Contacts of the helix formed by residues 140 - 156 (chain M) in PDB entry 3EXG
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 ALA 140 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135M ASN* 5.0 7.9 - - + -
137M ILE* 2.9 26.2 + - + +
139M GLY* 1.3 75.3 - - - +
141M GLN* 1.3 57.5 + - - +
143M PRO* 3.1 16.3 - - - +
144M LEU* 3.6 11.0 - - + +
174M GLN* 3.2 17.3 - - - +
91N ASP* 4.0 18.8 - - - +
92N GLN* 3.2 12.3 + - - +
95N ASN* 6.6 0.2 - - + -
96N SER* 4.1 15.7 - - - +
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Residues in contact with GLN 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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86M ILE* 3.6 21.9 - - + +
87M THR* 3.7 14.1 - - - +
88M ALA* 3.7 21.3 - - - +
135M ASN* 3.6 19.9 - - - +
137M ILE 4.3 2.3 - - - +
138M VAL* 5.0 0.2 - - - -
139M GLY* 3.2 23.2 + - - +
140M ALA* 1.3 73.4 + - - +
142M VAL* 1.3 67.5 + - + +
144M LEU* 3.7 11.6 - - - +
145M GLY* 3.0 16.5 + - - -
163M THR* 3.6 6.6 - - + +
164M LEU 2.8 27.8 + - - +
165M TYR* 3.6 17.8 - - - +
169M ALA* 5.6 0.8 - - - +
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Residues in contact with VAL 142 (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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139M GLY 2.7 18.7 + - - +
141M GLN* 1.3 76.0 - - - +
143M PRO* 1.3 62.5 - - + +
145M GLY* 3.1 4.2 + - - -
146M ALA* 2.8 23.4 + - - +
163M THR* 3.5 10.6 - - + +
165M TYR* 3.4 38.8 - - + -
175M ILE* 3.5 33.0 - - + +
178M ALA* 3.6 22.0 - - + -
191M PHE* 3.6 21.2 - - + -
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Residues in contact with PRO 143 (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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139M GLY 3.3 8.7 - - - +
140M ALA 3.1 12.8 - - - +
142M VAL* 1.3 90.8 - - + +
144M LEU* 1.3 64.9 + - - +
146M ALA* 2.9 9.0 + - + +
147M GLY 2.9 18.0 + - - -
174M GLN* 3.2 38.6 - - + +
178M ALA* 4.1 6.1 - - + -
61N GLY* 3.6 28.5 - - - +
64N GLY* 3.9 10.8 - - - -
65N ILE* 3.5 10.5 - - + +
92N GLN* 4.0 3.8 - - - +
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Residues in contact with LEU 144 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86M ILE* 3.9 13.7 - - + -
135M ASN* 3.7 23.3 - - - +
140M ALA* 3.6 15.3 - - + +
141M GLN* 3.7 9.6 - - - +
142M VAL 3.2 0.2 - - - -
143M PRO* 1.3 77.3 - - - +
145M GLY* 1.3 58.9 + - - +
147M GLY* 2.9 16.8 + - - -
148M ILE* 3.0 16.1 + - + +
64N GLY 3.5 18.8 - - - +
67N VAL* 3.7 27.4 - - + -
68N GLY* 3.3 15.1 - - - +
71N MET* 4.2 17.9 - - + -
92N GLN* 3.9 12.3 - - - +
96N SER* 4.1 16.2 - - - +
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Residues in contact with GLY 145 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86M ILE* 3.8 13.8 - - - +
141M GLN 3.0 13.9 + - - -
142M VAL 3.4 2.5 - - - -
144M LEU* 1.3 74.0 - - - +
146M ALA* 1.3 64.5 + - - +
147M GLY 3.0 1.5 + - - -
148M ILE* 3.3 6.0 + - - -
149M ALA* 3.2 17.5 + - - +
161M CYS* 3.5 11.5 - - - -
163M THR* 3.3 22.0 + - - -
189M CYS* 4.2 0.5 - - - -
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Residues in contact with ALA 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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142M VAL 2.8 15.7 + - - +
143M PRO* 2.9 11.1 + - + +
145M GLY* 1.3 72.4 - - - +
147M GLY* 1.3 57.5 + - - +
149M ALA* 3.2 5.6 + - - +
150M LEU* 2.9 21.7 + - - +
163M THR* 4.1 0.2 + - - -
178M ALA* 4.2 16.2 - - + +
182M ALA 5.5 0.2 - - - +
187M LEU* 3.5 17.4 - - + +
189M CYS* 4.3 11.2 - - - -
191M PHE* 4.5 10.1 - - + -
65N ILE* 3.8 20.6 - - + -
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Residues in contact with GLY 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 PRO 2.9 10.1 + - - -
144M LEU 2.9 5.8 + - - -
146M ALA* 1.3 77.6 - - - +
148M ILE* 1.3 63.6 + - - +
150M LEU* 3.1 12.5 + - - +
151M ALA 3.1 9.7 + - - -
65N ILE* 3.6 33.0 - - - -
69N ALA* 3.4 16.9 + - - -
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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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84M HIS* 3.5 38.1 - - + +
86M ILE* 4.3 10.8 - - + -
132M TYR* 3.2 49.8 - - + -
144M LEU* 3.0 16.5 + - + +
145M GLY* 3.3 15.0 + - - +
147M GLY* 1.3 77.6 - - - +
149M ALA* 1.3 55.0 + - - +
151M ALA* 3.3 3.6 + - - +
152M CYS* 3.1 26.7 + - - -
161M CYS* 3.9 8.7 - - + -
68N GLY* 3.8 17.3 - - - +
71N MET* 5.4 2.7 - - + -
72N ALA* 4.3 13.0 - - + -
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Residues in contact with ALA 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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145M GLY 3.2 8.3 + - - +
146M ALA 3.5 9.0 - - - +
147M GLY 3.1 0.8 - - - -
148M ILE* 1.3 75.0 - - - +
150M LEU* 1.3 65.6 + - - +
152M CYS* 3.3 8.9 - - - +
153M LYS* 3.1 19.9 + - - +
161M CYS* 4.0 6.4 - - + +
187M LEU* 3.8 6.1 - - + -
188M PRO* 3.5 24.7 - - - +
189M CYS* 3.5 31.4 - - + -
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Residues in contact with LEU 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 ALA 2.9 12.8 + - - +
147M GLY* 3.3 10.5 - - - +
149M ALA* 1.3 77.9 - - - +
151M ALA* 1.3 61.1 + - - +
153M LYS* 3.8 6.0 + - + +
154M TYR* 3.2 28.6 + - + +
185M TRP* 4.1 21.1 - - + -
187M LEU* 3.5 28.0 - - + +
24N PHE* 4.0 32.5 - - + -
26N LEU* 5.4 1.6 - - + -
53N ILE* 4.8 13.9 - - + -
65N ILE* 4.0 21.1 - - + -
69N ALA* 4.5 4.0 - - + -
74N LEU* 4.9 0.7 - - + -
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Residues in contact with ALA 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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147M GLY 3.1 9.4 + - - +
148M ILE 3.6 8.5 - - - +
149M ALA 3.2 0.2 - - - -
150M LEU* 1.3 73.4 - - - +
152M CYS* 1.3 68.4 + - - +
154M TYR* 3.1 1.2 + - - +
155M ASN* 2.9 37.7 + - - +
69N ALA* 4.5 2.0 - - - +
72N ALA* 3.6 27.1 - - + -
74N LEU* 3.5 28.9 - - + +
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Residues in contact with CYS 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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84M HIS* 3.8 30.5 - - - -
148M ILE* 3.1 20.2 + - - -
149M ALA* 3.3 12.1 - - - +
151M ALA* 1.3 80.6 - - - +
153M LYS* 1.3 63.6 + - - +
155M ASN* 3.2 12.5 + - - +
156M GLY* 3.2 11.4 + - - -
157M LYS* 4.1 4.5 + - - +
158M ASP 5.0 1.2 + - - -
159M GLU* 3.6 38.9 + - + +
160M VAL 4.2 7.4 - - - -
188M PRO* 3.8 7.0 - - + -
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Residues in contact with LYS 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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149M ALA 3.1 12.4 + - - +
150M LEU* 3.9 8.2 - - + +
152M CYS* 1.3 78.0 - - - +
154M TYR* 1.3 61.9 + - - +
156M GLY* 3.2 13.7 + - - -
185M TRP* 2.8 31.1 + - - +
186M LYS* 3.8 22.6 - - - +
187M LEU* 4.2 9.6 - - + +
188M PRO* 4.0 12.8 - - + +
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Residues in contact with TYR 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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150M LEU* 3.2 23.5 + - + +
151M ALA* 3.3 6.5 - - - +
152M CYS 3.1 0.2 - - - -
153M LYS* 1.3 80.9 - - - +
155M ASN* 1.3 68.5 + - - +
21N GLU* 2.8 29.8 + - + -
22N LYS* 4.6 3.1 - - + -
23N VAL 3.6 7.6 + - - -
24N PHE* 3.8 18.7 - + + +
50N LYS* 3.3 70.8 + - + +
51N ARG* 3.1 17.4 + - - -
53N ILE* 5.6 1.8 - - + -
74N LEU* 3.6 28.3 - - + -
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Residues in contact with ASN 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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151M ALA* 2.9 27.7 + - - +
152M CYS* 3.2 4.8 + - - +
154M TYR* 1.3 82.8 - - - +
156M GLY* 1.3 67.7 + - - +
157M LYS* 3.6 21.8 - - + +
159M GLU* 5.3 6.1 + - - +
22N LYS* 4.5 10.5 - - - +
72N ALA 5.0 5.1 + - - -
74N LEU* 3.6 26.7 - - - +
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Residues in contact with GLY 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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152M CYS 3.2 6.3 + - - -
153M LYS* 3.2 13.2 + - - -
154M TYR 3.3 1.0 + - - -
155M ASN* 1.3 82.3 - - - +
157M LYS* 1.3 65.6 + - - +
158M ASP 3.5 2.5 - - - -
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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