Contacts of the helix formed by residues 143 - 153 (chain E) in PDB entry 3J8B
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 ASN 143 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E GLN* 2.8 24.3 + - + +
139E TYR* 5.2 0.2 - - - -
141E CYS* 3.3 7.0 - - + +
142E GLY* 1.3 74.6 - - - +
144E TYR* 1.3 60.8 + - - +
145E SER 3.6 1.3 - - - -
146E GLY* 3.7 5.5 + - - +
147E ALA* 3.2 21.3 + - - +
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Residues in contact with TYR 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E TYR* 5.6 1.1 - - - +
142E GLY 3.4 7.7 + - - +
143E ASN* 1.3 71.8 - - - +
145E SER* 1.3 67.4 + - - +
147E ALA* 3.0 9.0 + - - +
148E ALA* 2.9 25.2 + - - +
175E SER* 5.0 10.4 - - - +
178E LEU* 6.0 4.0 - - + +
179E MET* 5.1 17.0 - - + +
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Residues in contact with SER 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E ASN 3.6 0.4 - - - -
144E TYR* 1.3 78.6 - - - +
146E GLY* 1.3 58.8 + - - +
148E ALA* 3.2 7.0 + - - +
149E GLU* 2.9 27.4 + - - +
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Residues in contact with GLY 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E GLN* 4.2 7.9 - - - -
143E ASN* 3.7 9.2 + - - +
144E TYR 3.2 0.2 - - - -
145E SER* 1.3 75.6 - - - +
147E ALA* 1.3 66.1 + - - +
149E GLU* 3.2 7.4 + - - +
150E TYR* 2.9 28.8 + - - +
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Residues in contact with ALA 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E ALA* 3.6 15.6 - - - +
138E GLN* 3.6 8.8 - - - +
139E TYR* 3.6 31.2 - - + +
143E ASN 3.2 15.2 + - - +
144E TYR* 3.0 11.8 + - - +
146E GLY* 1.3 74.7 - - - +
148E ALA* 1.3 58.4 + - - +
151E LEU* 2.8 31.6 + - - +
175E SER* 5.2 8.5 - - - -
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Residues in contact with ALA 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E TYR 2.9 12.0 + - - +
145E SER* 3.3 11.2 - - - +
147E ALA* 1.3 73.5 - - - +
149E GLU* 1.3 67.3 - - - +
151E LEU* 2.8 16.5 + - - +
152E TYR* 2.9 16.7 + - - +
172E LYS* 6.0 4.3 - - + +
175E SER* 4.6 17.1 - - - -
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Residues in contact with GLU 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E SER 2.9 16.4 + - - +
146E GLY* 3.2 8.9 + - - +
148E ALA* 1.3 73.4 - - - +
150E TYR* 1.3 59.0 + - - +
152E TYR* 3.2 4.7 + - - +
153E PHE* 2.9 28.0 + - - +
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Residues in contact with TYR 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E LEU* 3.1 42.3 - - - +
134E TYR* 3.9 20.4 - - + +
135E ALA 4.2 4.5 - - - +
146E GLY 2.9 17.6 + - - +
149E GLU* 1.3 74.5 - - - +
151E LEU* 1.3 62.6 + - - +
153E PHE* 3.6 12.1 + - + +
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Residues in contact with LEU 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E LEU 4.6 0.9 - - - -
132E TYR* 5.6 1.1 - - - +
135E ALA* 3.8 15.5 - - + +
147E ALA 2.8 23.2 + - - +
148E ALA* 2.8 12.1 + - - +
150E TYR* 1.3 80.1 - - - +
152E TYR* 1.3 58.0 + - - +
154E PHE* 3.5 18.2 + - - +
168E SER* 4.6 14.0 - - - +
171E GLY* 5.4 4.3 - - - -
172E LYS* 5.2 14.4 - - + +
175E SER* 6.1 1.3 - - - -
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Residues in contact with TYR 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E ALA 2.9 17.2 + - - +
149E GLU* 4.1 3.8 - - - +
151E LEU* 1.3 69.3 - - - +
153E PHE* 1.3 56.4 + - - +
154E PHE 2.9 5.8 - - - -
155E ARG* 3.0 29.4 + - - +
168E SER* 5.5 6.5 - - - -
172E LYS* 5.6 10.1 - - + +
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Residues in contact with PHE 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E LEU* 4.5 8.3 - - + +
149E GLU 2.9 16.2 + - - +
150E TYR* 3.7 14.6 - - - +
151E LEU 3.2 0.8 - - - -
152E TYR* 1.3 76.5 - - - +
154E PHE* 1.3 57.0 + - - +
155E ARG* 3.1 5.5 + - - +
156E VAL* 4.1 10.2 + - - +
157E LEU* 4.9 2.6 + - - +
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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