.1 + - - -
138P VAL* 1.3 81.3 - - + +
140P ASN* 1.3 72.8 + - - +
141P THR 3.7 0.2 - - - -
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Residues in contact with ASN 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137J LEU* 4.3 17.8 - - + +
141J THR* 4.9 11.2 + - + -
143J LEU* 4.2 26.2 - - + +
151J LYS* 4.9 8.1 - - - +
155J ILE* 5.7 1.4 - - - +
136P ALA* 3.2 24.0 + - - +
137P LEU 2.7 10.1 + - - -
139P GLU* 1.3 89.0 + - - +
141P THR* 1.3 60.5 + - - -
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Residues in contact with THR 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J ASN 4.4 14.3 + - - -
141J THR* 5.8 0.9 - - - -
8P ARG* 2.7 26.9 + - - -
137P LEU* 2.9 43.5 + - + +
138P VAL 3.6 7.0 - - - +
139P GLU 3.7 0.8 - - - -
140P ASN* 1.3 81.2 - - - +
142P GLU* 1.3 70.0 + - - +
143P LEU* 3.2 39.6 - - + +
148P ILE* 4.8 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