Contacts of the helix formed by residues 144 - 158 (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 SER 144 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8M ARG* 4.7 1.1 - - - +
9M ASN* 6.5 0.4 - - - -
11M GLN* 6.4 1.8 - - - -
143M LEU* 1.3 74.3 - - - +
145M ALA* 1.3 65.0 + - - +
146M HIS* 2.8 11.0 + - - +
147M GLU* 2.7 46.8 + - - +
148M ILE* 2.8 21.9 + - - +
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Residues in contact with ALA 145 (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* 3.4 32.1 - - - +
8M ARG* 3.7 35.8 + - + +
11M GLN* 3.8 12.0 - - + +
13M VAL* 3.4 11.2 - - + +
143M LEU 3.5 3.2 + - - -
144M SER* 1.3 72.0 - - - +
146M HIS* 1.3 59.0 + - - +
148M ILE* 4.0 1.6 - - - -
149M VAL* 3.2 29.5 + - - +
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Residues in contact with HIS 146 (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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11M GLN* 5.7 1.0 - - - +
13M VAL* 3.5 22.9 - - + +
144M SER* 2.8 9.1 + - - +
145M ALA* 1.3 75.4 - - - +
147M GLU* 1.3 75.3 + - - +
148M ILE 3.1 0.7 - - - -
149M VAL* 2.9 4.9 + - - +
150M GLU* 2.8 30.9 + - + +
169M ILE* 4.0 32.5 + - + +
171M GLU* 3.9 37.7 - - + +
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Residues in contact with GLU 147 (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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143M LEU* 3.3 31.0 - - + +
144M SER* 2.7 33.1 + - - +
146M HIS* 1.3 80.1 - - - +
148M ILE* 1.3 57.7 + - - +
150M GLU* 3.4 5.5 - - - +
151M LYS* 2.7 32.7 + - - +
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Residues in contact with ILE 148 (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 26.0 - - + -
8M ARG* 4.4 3.6 - - - +
134M ALA* 4.0 9.6 - - + -
137M LEU* 3.6 17.9 - - + -
138M VAL* 3.2 44.6 - - + +
143M LEU* 3.6 29.4 - - + +
144M SER 2.8 18.0 + - - +
145M ALA* 4.0 4.7 - - - +
147M GLU* 1.3 75.7 - - - +
149M VAL* 1.3 58.4 + - - +
150M GLU 2.9 0.9 + - - -
151M LYS* 2.9 1.7 + - - -
152M SER* 2.6 46.7 + - - +
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Residues in contact with VAL 149 (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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4M VAL* 3.6 14.3 - - + +
5M SER* 4.0 5.2 - - - +
6M VAL* 3.2 38.6 - - + +
13M VAL* 4.0 10.1 - - + -
14M VAL 4.3 0.7 - - - -
15M GLY* 3.4 35.2 - - - +
145M ALA 3.2 18.6 + - - +
146M HIS 2.9 3.9 + - - +
148M ILE* 1.3 80.7 - - - +
150M GLU* 1.3 60.3 + - - +
152M SER* 4.0 1.8 - - - -
153M LEU* 3.1 22.7 + - - +
169M ILE* 3.9 11.7 - - + -
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Residues in contact with GLU 150 (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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146M HIS* 2.8 21.5 + - + +
147M GLU* 3.4 12.3 - - + +
149M VAL* 1.3 75.2 - - - +
151M LYS* 1.3 75.3 + - - +
153M LEU* 2.8 18.1 + - - +
154M ARG* 3.3 25.3 + - - -
167M PHE* 4.0 22.3 - - + -
169M ILE* 3.7 26.2 - - + -
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Residues in contact with LYS 151 (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* 4.5 13.5 - - - +
137M LEU* 4.0 18.4 - - + -
143M LEU* 5.8 1.8 - - + -
147M GLU 2.7 21.5 + - - +
148M ILE* 3.6 2.5 - - - +
150M GLU* 1.3 81.3 + - - +
152M SER* 1.3 62.3 + - - +
154M ARG* 3.2 12.3 + - - +
155M ILE* 3.1 26.6 + - + +
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Residues in contact with SER 152 (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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4M VAL* 4.4 7.6 - - - -
130M ALA* 3.5 32.8 - - - +
133M ALA* 3.5 11.8 - - - -
134M ALA* 2.9 32.9 + - - +
137M LEU* 4.1 2.8 - - - +
148M ILE* 2.6 24.0 + - - +
149M VAL* 4.3 3.8 - - - -
151M LYS* 1.3 69.9 - - - +
153M LEU* 1.3 67.6 + - - +
155M ILE* 3.5 2.1 + - - +
156M ALA 3.3 13.9 + - - -
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Residues in contact with LEU 153 (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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2M THR* 3.5 32.3 - - + +
4M VAL* 3.3 25.8 - - + +
15M GLY* 3.6 7.4 - - - +
16M GLY* 3.3 25.8 - - - +
17M ASP* 4.9 0.4 - - + +
130M ALA* 4.7 0.2 - - + -
149M VAL 3.1 17.0 + - - +
150M GLU 2.8 6.9 + - - +
152M SER* 1.3 78.2 - - - +
154M ARG* 1.3 65.2 + - - +
156M ALA* 3.1 7.0 + - - +
157M GLY* 2.9 19.2 + - - -
163M THR* 4.9 2.4 - - - +
167M PHE* 3.2 46.6 - - + -
169M ILE* 4.8 5.4 - - + -
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Residues in contact with ARG 154 (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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139G GLU* 6.0 1.8 - - - -
150M GLU* 3.3 24.9 + - - +
151M LYS* 3.2 11.5 + - - +
153M LEU* 1.3 78.8 - - - +
155M ILE* 1.3 73.0 + - + +
157M GLY* 2.7 15.6 + - - -
158M ASP* 3.1 26.6 + - - +
165M THR* 3.5 33.5 + - + +
167M PHE* 3.6 22.2 - - + -
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Residues in contact with ILE 155 (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* 3.6 46.4 - - - +
135G ARG* 4.6 17.3 + - + +
136G ALA* 4.7 8.5 - - + +
139G GLU* 4.0 20.0 - - - +
140G ASN* 5.8 2.2 - - - +
129M TYR 4.8 1.8 - - - +
133M ALA* 4.1 17.5 - - + -
137M LEU* 6.4 0.9 - - + -
151M LYS* 3.1 23.1 + - + +
152M SER* 3.8 7.2 - - - +
153M LEU 3.4 0.2 - - - -
154M ARG* 1.3 80.3 - - + +
156M ALA* 1.3 62.6 + - - +
158M ASP* 3.2 18.7 + - - +
159M ILE* 3.6 14.6 + - + +
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Residues in contact with ALA 156 (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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2M THR* 3.6 31.6 - - + +
126M GLY 3.8 4.9 - - - +
129M TYR* 3.9 11.8 - - + -
130M ALA 3.8 14.6 - - - +
152M SER 3.3 9.1 + - - +
153M LEU 3.1 9.1 + - - +
154M ARG 3.1 0.6 - - - -
155M ILE* 1.3 78.4 - - - +
157M GLY* 1.3 60.7 + - - +
159M ILE* 3.0 2.0 + - - +
160M CYS* 2.9 32.7 + - - +
163M THR* 4.3 1.6 - - - -
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Residues in contact with GLY 157 (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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153M LEU 2.9 8.9 + - - -
154M ARG* 2.7 11.9 + - - -
156M ALA* 1.3 72.3 - - - +
158M ASP* 1.3 62.4 + - - +
159M ILE 3.2 3.2 + - - -
160M CYS 3.4 7.1 - - - +
163M THR* 3.2 41.1 - - - +
164M ASN* 4.4 8.0 - - - -
165M THR* 5.4 3.7 - - - +
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Residues in contact with ASP 158 (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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135G ARG* 4.2 13.9 + - - +
26H VAL* 4.2 16.2 - - - +
154M ARG* 3.1 26.0 + - - +
155M ILE* 3.5 12.6 - - - +
156M ALA 3.1 1.4 - - - -
157M GLY* 1.3 80.1 - - - +
159M ILE* 1.3 64.5 + - + +
165M THR* 4.3 15.1 - - - +
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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