Contacts of the helix formed by residues 145 - 154 (chain F) in PDB entry 3ZP0
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 145 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28F ASN* 3.5 4.5 - - - +
30F GLN* 3.2 22.9 - - - +
143F LYS 4.1 1.2 + - - -
144F CYS* 1.3 76.0 - - - +
146F ASN* 1.3 55.1 + - - +
147F GLU* 3.2 21.9 + - - +
148F CYS* 2.7 37.5 + - - +
149F MET* 2.8 31.9 + - - +
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Residues in contact with ASN 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F HIS* 3.7 23.1 + - - -
28F ASN* 3.0 27.1 + - - +
30F GLN* 3.5 30.1 + - - +
145F ASP* 1.3 75.3 - - - +
147F GLU* 1.3 52.7 + - - +
149F MET* 3.2 5.2 + - - +
150F GLU* 2.6 45.7 + - - +
153F ARG* 4.5 3.2 + - - +
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Residues in contact with GLU 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F ASP* 3.2 22.4 - - - +
146F ASN* 1.3 75.6 - - - +
148F CYS* 1.3 59.4 + - - +
150F GLU* 3.4 20.4 + - - +
151F SER* 3.1 24.8 + - - -
1160F NAG 2.5 48.5 + - + +
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Residues in contact with CYS 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F PHE* 4.8 0.7 - - - -
143F LYS 4.7 2.9 - - - -
144F CYS* 2.1 48.9 - - - -
145F ASP* 2.7 28.9 + - - +
147F GLU* 1.3 71.8 - - - +
149F MET* 1.3 61.1 + - - +
151F SER* 3.1 20.2 - - - -
152F VAL* 3.4 10.9 + - - +
157F TYR* 4.2 20.4 - - - -
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Residues in contact with MET 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ASP* 4.7 0.2 - - + -
6E GLN 3.9 19.7 - - - +
7E ILE* 4.0 15.4 - - + +
26F HIS* 3.4 31.6 - - + +
27F SER 3.9 11.7 - - - +
28F ASN* 3.6 14.6 - - + +
140F PHE* 4.2 15.3 - - + -
144F CYS* 3.4 39.9 - - + +
145F ASP 2.8 11.7 + - - +
146F ASN* 3.3 11.7 - - - +
148F CYS* 1.3 73.4 - - - +
150F GLU* 1.3 66.0 + - - +
152F VAL* 3.0 16.6 + - - +
153F ARG* 3.3 23.7 + - - +
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Residues in contact with GLU 150 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146F ASN* 2.6 29.0 + - + +
147F GLU* 3.4 23.8 + - - +
149F MET* 1.3 72.6 - - - +
151F SER* 1.3 62.8 + - - +
153F ARG* 3.1 41.2 + - - +
154F ASN* 3.2 16.1 + - - +
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Residues in contact with SER 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F GLU 3.1 15.3 + - - -
148F CYS* 3.1 17.7 - - - -
149F MET 3.0 0.4 - - - -
150F GLU* 1.3 76.5 - - - +
152F VAL* 1.3 58.6 + - - +
154F ASN* 2.9 21.2 - - - +
155F GLY 3.4 0.2 + - - -
156F THR* 3.0 29.0 + - - +
157F TYR* 3.1 29.5 + - - -
158F ASP 4.7 0.2 + - - -
1160F NAG 5.9 5.6 - - - -
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Residues in contact with VAL 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ILE* 4.0 21.8 - - + -
24F TYR* 4.8 3.1 + - + -
121F LYS* 5.9 0.9 + - - -
122F VAL* 4.1 32.1 - - + +
125F GLN* 3.6 14.8 - - - +
126F LEU* 4.3 10.5 - - + -
140F PHE* 4.0 21.5 - - + -
148F CYS 3.5 15.3 - - - +
149F MET* 3.0 10.3 + - - +
151F SER* 1.3 75.7 - - - +
153F ARG* 1.3 63.3 + - - +
154F ASN 3.4 0.3 + - - -
155F GLY 3.4 8.3 + - - -
157F TYR* 3.9 26.0 - - + -
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Residues in contact with ARG 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ILE* 4.4 6.7 - - + +
24F TYR* 3.6 53.3 + - + +
26F HIS* 3.6 31.3 + - - +
35F ALA* 3.8 31.3 - - - +
37F ASP* 4.3 6.1 - - - +
121F LYS* 5.3 3.1 + - - -
146F ASN* 4.5 2.6 + - - +
149F MET* 3.7 23.0 + - - +
150F GLU* 3.1 47.1 + - - +
152F VAL* 1.3 78.3 - - - +
154F ASN* 1.3 58.5 + - + +
155F GLY 3.4 0.4 + - - -
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Residues in contact with ASN 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F GLU 3.2 13.0 + - - +
151F SER* 2.9 28.8 - - - +
153F ARG* 1.3 76.5 - - + +
155F GLY* 1.3 57.8 + - - +
156F THR* 2.7 30.0 + - - +
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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
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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