Contacts of the helix formed by residues 126 - 141 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1M THR 3.2 4.6 + - - -
2M THR* 3.1 30.6 + - - +
125M SER* 1.3 81.5 + - - +
127M GLY* 1.3 68.6 + - - +
128M ASN 3.8 0.4 - - - -
129M TYR* 3.4 25.4 + - - +
130M ALA 3.3 8.3 + - - -
156M ALA* 3.8 0.8 - - - +
160M CYS* 4.1 9.3 - - - -
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Residues in contact with GLY 127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M THR* 4.2 2.4 - - - +
122M ALA* 4.1 17.2 - - - +
123M ILE* 4.2 13.5 - - - -
124M GLY 3.2 12.0 + - - -
125M SER 2.9 10.7 + - - -
126M GLY* 1.3 79.9 - - - +
128M ASN* 1.3 55.3 + - - -
129M TYR 2.5 16.5 + - - -
130M ALA* 2.7 11.4 + - - +
131M LEU 3.0 7.5 + - - -
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Residues in contact with ASN 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G TYR* 3.5 33.2 + - + -
159G ILE* 3.8 24.5 - - + +
122M ALA* 4.9 0.6 + - - +
125M SER 5.0 5.9 + - - -
127M GLY* 1.3 70.8 - - - +
129M TYR* 1.3 55.7 + - + +
131M LEU* 3.4 20.3 - - - +
132M SER* 2.7 38.4 + - - -
25R THR* 3.6 19.5 + - - +
26R VAL 5.2 3.5 - - - +
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Residues in contact with TYR 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G ASN* 3.2 34.0 + - + -
129G TYR* 3.4 28.2 + + - -
132G SER* 3.6 23.0 - - - +
25H THR* 3.3 23.3 - - + +
125M SER 4.7 4.7 - - - -
126M GLY* 3.5 27.1 - - - +
127M GLY 2.5 6.1 + - - -
128M ASN* 1.3 79.9 - - + +
130M ALA* 1.3 62.6 + - - +
132M SER* 2.9 10.7 + - - -
133M ALA* 3.0 10.3 + - - +
155M ILE* 5.0 0.7 - - - -
156M ALA* 3.9 14.1 - - + -
159M ILE* 3.6 26.0 - - + -
160M CYS* 4.3 13.9 - - + -
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Residues in contact with ALA 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M THR* 3.8 22.9 - - + -
4M VAL* 3.9 25.7 - - + +
122M ALA* 4.9 0.9 - - + -
126M GLY 3.3 1.0 + - - -
127M GLY 2.7 12.4 + - - +
129M TYR* 1.3 74.4 - - - +
131M LEU* 1.3 52.2 + - - +
133M ALA* 3.2 4.4 + - - +
134M ALA* 2.7 35.4 + - - +
152M SER* 3.5 28.3 + - - +
153M LEU* 4.7 0.2 - - + -
156M ALA* 3.8 1.9 - - + +
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Residues in contact with LEU 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159G ILE* 4.0 15.5 - - + -
4M VAL* 4.9 1.1 - - - -
120M ILE* 4.2 22.4 - - + +
122M ALA* 4.0 19.4 - - + +
127M GLY 3.0 5.5 + - - +
128M ASN* 3.4 25.4 - - - +
130M ALA* 1.3 77.3 - - - +
132M SER* 1.3 64.5 + - - +
134M ALA* 3.0 5.2 + - - +
135M ARG* 2.9 76.6 + - + +
26R VAL 5.3 4.0 - - - +
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Residues in contact with SER 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G TYR* 3.6 32.5 - - - +
132G SER* 4.0 4.0 - - - -
133G ALA* 3.9 3.3 - - - -
155G ILE* 3.7 26.0 - - - +
159G ILE* 3.1 18.2 - - - +
128M ASN 2.7 26.7 + - - -
129M TYR 3.4 3.8 - - - -
131M LEU* 1.3 73.3 - - - +
133M ALA* 1.3 58.1 + - - +
135M ARG* 4.7 0.9 - - - -
136M ALA* 3.0 28.6 + - - +
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Residues in contact with ALA 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G SER* 4.3 4.5 - - - +
136G ALA* 4.2 7.2 - - + -
129M TYR 3.0 11.0 + - - +
130M ALA 3.3 9.4 - - - +
132M SER* 1.3 75.5 - - - +
134M ALA* 1.3 70.2 + - - +
136M ALA* 3.0 9.2 + - - +
137M LEU* 2.8 23.4 + - + +
152M SER* 3.5 22.2 - - - +
155M ILE* 4.1 25.8 - - + -
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Residues in contact with ALA 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M VAL* 4.5 2.0 - - + -
6M VAL* 4.1 12.3 - - + -
120M ILE* 3.5 33.4 - - + -
130M ALA 2.7 16.9 + - - +
131M LEU* 3.3 8.1 - - - +
133M ALA* 1.3 69.7 - - - +
135M ARG* 1.3 56.2 + - - +
137M LEU* 2.5 25.6 + - - -
138M VAL* 2.7 14.0 + - - -
148M ILE* 4.0 6.7 - - - -
152M SER* 2.9 15.7 + - - +
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Residues in contact with ARG 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155G ILE* 4.4 18.0 + - + +
158G ASP* 4.4 17.0 + - - +
159G ILE* 3.7 22.2 - - - +
116M GLU* 6.2 2.0 - - - +
118M ASP* 4.2 16.6 + - - +
120M ILE* 3.4 19.0 + - + +
131M LEU* 2.9 56.9 + - + +
132M SER 4.0 3.4 - - - +
134M ALA* 1.3 75.7 - - - +
136M ALA* 1.3 64.1 + - - +
138M VAL* 4.6 0.4 - - - -
139M GLU* 3.0 49.5 + - - +
26R VAL 4.7 10.1 + - - -
27R MET 5.1 6.7 + - - -
28R LYS* 6.2 0.2 - - - +
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Residues in contact with ALA 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G ALA* 3.9 4.9 - - - -
136G ALA* 3.9 9.0 - - + -
137G LEU* 3.2 27.7 - - + +
155G ILE* 3.5 19.0 - - + +
132M SER 3.0 18.3 + - - +
133M ALA 3.0 13.2 - - - +
135M ARG* 1.3 78.3 - - - +
137M LEU* 1.3 61.7 + - - +
140M ASN* 3.2 27.6 + - - +
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Residues in contact with LEU 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G ALA* 3.6 31.6 - - + +
137G LEU* 4.5 2.5 - - + -
140G ASN* 3.9 21.1 - - + +
141G THR* 6.3 0.7 - - + -
133M ALA* 2.8 11.6 + - + +
134M ALA 2.5 11.9 + - - +
136M ALA* 1.3 69.2 - - - +
138M VAL* 1.3 70.0 + - - +
139M GLU 2.7 3.6 + - - -
140M ASN 2.8 13.0 + - - -
141M THR* 2.9 30.5 - - + +
143M LEU* 4.1 9.4 - - + -
148M ILE* 3.6 22.9 - - + -
151M LYS* 4.0 27.4 - - + -
152M SER* 4.1 13.5 - - - +
155M ILE* 6.4 0.7 - - + -
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Residues in contact with VAL 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6M VAL* 3.5 25.8 - - + -
8M ARG* 3.9 29.2 + - + +
118M ASP* 4.8 12.3 - - + +
120M ILE* 3.7 24.7 - - + -
134M ALA 2.7 14.1 + - - +
135M ARG 4.2 0.9 - - - +
137M LEU* 1.3 74.0 - - - +
139M GLU* 1.3 66.4 + - + +
141M THR 3.6 10.4 - - - +
148M ILE* 3.2 26.2 - - + +
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Residues in contact with GLU 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155G ILE* 4.9 10.5 - - - +
118M ASP* 4.7 11.6 - - + +
135M ARG* 3.0 41.5 + - - +
137M LEU 2.7 4.0 + - - -
138M VAL* 1.3 81.4 - - + +
140M ASN* 1.3 70.4 + - - +
141M THR 3.6 0.2 - - - -
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Residues in contact with ASN 140 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G LEU* 4.1 19.7 - - + +
141G THR* 5.0 11.3 + - + -
143G LEU* 4.3 25.0 - - + +
151G LYS* 4.8 9.2 - - - +
155G ILE* 5.7 1.4 - - - +
136M ALA* 3.2 23.8 + - - +
137M LEU 2.8 10.3 + - - -
139M GLU* 1.3 87.5 + - - +
141M THR* 1.3 59.6 + - - -
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Residues in contact with THR 141 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G ASN 4.6 13.2 + - - +
141G THR* 5.9 1.3 - - - -
8M ARG* 2.7 26.0 + - - -
137M LEU* 2.9 42.9 + - + +
138M VAL 3.6 6.5 - - - +
139M GLU 3.6 1.0 + - - -
140M ASN* 1.3 81.8 - - - +
142M GLU* 1.3 68.9 + - - +
143M LEU* 3.2 39.0 - - + +
148M ILE* 4.8 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
------------------------------------------------------------
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