Contacts of the helix formed by residues 126 - 141 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1O THR 3.2 5.1 + - - -
2O THR* 3.2 30.4 - - - +
125O SER* 1.3 80.7 + - - +
127O GLY* 1.3 67.6 + - - +
128O ASN 3.8 0.4 - - - -
129O TYR* 3.3 25.1 + - - +
130O ALA 3.3 8.5 + - - -
156O ALA* 3.8 0.8 - - - +
160O CYS* 4.0 9.6 - - - -
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Residues in contact with GLY 127 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2O THR* 4.2 3.1 - - - +
122O ALA* 4.2 17.0 - - - -
123O ILE* 4.1 14.6 + - - -
124O GLY 3.2 13.0 + - - -
125O SER 3.0 9.1 + - - -
126O GLY* 1.3 78.1 - - - +
128O ASN* 1.3 54.6 + - - -
129O TYR 2.5 15.2 + - - -
130O ALA* 2.7 12.6 + - - +
131O LEU 2.9 7.4 + - - -
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Residues in contact with ASN 128 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129I TYR* 3.6 25.3 + - + -
159I ILE* 3.8 17.0 - - + +
25N THR* 3.7 32.4 + - - +
26N VAL 5.2 3.3 - - - +
122O ALA* 4.8 0.2 - - - +
124O GLY 5.7 1.2 + - - -
125O SER 5.1 5.5 + - - -
126O GLY 3.8 0.2 - - - -
127O GLY* 1.3 71.0 - - - +
129O TYR* 1.3 52.4 + - + +
131O LEU* 3.4 20.3 - - - +
132O SER* 2.7 41.6 + - - -
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Residues in contact with TYR 129 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I ASN* 3.3 30.9 + - + -
129I TYR* 3.4 28.5 + + - -
132I SER* 3.7 22.2 - - - +
24J ASN 5.9 0.2 - - - -
25J THR* 3.4 22.1 - - + +
125O SER 4.6 5.4 - - - -
126O GLY* 3.4 27.6 - - - +
127O GLY 2.5 6.1 + - - -
128O ASN* 1.3 76.0 - - + +
130O ALA* 1.3 65.0 + - - +
132O SER* 3.0 3.4 + - - -
133O ALA* 3.0 16.9 + - - +
155O ILE* 5.0 0.7 - - - -
156O ALA* 4.0 14.6 - - + -
159O ILE* 3.6 31.4 - - + -
160O CYS* 4.4 13.0 - - + -
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Residues in contact with ALA 130 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2O THR* 3.8 23.1 - - + -
4O VAL* 3.9 26.7 - - + -
122O ALA* 4.9 0.7 - - + -
126O GLY 3.3 0.6 + - - -
127O GLY 2.7 12.2 + - - +
129O TYR* 1.3 75.9 - - - +
131O LEU* 1.3 50.9 + - - +
133O ALA* 3.2 4.3 + - - +
134O ALA* 2.7 36.1 + - - +
152O SER* 3.5 26.2 + - - +
153O LEU* 4.7 0.4 - - + -
156O ALA* 3.8 1.9 - - + +
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Residues in contact with LEU 131 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159I ILE* 4.2 13.0 - - + -
26N VAL 5.3 4.9 - - - +
27N MET* 6.5 0.2 - - - -
4O VAL* 5.0 0.9 - - - -
120O ILE* 4.1 22.4 - - + +
122O ALA* 4.0 20.8 - - + +
127O GLY 2.9 5.5 + - - +
128O ASN* 3.4 26.0 - - - +
130O ALA* 1.3 78.3 - - - +
132O SER* 1.3 64.5 + - - +
134O ALA* 3.0 5.6 + - - +
135O ARG* 2.9 76.4 + - + +
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Residues in contact with SER 132 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129I TYR* 3.7 31.0 - - - +
132I SER* 4.0 4.7 - - - -
133I ALA* 4.1 2.8 - - - -
155I ILE* 3.7 25.6 - - - +
159I ILE* 3.0 20.3 - - - +
128O ASN 2.7 27.5 + - - -
129O TYR 3.5 4.0 - - - -
131O LEU* 1.3 73.0 - - - +
133O ALA* 1.3 57.3 + - - +
135O ARG* 4.6 1.1 - - - -
136O ALA* 2.9 28.6 + - - +
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Residues in contact with ALA 133 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I SER* 4.4 5.3 - - - +
136I ALA* 4.3 7.2 - - + -
129O TYR 3.0 11.9 + - - +
130O ALA 3.3 10.1 - - - +
132O SER* 1.3 73.8 - - - +
134O ALA* 1.3 70.8 + - - +
136O ALA* 2.9 9.9 + - - +
137O LEU* 2.8 23.2 + - + +
152O SER* 3.5 21.1 - - - +
155O ILE* 4.1 24.9 - - + -
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Residues in contact with ALA 134 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4O VAL* 4.5 2.9 - - + -
6O VAL* 4.1 11.9 - - + -
120O ILE* 3.5 32.8 - - + -
130O ALA 2.7 17.0 + - - +
131O LEU* 3.4 7.6 - - - +
133O ALA* 1.3 69.2 - - - +
135O ARG* 1.3 56.1 + - - +
137O LEU* 2.5 26.2 + - - -
138O VAL* 2.8 13.7 + - - -
148O ILE* 4.0 7.0 - - - -
152O SER* 2.9 16.8 + - - +
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Residues in contact with ARG 135 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155I ILE* 4.5 15.5 + - + +
158I ASP* 4.4 17.6 + - - +
159I ILE* 3.8 21.8 - - - +
26N VAL 4.6 10.3 + - - -
27N MET 5.0 6.7 + - - -
28N LYS* 6.2 0.6 - - - +
118O ASP* 4.2 17.7 + - - +
120O ILE* 3.5 19.3 + - + +
131O LEU* 2.9 58.1 + - + +
132O SER* 4.0 4.5 - - - +
134O ALA* 1.3 76.1 - - - +
136O ALA* 1.3 64.1 + - - +
138O VAL* 4.6 0.2 - - - -
139O GLU* 3.1 46.4 + - - +
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Residues in contact with ALA 136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I ALA* 3.9 10.3 - - - -
136I ALA* 3.9 4.0 - - + -
137I LEU* 3.2 27.9 - - + +
155I ILE* 3.6 18.3 - - + +
132O SER 2.9 17.0 + - - +
133O ALA 2.9 15.0 + - - +
134O ALA 2.9 0.2 + - - -
135O ARG* 1.3 78.7 - - - +
137O LEU* 1.3 61.4 + - - +
139O GLU* 5.4 0.2 - - - -
140O ASN* 3.2 27.7 + - - +
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Residues in contact with LEU 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136I ALA* 3.6 31.6 - - + +
137I LEU* 4.7 1.8 - - + -
140I ASN* 3.8 20.9 - - + +
133O ALA* 2.8 10.9 + - + +
134O ALA 2.5 12.0 + - - +
136O ALA* 1.3 68.8 - - - +
138O VAL* 1.3 68.6 + - - +
139O GLU 2.7 4.0 + - - -
140O ASN* 2.8 13.8 + - - +
141O THR* 2.9 30.8 + - + +
143O LEU* 4.1 7.9 - - + -
148O ILE* 3.6 28.7 - - + -
151O LYS* 4.0 28.0 - - + -
152O SER* 4.1 6.7 - - - +
155O ILE* 6.3 0.7 - - + -
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Residues in contact with VAL 138 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6O VAL* 3.5 24.9 - - + -
8O ARG* 3.9 28.4 + - + +
118O ASP* 4.7 14.1 - - + +
120O ILE* 3.6 26.2 - - + -
134O ALA 2.8 13.9 + - - +
135O ARG 4.2 1.1 - - - +
137O LEU* 1.3 72.5 - - - +
139O GLU* 1.3 66.4 + - + +
141O THR 3.6 9.9 - - - +
148O ILE* 3.2 26.4 - - + +
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Residues in contact with GLU 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151I LYS* 6.1 0.7 - - - +
155I ILE* 5.0 9.7 - - - +
118O ASP* 4.7 12.5 - - + +
135O ARG* 3.1 39.8 + - - +
137O LEU 2.7 5.9 + - - -
138O VAL* 1.3 82.2 - - + +
140O ASN* 1.3 70.9 + - - +
141O THR 3.7 0.2 - - - -
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Residues in contact with ASN 140 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137I LEU* 4.4 12.5 - - + +
141I THR* 5.0 11.6 + - + -
143I LEU* 4.4 22.9 - - + +
151I LYS* 3.7 38.0 + - - +
155I ILE* 5.6 1.6 - - - +
136O ALA* 3.2 24.6 + - - +
137O LEU* 2.8 10.0 + - - -
139O GLU* 1.3 87.6 + - - +
141O THR* 1.3 59.9 + - - -
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Residues in contact with THR 141 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I ASN 4.6 13.4 + - - -
141I THR* 6.0 1.1 - - - -
8O ARG* 2.7 26.7 + - - -
137O LEU* 2.9 42.8 + - + +
138O VAL 3.6 6.7 - - - +
139O GLU 3.7 1.4 - - - -
140O ASN* 1.3 81.6 - - - +
142O GLU* 1.3 69.6 + - - +
143O LEU* 3.2 41.1 - - + +
148O ILE* 4.7 0.4 - - + -
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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