Contacts of the helix formed by residues 126 - 140 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1I THR 3.2 4.9 + - - -
2I THR* 3.1 18.3 + - - +
125I SER* 1.3 81.5 + - - +
127I GLY* 1.3 62.1 + - - +
128I ASN 3.7 0.9 - - - -
129I TYR* 3.4 21.9 - - - +
130I ALA 3.1 17.0 + - - -
156I ALA* 3.3 11.9 - - - +
160I CYS* 4.2 10.4 - - - -
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Residues in contact with GLY 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I THR* 4.1 4.2 + - - -
122I ALA* 3.7 19.8 - - - +
123I ILE 4.3 10.5 - - - -
124I GLY 3.4 12.5 + - - -
125I SER 3.2 6.1 + - - -
126I GLY* 1.3 72.5 - - - +
128I ASN* 1.3 55.0 + - - +
129I TYR 2.9 2.7 + - - -
130I ALA* 2.9 3.8 + - - +
131I LEU* 2.6 38.3 + - - +
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Residues in contact with ASN 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I GLY 5.6 2.0 + - - -
125I SER 5.0 7.5 + - - -
126I GLY 3.7 0.2 - - - -
127I GLY* 1.3 73.9 - - - +
129I TYR* 1.3 56.6 + - + +
131I LEU* 3.3 16.9 - - - +
132I SER* 2.7 38.8 + - - -
25J THR* 3.5 38.7 + - - +
26J VAL 5.5 1.9 + - - +
129O TYR* 3.3 27.1 + - + -
159O ILE* 4.3 10.8 - - + +
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Residues in contact with TYR 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125I SER 4.5 5.6 - - - -
126I GLY* 3.4 27.6 - - - +
127I GLY 2.9 0.6 + - - -
128I ASN* 1.3 77.6 - - + +
130I ALA* 1.3 65.6 + - - +
131I LEU 2.8 4.6 + - - -
132I SER* 2.8 10.4 + - - -
133I ALA* 3.0 12.5 + - - +
156I ALA* 3.8 17.3 - - + -
159I ILE* 3.7 25.8 - - + -
160I CYS* 4.6 8.3 - - + -
25N THR* 3.3 22.7 - - + +
128O ASN* 3.6 25.4 + - + -
129O TYR* 3.4 33.9 + + - -
132O SER* 3.7 25.3 - - - +
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Residues in contact with ALA 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I THR* 3.6 28.5 - - + -
4I VAL* 4.0 24.2 - - + +
126I GLY 3.1 1.0 + - - -
127I GLY* 2.9 7.2 + - - +
129I TYR* 1.3 78.8 - - - +
131I LEU* 1.3 61.6 + - - +
133I ALA* 4.3 1.3 - - - -
134I ALA* 3.0 21.7 + - - +
152I SER* 3.3 24.4 - - - +
156I ALA* 3.5 10.8 - - + +
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Residues in contact with LEU 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I VAL* 4.8 0.9 - - - -
120I ILE* 3.7 27.1 - - + +
122I ALA* 4.0 17.4 - - + +
127I GLY 2.6 20.8 + - - +
128I ASN* 3.3 15.9 - - - +
129I TYR 2.8 0.4 + - - -
130I ALA* 1.3 70.6 - - - +
132I SER* 1.3 68.1 + - - +
134I ALA* 2.7 17.3 + - - +
135I ARG* 2.7 66.7 + - + +
26J VAL 5.7 2.0 - - - +
159O ILE* 3.7 16.8 - - + -
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Residues in contact with SER 132 (chain I).
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 2.7 25.5 + - - -
129I TYR 2.8 3.6 + - - -
131I LEU* 1.3 74.2 - - - +
133I ALA* 1.3 62.6 + - - +
135I ARG* 3.5 4.6 + - - +
136I ALA* 2.9 24.1 + - - +
129O TYR* 3.7 29.7 - - - +
132O SER* 4.0 5.6 - - - -
133O ALA* 4.4 3.9 - - - -
155O ILE* 3.6 26.9 - - - +
159O ILE* 3.5 17.2 - - - +
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Residues in contact with ALA 133 (chain I).
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 3.0 10.4 + - - +
130I ALA 3.6 6.1 - - - +
131I LEU 2.9 0.4 + - - -
132I SER* 1.3 76.5 - - - +
134I ALA* 1.3 63.9 + - - +
136I ALA* 2.9 6.1 + - - +
137I LEU* 2.8 26.0 + - + +
152I SER* 3.3 20.0 - - - +
155I ILE* 3.5 33.2 - - + -
132O SER* 4.1 5.3 - - - +
136O ALA* 3.9 11.7 - - + -
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Residues in contact with ALA 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I VAL* 4.5 3.6 - - + -
6I VAL* 3.9 18.2 - - + -
120I ILE* 3.9 12.3 - - + -
130I ALA 3.0 10.2 + - - +
131I LEU* 2.7 11.9 + - - +
133I ALA* 1.3 74.5 - - - +
135I ARG* 1.3 54.2 + - - +
137I LEU 3.0 1.7 + - - -
138I VAL* 2.6 41.3 + - - +
148I ILE* 3.5 17.0 - - + -
152I SER* 3.0 14.6 + - - +
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Residues in contact with ARG 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I GLU* 4.7 18.9 + - - +
118I ASP* 3.8 27.9 + - - -
120I ILE* 4.0 18.1 + - + +
131I LEU* 2.7 64.2 + - + +
132I SER* 3.7 6.3 - - - +
134I ALA* 1.3 72.3 - - - +
136I ALA* 1.3 64.5 + - - +
138I VAL* 3.7 0.7 - - - -
139I GLU* 2.9 44.9 + - - +
26J VAL 4.6 8.7 + - - -
27J MET 5.4 4.4 + - - -
155O ILE* 4.8 13.0 + - + +
158O ASP* 4.4 12.2 + - - +
159O ILE* 4.0 20.6 - - - +
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Residues in contact with ALA 136 (chain I).
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 2.9 13.7 + - - +
133I ALA 2.9 9.5 + - - +
135I ARG* 1.3 76.6 - - - +
137I LEU* 1.3 57.4 + - - +
139I GLU* 3.8 2.6 - - - -
140I ASN* 2.9 38.7 + - - +
133O ALA* 4.2 11.9 - - + +
136O ALA* 3.9 11.9 - - + -
137O LEU* 3.6 25.0 - - + +
155O ILE* 4.7 10.2 - - + +
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Residues in contact with LEU 137 (chain I).
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* 2.8 13.0 + - + +
134I ALA 3.6 5.6 - - - +
136I ALA* 1.3 74.5 - - + +
138I VAL* 1.3 60.3 + - - +
141I THR* 2.7 36.0 - - + +
143I LEU* 4.4 14.4 - - + -
148I ILE* 3.4 35.4 - - + +
151I LYS* 4.0 28.3 - - + -
152I SER* 4.1 9.0 - - - +
155I ILE* 5.2 1.1 - - + -
136O ALA* 3.2 45.3 - - + +
137O LEU* 4.7 2.2 - - + -
140O ASN* 4.4 9.6 - - + +
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Residues in contact with VAL 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I VAL* 4.1 13.9 - - + -
7I ARG 6.1 0.4 - - - +
8I ARG* 3.4 35.9 + - + +
118I ASP* 4.9 15.3 - - + +
120I ILE* 3.5 27.4 - - + -
134I ALA 2.6 24.8 + - - +
135I ARG 3.7 3.1 - - - +
137I LEU* 1.3 76.4 - - - +
139I GLU* 1.3 66.0 + - + +
140I ASN 3.7 0.2 + - - -
141I THR 3.8 2.8 + - - +
148I ILE* 3.2 22.9 - - + -
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Residues in contact with GLU 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118I ASP* 5.0 9.6 - - + +
135I ARG* 2.9 38.5 + - - +
136I ALA* 4.0 2.4 - - - +
138I VAL* 1.3 82.2 - - + +
140I ASN* 1.3 71.4 + - - +
141I THR 3.7 0.4 + - - -
154O ARG* 6.0 1.4 - - - -
155O ILE* 4.2 18.9 - - - +
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Residues in contact with ASN 140 (chain I).
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* 2.9 24.1 + - - +
139I GLU* 1.3 91.0 + - - +
141I THR* 1.3 65.7 + - + +
137O LEU* 3.8 29.7 - - + +
141O THR* 4.6 12.3 + - - +
143O LEU* 4.5 18.1 - - + +
151O LYS* 4.6 10.8 - - - +
155O ILE* 6.0 2.2 - - - +
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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