Contacts of the helix formed by residues 125 - 132 (chain C) in PDB entry 1PFX
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 125 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124C ALA* 1.3 72.7 - - - +
126C LYS* 1.3 67.0 + - - +
127C GLU* 3.7 14.7 + - - +
128C TYR* 3.0 33.0 + - - +
129C THR* 2.7 22.0 + - - -
235C VAL* 3.7 5.4 - - - -
239C LYS* 6.5 0.9 - - - +
98L PHE* 4.7 11.5 - - + -
100L LYS* 3.3 31.0 + - - +
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Residues in contact with LYS 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C ASP* 1.3 76.8 + - - +
127C GLU* 1.3 67.3 + - - +
129C THR* 3.4 18.8 + - - +
232C SER* 3.5 27.4 - - - +
233C ARG* 5.2 12.5 - - - +
235C VAL* 3.6 14.5 - - + +
236C ASN* 6.1 5.8 - - + +
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Residues in contact with GLU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C ASP* 3.4 13.4 + - - +
126C LYS* 1.3 81.2 - - - +
128C TYR* 1.3 88.0 + - + +
129C ASN* 3.0 44.0 + - + +
99L CYS 5.1 2.2 - - - +
100L LYS* 4.8 12.8 - - - +
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Residues in contact with TYR 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ALA* 4.0 7.4 - - + -
125C ASP* 3.0 30.0 + - - +
127C GLU* 1.3 98.8 + - + +
129C THR* 1.3 72.8 + + - +
130C PHE* 2.7 67.1 + + + -
88L CYS* 5.3 1.2 + - - +
92L ASN* 3.4 20.8 + - - -
97L GLN 3.6 14.4 - - - -
98L PHE* 3.7 23.8 - + + -
99L CYS* 3.1 34.7 + - - -
100L LYS* 4.0 16.8 - - - -
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Residues in contact with THR 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ALA* 3.2 23.7 + - - +
125C ASP 2.7 23.1 + - - -
126C LYS 3.7 3.8 - - - -
127C GLU 3.1 1.2 + - - -
128C TYR* 1.3 77.1 - - - +
129C ASN* 1.3 63.3 + - - +
130C PHE* 4.3 2.5 - - - -
131C LEU* 3.0 17.8 + - - +
208C PHE* 6.5 0.2 - - - -
209C LEU 3.5 23.8 - - - +
210C THR* 3.3 21.9 - - + +
231C VAL* 4.1 6.7 - - + -
232C SER* 3.7 30.1 - - - +
235C VAL* 3.9 5.4 - - - +
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Residues in contact with ASN 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C LYS 3.5 6.1 + - - +
127C GLU* 3.0 10.5 + - - +
129C THR* 1.3 143.0 - - + +
131C LEU* 2.9 24.8 + - + +
132C LYS* 3.1 42.6 + - + +
230C LYS* 3.8 18.4 - - + -
232C SER* 3.1 23.4 + - - +
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Residues in contact with ILE 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C GLU* 3.1 44.1 + - + -
128C TYR* 3.3 33.9 - - - +
129C ASN* 1.3 78.8 - - - +
130C PHE* 1.3 61.1 - - - +
131C LEU 3.3 0.3 - - - -
132C LYS* 3.5 27.8 - - + +
133C PHE* 3.0 45.9 - + - -
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Residues in contact with PHE 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ALA* 4.5 7.9 - - + -
128C TYR* 2.7 66.7 + + + +
129C ILE* 1.3 77.9 - + - +
131C LEU* 1.3 64.0 + - - +
133C PHE* 3.4 40.0 - + - +
201C THR* 3.4 38.9 - - - +
203C VAL* 3.5 42.8 - - + -
208C PHE* 4.5 15.5 - + + -
210C THR* 4.1 2.9 - - + -
92L ASN* 6.2 1.6 - - - -
97L GLN* 5.5 2.5 - - - -
98L PHE* 4.4 12.3 - + - -
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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