Contacts of the helix formed by residues 142 - 152 (chain B) in PDB entry 4JU5
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 ASP 142 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LEU* 3.4 3.1 + - - +
141B PRO* 1.3 91.1 - - - +
143B GLY* 1.3 62.9 + - - +
144B ALA* 3.2 11.1 + - - +
145B ALA* 2.9 27.9 + - - +
146B ALA* 3.4 15.8 + - - +
189B ASN* 4.5 1.6 - - - +
192B VAL* 3.7 14.9 - - - +
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Residues in contact with GLY 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ASP* 1.3 73.7 - - - +
144B ALA* 1.3 64.8 + - - +
146B ALA* 3.4 6.8 + - - +
147B GLU* 3.1 27.6 + - - +
192B VAL* 4.0 7.7 - - - +
195B LYS* 4.0 27.1 - - - -
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ASP* 3.2 10.1 + - - +
143B GLY* 1.3 75.0 - - - +
145B ALA* 1.3 57.2 + - - +
147B GLU* 3.4 7.8 + - - +
148B SER* 2.8 34.9 + - - +
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B THR 5.3 0.4 - - - +
140B LEU* 3.7 17.1 - - + +
141B PRO* 4.1 17.9 - - + -
142B ASP* 2.9 20.5 + - - +
144B ALA* 1.3 74.5 - - - +
146B ALA* 1.3 65.1 + - - +
148B SER* 3.4 7.5 + - - -
149B LEU* 3.0 26.0 + - - +
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Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LEU* 3.8 20.9 - - + +
142B ASP 3.4 5.6 + - - +
143B GLY* 3.5 8.1 - - - +
145B ALA* 1.3 79.4 - - - +
147B GLU* 1.3 57.3 + - - +
149B LEU* 3.2 2.8 + - - +
150B VAL* 3.0 32.3 + - - +
158B ILE* 4.1 3.7 - - + +
192B VAL* 3.9 18.4 - - + -
196B TYR* 3.5 29.8 - - + +
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Residues in contact with GLU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B GLY 3.1 17.4 + - - +
144B ALA* 3.7 9.9 - - - +
146B ALA* 1.3 73.0 - - - +
148B SER* 1.3 65.1 + - - +
150B VAL* 3.1 13.5 + - - +
151B GLU* 2.9 35.4 + - + +
195B LYS* 3.7 22.6 + - - +
196B TYR* 2.9 24.3 + - - -
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Residues in contact with SER 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ALA* 2.8 24.3 + - - +
145B ALA* 3.4 8.3 + - - -
147B GLU* 1.3 71.7 - - - +
149B LEU* 1.3 57.4 + - - +
151B GLU* 3.3 8.2 + - - +
152B SER* 3.0 33.4 + - - -
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B THR* 4.3 23.1 - - + +
140B LEU* 4.2 10.8 - - + -
145B ALA 3.0 16.6 + - - +
146B ALA* 3.5 3.6 - - - +
148B SER* 1.3 73.4 - - - +
150B VAL* 1.3 67.2 - - + +
152B SER* 3.3 19.4 + - - -
153B SER 4.2 1.2 + - - -
156B ALA* 3.8 23.7 - - + +
157B VAL 4.3 2.2 - - - +
158B ILE* 4.1 23.8 - - + -
183B PRO* 3.7 30.5 - - + +
184B PHE 4.6 1.3 - - - +
185B GLY 4.2 11.7 - - - +
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ALA 3.0 17.7 + - - +
147B GLU* 3.6 15.5 - - - +
149B LEU* 1.3 80.6 - - + +
151B GLU* 1.3 71.2 + - - +
153B SER 3.4 15.8 + - - +
156B ALA* 4.1 10.7 - - + +
158B ILE* 4.1 8.1 - - + -
196B TYR* 4.3 8.1 - - - +
206B PHE* 3.7 55.5 - - + +
207B LYS 6.5 0.4 - - - -
208B LYS* 4.0 6.2 - - + +
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Residues in contact with GLU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B GLU* 2.9 27.3 + - + +
148B SER* 3.7 6.7 - - - +
149B LEU 3.2 0.2 - - - -
150B VAL* 1.3 90.3 - - - +
152B SER* 1.3 56.0 + - - +
153B SER 3.1 8.8 + - - -
208B LYS* 2.7 42.0 + - - +
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Residues in contact with SER 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B SER* 3.0 20.6 + - - -
149B LEU* 3.3 18.4 + - - -
151B GLU* 1.3 76.5 - - - +
153B SER* 1.3 62.1 + - - +
183B PRO* 5.3 3.5 - - - +
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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