Contacts of the helix formed by residues 144 - 159 (chain M) in PDB entry 2ZHX
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 144 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M GLN* 2.6 32.6 + - - -
27M HIS* 5.2 3.8 - - - -
28M MET* 3.5 13.2 - - - +
142M GLY 3.1 7.5 + - - -
143M LYS* 1.3 78.3 - - - +
145M TRP* 1.3 63.0 + - - +
146M GLU* 3.5 3.1 + - - -
147M ALA* 3.9 5.7 + - - +
148M VAL* 4.0 2.8 - - - +
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Residues in contact with TRP 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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25M VAL* 5.2 6.7 - - + -
28M MET* 3.5 40.9 - - + +
32M LEU* 4.5 8.7 - - + +
49M VAL* 3.7 32.3 - - + -
50M LEU* 3.7 13.5 - - + -
128M ARG 4.0 7.5 - - - +
129M VAL* 4.1 5.8 - - + -
130M LEU* 3.7 40.2 - - + +
131M THR* 2.5 43.2 + - + +
140M HIS* 4.4 16.6 - - + +
143M LYS 3.5 1.8 + - - -
144M GLY* 1.3 76.3 - - - +
146M GLU* 1.3 71.5 + - - +
148M VAL* 2.9 48.0 + - + +
149M THR* 3.3 4.9 + - - +
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Residues in contact with GLU 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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128M ARG* 4.0 23.8 - - + +
129M VAL* 3.8 14.9 - - + +
140M HIS 4.5 0.3 - - - +
141M ARG* 3.4 17.2 + - - +
142M GLY* 2.6 39.4 + - - -
143M LYS 4.0 0.5 + - - -
144M GLY 3.5 1.1 + - - -
145M TRP* 1.3 84.9 + - - +
147M ALA* 1.3 61.3 + - - +
149M THR* 3.0 9.6 + - - +
150M GLU* 2.9 43.7 + - + +
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Residues in contact with ALA 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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21M VAL* 4.1 6.7 - - + +
24M GLN* 4.0 28.7 - - + +
144M GLY 3.9 1.9 + - - +
145M TRP 3.2 0.6 - - - -
146M GLU* 1.3 74.7 - - - +
148M VAL* 1.3 67.5 + - - +
150M GLU* 3.5 12.9 - - - +
151M CYS* 3.0 24.4 + - - +
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Residues in contact with VAL 148 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M LEU* 3.9 22.0 - - + +
21M VAL* 4.2 15.9 - - + +
24M GLN* 4.5 7.6 - - + +
25M VAL* 4.6 22.7 - - + +
28M MET* 4.8 1.1 - - + -
50M LEU* 5.5 2.0 - - + -
53M PHE* 4.6 13.7 - - + -
130M LEU* 4.9 1.3 - - + -
144M GLY 4.0 9.9 - - - +
145M TRP* 2.9 42.8 + - + +
147M ALA* 1.3 75.1 - - - +
149M THR* 1.3 65.6 + - + +
151M CYS* 2.9 17.0 + - - +
152M ALA* 2.9 11.1 + - - +
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Residues in contact with THR 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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53M PHE* 5.3 0.2 - - - -
126M LEU* 3.7 18.9 - - + +
127M ASN 2.9 28.7 - - - +
128M ARG* 2.9 38.7 + - - +
130M LEU* 3.8 17.9 - - + -
145M TRP 3.3 2.9 + - - +
146M GLU* 3.0 17.3 + - - -
148M VAL* 1.3 79.1 - - - +
150M GLU* 1.3 55.3 + - - +
152M ALA* 3.2 9.3 - - - +
153M ILE* 3.0 34.7 + - - +
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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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128M ARG* 4.0 21.1 + - - +
146M GLU* 2.9 36.4 + - - +
147M ALA* 3.5 11.5 - - - +
149M THR* 1.3 74.7 + - - +
151M CYS* 1.3 61.5 + - - +
153M ILE* 2.9 9.1 + - + +
154M ARG* 2.8 46.9 + - - +
178M MET* 3.9 32.3 - - + +
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Residues in contact with CYS 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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17M ALA 3.9 20.0 - - - -
18M LEU* 4.7 2.5 - - + -
20M PRO* 4.3 15.9 - - - -
21M VAL* 3.5 38.1 - - + -
147M ALA 3.0 7.0 + - - +
148M VAL 2.9 11.8 + - - +
150M GLU* 1.3 72.9 - - - +
152M ALA* 1.3 57.3 + - - +
154M ARG* 3.6 10.9 - - - +
155M ALA* 2.8 29.6 + - - +
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Residues in contact with ALA 152 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M TRP* 3.8 17.1 - - + -
17M ALA* 6.1 0.2 - - - -
18M LEU* 4.3 8.6 - - + +
53M PHE* 3.8 32.8 - - + -
124M LEU* 5.7 0.7 - - + -
126M LEU* 4.7 5.6 - - + -
148M VAL 2.9 10.6 + - - +
149M THR* 3.2 12.1 - - - +
150M GLU 3.0 0.2 - - - -
151M CYS* 1.3 77.7 - - - +
153M ILE* 1.3 62.9 + - - +
155M ALA* 3.3 4.7 + - - +
156M LEU* 2.9 25.2 + - - +
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Residues in contact with ILE 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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63M LEU* 3.9 24.2 - - + -
65M VAL* 5.3 1.3 - - + -
124M LEU* 6.3 0.2 - - - -
126M LEU* 3.7 22.0 - - + +
128M ARG* 5.2 4.5 - - + -
149M THR* 3.0 20.1 + - - +
150M GLU* 2.9 11.9 + - + +
152M ALA* 1.3 73.5 - - - +
154M ARG* 1.3 52.8 + - - +
156M LEU* 2.9 13.3 + - + +
157M ALA* 2.8 33.0 + - - +
163M LEU* 5.1 0.8 - - + +
175M LEU* 3.4 34.5 - - + -
178M MET* 4.8 14.8 - - + -
179M LEU* 4.8 24.0 - - + -
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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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150M GLU* 2.8 37.4 + - - +
151M CYS* 3.6 11.2 - - - +
153M ILE* 1.3 73.9 - - - +
155M ALA* 1.3 61.3 + - - +
157M ALA* 3.4 9.0 + - - +
158M ALA* 3.1 23.9 + - - +
178M MET* 3.7 53.4 + - + +
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Residues in contact with ALA 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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17M ALA* 3.6 37.9 - - + +
57M PHE* 3.8 6.4 - - + -
151M CYS* 2.8 18.1 + - - +
152M ALA* 3.5 6.3 - - - +
154M ARG* 1.3 74.1 - - - +
156M LEU* 1.3 65.0 + - - +
158M ALA* 3.1 16.1 + - - +
159M ARG* 3.4 15.9 + - - +
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Residues in contact with LEU 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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14M TRP* 4.6 1.6 - - + -
57M PHE* 4.2 13.4 - - + +
60M VAL* 3.7 22.9 - - + -
63M LEU* 4.6 13.7 - - + -
124M LEU* 3.5 31.9 - - + -
152M ALA 2.9 13.7 + - - +
153M ILE* 2.9 13.9 + - - +
155M ALA* 1.3 78.5 - - - +
157M ALA* 1.3 58.4 + - - +
159M ARG* 3.2 64.2 + - - +
161M ALA 5.1 1.9 - - - +
163M LEU* 3.9 28.8 - - + +
184M CYS* 4.8 0.3 - - - -
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Residues in contact with ALA 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 ILE 2.8 11.7 + - - +
154M ARG 3.6 9.4 - - - +
155M ALA 3.2 0.2 - - - -
156M LEU* 1.3 75.5 - - - +
158M ALA* 1.3 62.5 + - - +
159M ARG 3.3 3.1 + - - +
163M LEU* 4.3 1.7 - - - +
178M MET 4.3 5.8 - - - +
179M LEU* 3.7 34.8 - - + -
180M ALA 5.1 1.6 - - - +
183M ASN* 3.4 22.0 + - - +
184M CYS* 3.6 14.5 - - - -
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Residues in contact with ALA 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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154M ARG 3.1 16.9 + - - +
155M ALA* 3.1 9.8 + - - +
157M ALA* 1.3 73.6 - - - +
159M ARG* 1.3 66.5 + - - +
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Residues in contact with ARG 159 (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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57M PHE* 3.0 55.1 + - + -
58M ASP* 3.9 11.5 + - - +
60M VAL 3.0 30.7 + - - +
155M ALA 3.4 15.0 + - - +
156M LEU* 3.2 33.3 + - - +
157M ALA 3.2 2.5 - - - +
158M ALA* 1.3 82.3 - - - +
160M ALA* 1.3 57.5 + - - +
161M ALA* 3.9 19.9 + - + +
162M PRO 3.6 18.6 + - - -
163M LEU* 4.1 8.7 - - - +
183M ASN* 2.8 27.0 + - - -
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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
------------------------------------------------------------
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