Contacts of the helix formed by residues 133 - 145 (chain C) in PDB entry 4PP8
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 133 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117C SER 4.8 7.9 + - - +
118C TYR* 5.2 0.2 - - - -
119C PHE* 5.4 3.2 - - - -
131C SER* 3.3 9.8 + - - -
132C ALA* 1.3 85.8 + - - +
134C ASP* 1.3 60.9 + - - +
135C GLU* 3.4 23.8 + - - +
136C SER* 2.7 43.6 + - - -
137C GLY 2.8 23.6 + - - -
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Residues in contact with ASP 134 (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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131C SER* 5.2 0.9 + - - -
133C ASN* 1.3 72.4 - - - +
135C GLU* 1.3 62.1 + - + +
137C GLY* 3.2 3.3 + - - +
138C VAL* 2.9 32.9 + - + +
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Residues in contact with GLU 135 (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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117C SER 5.2 2.9 - - - +
118C TYR* 4.0 28.1 - - + -
133C ASN* 3.3 20.0 + - - +
134C ASP* 1.3 77.5 + - + +
136C SER* 1.3 63.1 + - - +
138C VAL* 3.5 16.4 + - - +
139C ILE* 3.6 10.9 + - - +
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Residues in contact with SER 136 (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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117C SER 4.2 0.2 + - - -
118C TYR* 3.3 18.9 - - - -
119C PHE 3.0 45.1 + - - -
120C PHE* 3.9 3.4 - - - -
131C SER* 4.1 3.8 - - - -
132C ALA* 4.5 0.3 - - - +
133C ASN* 2.7 38.9 + - - -
135C GLU* 1.3 71.8 - - - +
137C GLY* 1.3 58.9 + - - +
139C ILE* 3.3 4.2 + - - +
140C MET* 2.8 29.1 + - - +
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Residues in contact with GLY 137 (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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131C SER* 3.6 21.9 - - - -
133C ASN 2.8 11.2 + - - -
134C ASP* 3.2 7.1 + - - -
136C SER* 1.3 74.5 - - - +
138C VAL* 1.3 58.5 + - - +
140C MET* 3.6 6.6 - - - +
141C ASN* 2.8 41.8 + - - -
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Residues in contact with VAL 138 (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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134C ASP* 2.9 21.5 + - + +
135C GLU* 3.7 10.8 - - - +
136C SER 3.2 0.4 - - - -
137C GLY* 1.3 77.2 - - - +
139C ILE* 1.3 65.0 + - + +
141C ASN* 3.4 8.4 + - - +
142C LYS* 3.1 47.7 + - + +
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Residues in contact with ILE 139 (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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79C THR* 4.5 15.7 - - + -
114C ILE* 3.6 26.2 - - + -
118C TYR* 3.5 49.6 - - + -
120C PHE* 4.1 5.6 - - + -
135C GLU 3.6 4.9 + - - +
136C SER* 3.3 7.0 + - - +
138C VAL* 1.3 78.3 - - + +
140C MET* 1.3 66.5 + - - +
142C LYS* 3.1 12.0 + - + +
143C TRP* 2.9 40.2 + - + +
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Residues in contact with MET 140 (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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120C PHE* 3.7 42.8 - - + -
129C TRP* 3.6 51.1 - - + -
130C ARG* 3.9 11.9 - - - +
131C SER* 3.9 16.4 - - - +
136C SER 2.8 17.3 + - - +
137C GLY* 3.6 6.3 - - - +
139C ILE* 1.3 76.9 - - - +
141C ASN* 1.3 75.5 + - - +
143C TRP* 3.2 2.3 + - - +
144C LYS* 2.9 34.2 + - + +
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Residues in contact with ASN 141 (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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137C GLY* 2.8 30.8 + - - +
138C VAL* 3.7 8.2 - - - +
140C MET* 1.3 86.7 - - - +
142C LYS* 1.3 62.1 + - - +
144C LYS* 3.3 30.3 + - - +
145C ASP* 3.3 28.1 + - - +
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Residues in contact with LYS 142 (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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75C LYS* 5.1 1.9 + - - -
138C VAL* 3.1 34.0 + - + +
139C ILE* 3.1 13.3 + - + +
141C ASN* 1.3 77.7 - - + +
143C TRP* 1.3 69.5 + - + +
145C ASP* 3.4 22.1 + - - +
146C ASP* 4.1 2.9 + - - +
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Residues in contact with TRP 143 (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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72C LEU* 4.1 19.7 - - + -
75C LYS* 3.9 38.1 + - + +
76C VAL* 4.3 6.7 - - + -
79C THR* 3.2 28.2 + - - +
92C LEU* 3.9 22.4 - - + -
112C PHE* 4.1 14.8 - + - -
114C ILE* 3.8 23.6 - - + -
120C PHE* 4.0 18.4 - + + -
129C TRP* 5.6 0.7 - - + -
139C ILE* 2.9 35.4 + - + +
140C MET* 3.7 6.7 - - - +
142C LYS* 1.3 78.1 - - + +
144C LYS* 1.3 58.2 + - - +
146C ASP* 3.1 26.9 + - - +
149C PHE* 3.4 34.2 - + + -
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Residues in contact with LYS 144 (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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129C TRP* 3.4 57.6 - - + +
140C MET* 2.9 23.6 + - + +
141C ASN* 3.3 33.7 + - - +
142C LYS 3.4 0.2 - - - -
143C TRP* 1.3 72.4 - - - +
145C ASP* 1.3 66.9 + - - +
146C ASP 3.1 6.8 + - - +
147C GLY* 4.6 1.0 + - - -
149C PHE* 4.8 0.2 - - - -
150C VAL* 3.6 20.8 - - + +
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Residues in contact with ASP 145 (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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141C ASN 3.3 16.7 + - - +
142C LYS* 3.5 15.3 - - - +
143C TRP 3.2 0.8 - - - -
144C LYS* 1.3 82.9 + - - +
146C ASP* 1.3 56.6 + - - +
147C GLY* 3.2 7.2 + - - -
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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