Contacts of the helix formed by residues 144 - 158 (chain G) in PDB entry 2OX4
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 ARG 144 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143G GLY* 1.3 73.2 - - - -
145G LYS* 1.3 61.2 + - - +
146G GLU* 3.8 22.4 + - - +
147G GLU* 2.8 70.4 + - + +
148G TYR* 3.3 8.1 - - - -
150G GLU* 4.4 13.3 + - - -
172G ARG* 4.3 12.1 - - + +
195G GLU* 5.8 0.2 - - - -
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Residues in contact with LYS 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143G GLY 3.8 1.6 + - - -
144G ARG* 1.3 73.2 - - - +
146G GLU* 1.3 88.6 + - + +
148G TYR* 3.2 21.4 + - - +
149G ALA 3.2 9.5 + - - -
195G GLU* 3.8 65.7 + - + +
196G ARG* 4.4 5.4 - - + +
199G ALA* 3.6 14.5 - - + +
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Residues in contact with GLU 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G ARG* 3.8 26.5 + - - +
145G LYS* 1.3 110.7 + - + +
147G GLU* 1.3 57.6 + - - +
149G ALA* 3.4 7.9 + - - +
150G GLU* 2.9 44.1 + - - +
199G ALA* 5.4 0.9 - - - -
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Residues in contact with GLU 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G SER 5.6 0.2 - - - +
142G LYS* 3.9 31.2 + - + +
143G GLY* 2.9 15.6 + - - -
144G ARG* 2.8 72.1 + - - +
146G GLU* 1.3 74.9 - - - +
148G TYR* 1.3 60.6 + - - +
150G GLU* 3.3 15.4 + - - +
151G GLU* 3.0 35.0 + - - +
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Residues in contact with TYR 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G LEU* 4.5 4.3 - - + +
132G GLN* 3.7 33.8 - - + +
142G LYS* 2.8 43.6 + - + -
143G GLY 4.0 0.7 - - - -
144G ARG 3.3 15.0 - - - -
145G LYS 3.2 7.9 + - - +
147G GLU* 1.3 74.3 - - - +
149G ALA* 1.3 64.5 + - - +
151G GLU* 3.4 5.6 + - - +
152G ALA* 3.1 22.7 + - - +
165G VAL* 3.6 24.9 - - + -
166G ASP 4.0 4.9 + - - -
167G VAL* 4.6 0.2 - - + -
170G HIS* 4.1 6.1 + - - +
196G ARG* 3.3 61.2 + - + +
200G ILE* 3.7 18.4 - - + +
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Residues in contact with ALA 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145G LYS 3.2 7.7 + - - +
146G GLU* 3.6 10.3 - - - +
148G TYR* 1.3 77.2 - - - +
150G GLU* 1.3 63.6 + - - +
152G ALA* 3.2 4.9 + - - +
153G LEU* 2.9 30.1 + - + +
199G ALA* 3.6 27.8 - - + +
200G ILE* 4.0 9.5 - - - +
203G ALA* 3.9 11.3 - - + +
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Residues in contact with GLU 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G ARG* 4.4 8.0 + - - -
146G GLU* 2.9 32.6 + - - +
147G GLU* 3.4 20.7 - - - +
149G ALA* 1.3 77.0 - - + +
151G GLU* 1.3 71.5 + - - +
153G LEU* 3.2 11.9 + - + +
154G LYS* 3.0 33.3 + - - +
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Residues in contact with GLU 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G LEU* 3.7 33.6 - - + +
134G GLY* 3.4 1.7 - - - -
135G TRP* 2.6 44.8 + - - +
142G LYS* 3.7 31.0 + - + -
147G GLU* 3.0 21.4 + - - +
148G TYR* 3.9 4.0 - - - +
150G GLU* 1.3 78.6 - - - +
152G ALA* 1.3 65.3 + - - +
154G LYS* 2.9 35.0 + - - +
155G ALA* 3.2 19.6 + - - +
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Residues in contact with ALA 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G LEU* 3.7 22.8 - - + +
148G TYR 3.1 14.1 + - - +
149G ALA* 3.2 9.2 + - - +
151G GLU* 1.3 76.9 - - - +
153G LEU* 1.3 56.0 + - - +
155G ALA* 3.2 4.5 + - - +
156G VAL* 3.0 32.2 + - - +
163G VAL* 4.5 5.8 - - + +
200G ILE* 3.8 15.9 - - + -
204G VAL* 3.7 21.1 - - + -
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Residues in contact with LEU 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149G ALA* 2.9 20.9 + - + +
150G GLU* 3.2 11.4 + - + +
152G ALA* 1.3 74.0 - - - +
154G LYS* 1.3 59.4 + - + +
156G VAL* 3.8 11.4 - - + +
157G ALA* 2.9 30.7 + - - +
203G ALA* 3.5 39.5 - - + +
204G VAL* 4.7 6.1 - - + +
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Residues in contact with LYS 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G TRP* 3.9 22.1 + - + +
142G LYS* 5.6 1.4 - - - +
150G GLU* 3.0 23.0 + - - +
151G GLU* 2.9 47.0 + - - +
153G LEU* 1.3 75.8 - - - +
155G ALA* 1.3 61.8 + - - +
157G ALA* 3.4 7.6 + - - +
158G GLU* 3.3 26.3 + - - +
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Residues in contact with ALA 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G ALA* 3.6 31.4 - - + -
131G LEU* 4.5 1.6 - - + -
135G TRP* 3.8 18.5 - - + +
151G GLU 3.2 9.0 + - - +
152G ALA 3.5 7.9 - - - +
154G LYS* 1.3 76.7 - - - +
156G VAL* 1.3 65.6 + - - +
158G GLU 3.0 10.6 + - - -
160G TYR* 3.2 25.2 + - + -
163G VAL* 4.0 12.1 - - + -
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Residues in contact with VAL 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G ALA 3.0 20.7 + - - +
153G LEU* 3.8 13.9 - - + +
155G ALA* 1.3 75.4 - - - +
157G ALA* 1.3 59.8 + - - +
159G GLY* 2.8 21.8 + - - -
160G TYR 3.7 13.1 - - - +
163G VAL* 5.1 2.5 - - + -
204G VAL* 3.8 26.5 - - + +
208G VAL* 3.9 30.1 - - + -
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Residues in contact with ALA 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153G LEU 2.9 18.5 + - - +
154G LYS* 3.5 9.2 - - - +
155G ALA 3.2 0.2 - - - -
156G VAL* 1.3 78.4 - - - +
158G GLU* 1.3 60.7 + - + +
159G GLY* 3.2 1.1 + - - -
362G LYS* 5.3 4.9 + - - -
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Residues in contact with GLU 158 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135G TRP* 2.9 35.8 + - - -
154G LYS* 3.3 9.5 + - - +
155G ALA 3.0 10.6 + - - +
157G ALA* 1.3 76.9 - - + +
159G GLY* 1.3 56.9 + - - +
160G TYR* 3.5 17.0 + - + -
343G GLN* 3.3 17.7 + - - +
362G LYS* 3.6 27.3 + - - +
363G GLY 4.3 1.2 + - - -
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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