Contacts of the helix formed by residues 126 - 140 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2H THR* 3.2 28.0 + - - +
125H SER* 1.3 82.7 + - - +
127H GLY* 1.3 65.7 + - - +
128H ASN 3.6 1.1 - - - -
129H TYR* 3.2 26.8 - - - +
130H ALA 3.1 15.4 + - - -
156H ALA* 3.7 1.4 - - - +
160H CYS* 4.2 8.5 - - - -
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Residues in contact with GLY 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H THR* 4.2 5.7 - - - +
122H ALA* 3.7 22.1 - - - +
123H ILE* 4.2 11.4 - - - -
124H GLY 3.3 12.2 + - - -
125H SER 3.1 6.3 + - - -
126H GLY* 1.3 76.1 - - - +
128H ASN* 1.3 65.0 + - - +
129H TYR 2.9 1.0 + - - -
130H ALA* 2.9 6.4 + - - +
131H LEU* 2.7 20.6 + - - +
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Residues in contact with ASN 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H GLY 5.7 1.4 + - - -
125H SER 4.8 7.5 + - - -
127H GLY* 1.3 72.4 - - - +
129H TYR* 1.3 55.3 + - + +
131H LEU* 2.9 16.9 + - - +
132H SER* 2.5 39.9 + - - -
25I THR* 3.5 39.4 + - - +
26I VAL 5.3 2.8 + - - +
27I MET* 6.1 0.2 - - - -
129N TYR* 3.5 26.0 + - + -
159N ILE* 4.2 11.4 - - + +
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Residues in contact with TYR 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H SER 4.6 5.4 - - - -
126H GLY* 3.2 27.4 - - - +
127H GLY 2.9 0.6 + - - -
128H ASN* 1.3 82.5 - - + +
130H ALA* 1.3 56.3 + - - +
131H LEU 2.6 7.8 + - - -
132H SER* 2.8 11.3 + - - -
133H ALA* 2.9 11.8 + - - +
156H ALA* 3.8 17.9 - - + -
159H ILE* 3.8 22.9 - - + -
160H CYS* 4.5 8.7 - - + -
25M THR* 3.3 23.2 - - + +
128N ASN* 3.5 25.6 + - + -
129N TYR* 3.5 33.2 + + - -
132N SER* 3.7 25.8 - - - +
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Residues in contact with ALA 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H THR* 3.7 26.7 - - + -
4H VAL* 4.0 26.3 - - + +
126H GLY 3.1 1.0 + - - -
127H GLY* 2.9 9.9 + - - +
129H TYR* 1.3 76.5 - - - +
131H LEU* 1.3 56.3 + - - +
133H ALA* 3.5 1.5 - - - +
134H ALA* 2.9 25.6 + - - +
152H SER* 3.2 28.1 - - - +
156H ALA* 3.5 6.7 - - + +
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Residues in contact with LEU 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H VAL* 5.1 0.4 - - - -
120H ILE* 3.7 27.6 - - + +
122H ALA* 4.1 17.9 - - + +
127H GLY 2.7 14.5 + - - +
128H ASN* 2.9 19.5 - - - +
129H TYR 2.6 4.2 + - - -
130H ALA* 1.3 67.7 - - - +
132H SER* 1.3 68.5 + - - +
133H ALA 2.9 1.1 - - - -
134H ALA* 2.8 4.4 + - - -
135H ARG* 2.7 79.4 + - + +
26I VAL 5.5 2.5 - - - +
27I MET* 6.5 0.7 - - - -
159N ILE* 3.8 15.5 - - + -
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Residues in contact with SER 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H ASN 2.5 16.8 + - - -
129H TYR 3.4 7.2 - - - -
131H LEU* 1.3 73.1 - - - +
133H ALA* 1.3 64.1 + - - +
135H ARG* 3.5 4.1 + - - +
136H ALA* 2.9 23.7 + - - +
129N TYR* 3.6 31.3 - - - +
132N SER* 4.0 5.8 - - - -
133N ALA* 4.3 3.3 - - - -
155N ILE* 3.5 27.2 - - - +
159N ILE* 3.4 17.7 - - - +
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Residues in contact with ALA 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H TYR 2.9 10.2 + - - +
130H ALA* 3.5 10.5 - - - +
131H LEU 2.9 0.4 + - - -
132H SER* 1.3 77.4 - - - +
134H ALA* 1.3 65.2 + - - +
136H ALA* 2.8 14.0 + - - +
137H LEU* 2.9 17.1 + - + +
152H SER* 3.5 16.2 - - - +
155H ILE* 3.6 31.9 - - + -
132N SER* 4.1 4.9 - - - +
136N ALA* 4.0 11.0 - - + -
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Residues in contact with ALA 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H VAL* 4.5 3.4 - - + -
6H VAL* 3.9 7.2 - - + -
120H ILE* 3.8 24.5 - - + -
130H ALA 2.9 17.9 + - - +
131H LEU 2.8 7.7 + - - +
133H ALA* 1.3 72.6 - - - +
135H ARG* 1.3 65.4 + - - +
137H LEU* 3.1 1.2 + - - -
138H VAL* 2.8 27.7 + - - +
148H ILE* 3.6 17.0 - - + -
152H SER* 3.0 13.9 + - - +
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Residues in contact with ARG 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116H GLU* 4.7 21.6 + - - +
118H ASP* 3.7 28.3 + - - -
120H ILE* 4.0 17.1 + - + +
131H LEU* 2.7 65.2 + - + +
132H SER* 3.6 7.2 - - - +
134H ALA* 1.3 72.3 - - - +
136H ALA* 1.3 63.2 + - - +
138H VAL* 3.8 0.5 - - - +
139H GLU* 3.0 43.8 + - - +
26I VAL 4.3 9.5 + - - -
27I MET 5.3 4.8 + - - -
155N ILE* 4.7 14.0 + - + +
158N ASP* 4.3 13.7 + - - +
159N ILE* 4.0 19.8 - - - +
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Residues in contact with ALA 136 (chain H).
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 2.9 13.0 + - - +
133H ALA 2.8 13.8 + - - +
135H ARG* 1.3 72.3 - - - +
137H LEU* 1.3 62.3 + - + +
138H VAL 3.1 0.3 + - - -
139H GLU* 3.8 1.7 - - - -
140H ASN* 2.9 37.6 + - - +
133N ALA* 4.3 12.6 - - + +
136N ALA* 4.1 8.1 - - + -
137N LEU* 3.7 25.8 - - + -
155N ILE* 4.6 11.3 - - + +
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Residues in contact with LEU 137 (chain H).
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* 2.9 11.5 + - + +
134H ALA 3.8 5.6 - - - +
136H ALA* 1.3 73.4 - - + +
138H VAL* 1.3 59.7 + - - +
141H THR* 2.6 38.0 - - + +
143H LEU* 4.2 14.1 - - + -
148H ILE* 3.5 34.8 - - + +
151H LYS* 3.9 28.5 - - + -
152H SER* 4.4 4.9 - - - +
155H ILE* 5.3 0.7 - - + -
136N ALA* 3.2 45.5 - - + +
137N LEU* 4.5 3.6 - - + +
140N ASN* 4.3 12.3 - - + +
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Residues in contact with VAL 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H VAL* 4.1 13.5 - - + -
7H ARG 6.0 0.4 - - - +
8H ARG* 3.4 38.7 + - + +
118H ASP* 4.8 16.2 - - + +
120H ILE* 3.5 26.0 - - + -
134H ALA 2.8 25.5 + - - +
135H ARG 3.8 3.4 - - - +
137H LEU* 1.3 73.7 - - - +
139H GLU* 1.3 66.7 + - + +
140H ASN 3.6 0.3 + - - -
141H THR 3.6 4.5 + - - +
148H ILE* 3.3 19.1 - - + -
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Residues in contact with GLU 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118H ASP* 5.1 9.4 - - + +
135H ARG* 3.0 37.0 + - - +
136H ALA* 3.9 2.3 - - - +
138H VAL* 1.3 82.0 - - + +
140H ASN* 1.3 68.5 + - - +
141H THR 3.6 0.7 + - - -
154N ARG* 5.8 3.1 - - - -
155N ILE* 4.1 19.3 - - - +
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Residues in contact with ASN 140 (chain H).
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* 2.9 23.9 + - - +
139H GLU* 1.3 88.6 + - - +
141H THR* 1.3 66.9 + - + +
137N LEU* 3.8 31.5 - - + +
141N THR* 4.7 12.7 + - - +
143N LEU* 4.6 16.5 - - + +
151N LYS* 4.4 12.9 - - - +
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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