Contacts of the helix formed by residues 130 - 144 (chain C) in PDB entry 1PR1
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 130 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C LYS* 5.7 0.3 - - - -
129C ALA* 1.3 72.3 - - - +
131C PHE* 1.3 65.8 + - - +
132C ASP* 3.3 16.2 + - - +
133C MET* 2.9 53.2 + - - +
134C VAL* 3.2 13.2 + - - +
195C LYS* 3.4 52.7 + - + +
196C ALA 3.2 7.1 + - - +
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Residues in contact with PHE 131 (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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107C MET* 5.6 11.2 - - - -
129C ALA 3.3 5.6 + - - -
130C ASP* 1.3 72.2 + - - +
132C ASP* 1.3 75.6 + - - +
134C VAL* 3.0 22.5 + - + +
135C ARG* 3.0 52.3 + - + +
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Residues in contact with ASP 132 (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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84C LYS* 6.3 0.4 - - - +
130C ASP* 3.3 12.9 + - - +
131C PHE* 1.3 86.4 - - - +
133C MET* 1.3 57.3 + - + +
135C ARG* 2.6 39.2 + - - +
136C ASN* 2.8 42.3 + - - +
195C LYS* 5.8 1.4 + - - -
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Residues in contact with MET 133 (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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84C LYS* 4.0 40.6 - - + +
85C ILE 3.7 13.9 - - - +
86C ILE* 3.5 34.8 - - + -
130C ASP* 2.9 24.3 + - + +
132C ASP* 1.3 76.9 - - + +
134C VAL* 1.3 58.9 + - - +
136C ASN* 3.6 8.3 - - - +
137C ALA* 3.0 29.5 + - - +
195C LYS* 3.8 29.2 - - - -
196C ALA* 3.9 8.7 - - - -
197C LEU* 3.6 23.0 - - + +
231C SER* 4.9 1.2 + - - -
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Residues in contact with VAL 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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105C ILE* 3.9 18.4 - - + -
107C MET* 4.4 19.7 - - + -
129C ALA* 3.9 11.0 - - + -
130C ASP 3.3 17.0 - - - +
131C PHE* 3.0 13.8 + - + +
133C MET* 1.3 76.3 - - - +
135C ARG* 1.3 58.6 + - - +
137C ALA* 3.3 3.8 + - - +
138C VAL* 2.9 32.5 + - + +
150C VAL* 3.9 22.0 - - + -
197C LEU* 3.5 24.2 - - + -
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Residues in contact with ARG 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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131C PHE* 3.0 41.8 + - + +
132C ASP* 2.6 40.5 + - - +
134C VAL* 1.3 76.0 - - - +
136C ASN* 1.3 71.1 + - - +
138C VAL* 3.2 6.4 + - + +
139C ASP* 2.9 45.7 + - - +
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Residues in contact with ASN 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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84C LYS* 4.2 10.5 - - - +
132C ASP* 2.8 39.2 + - - +
133C MET* 3.6 9.4 - - - +
135C ARG* 1.3 79.8 + - - +
137C ALA* 1.3 57.6 + - - +
139C ASP* 3.3 2.8 + - - +
140C ALA* 2.8 30.7 + - - +
231C SER* 3.4 25.7 + - - +
234C LEU* 3.5 21.9 - - + +
235C GLY* 3.4 25.3 + - - -
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Residues in contact with ALA 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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105C ILE* 4.0 15.7 - - + +
133C MET 3.0 18.1 + - - +
134C VAL* 3.6 4.9 - - - +
135C ARG 3.2 0.2 - - - -
136C ASN* 1.3 75.1 - - - +
138C VAL* 1.3 63.9 + - - +
140C ALA* 4.3 0.2 - - - -
141C ALA* 3.1 23.2 + - - +
197C LEU* 3.7 20.0 - - + -
199C ILE* 4.5 4.0 - - + -
227C ILE* 3.5 17.9 - - + +
231C SER* 3.6 12.7 - - - -
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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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105C ILE* 3.9 9.0 - - + -
134C VAL* 2.9 25.2 + - + +
135C ARG* 3.2 7.8 + - + +
137C ALA* 1.3 75.7 - - - +
139C ASP* 1.3 69.5 + - - +
141C ALA* 3.4 6.3 - - - +
142C LYS* 3.2 22.3 + - + +
148C ALA* 5.9 1.1 - - + +
150C VAL* 3.5 32.3 - - + -
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Residues in contact with ASP 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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135C ARG* 2.9 37.4 + - - +
136C ASN* 3.7 5.7 - - - +
138C VAL* 1.3 83.2 - - - +
140C ALA* 1.3 66.0 + - - +
142C LYS* 3.3 8.2 + - - +
143C ALA* 3.0 23.7 + - - +
234C LEU* 3.8 15.0 - - + +
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Residues in contact with ALA 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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136C ASN 2.8 18.1 + - - +
137C ALA 3.8 4.9 - - - +
139C ASP* 1.3 75.3 - - - +
141C ALA* 1.3 63.2 + - - +
143C ALA* 3.2 7.6 + - - +
144C LEU* 3.0 28.1 + - - +
227C ILE* 3.6 26.2 - - - +
230C GLU* 3.9 13.0 - - + +
231C SER* 3.7 13.0 - - - +
234C LEU* 3.8 7.8 - - + +
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Residues in contact with ALA 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 ALA 3.1 15.0 + - - +
138C VAL* 3.4 11.9 - - - +
140C ALA* 1.3 75.5 - - - +
142C LYS* 1.3 55.8 + - - +
144C LEU* 2.7 23.8 + - - -
145C GLY 2.9 9.2 + - - -
146C ILE* 3.1 25.1 + - - +
148C ALA* 4.4 12.6 - - + -
227C ILE* 4.0 26.6 - - + +
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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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138C VAL* 3.2 11.7 + - + +
139C ASP* 3.3 11.4 + - - +
141C ALA* 1.3 77.4 - - - +
143C ALA* 1.3 57.2 + - - +
145C GLY* 3.1 17.7 + - - +
146C ILE 4.3 2.9 + - - -
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Residues in contact with ALA 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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139C ASP 3.0 17.1 + - - +
140C ALA* 3.5 8.5 - - - +
142C LYS* 1.3 76.9 - - - +
144C LEU* 1.3 62.9 + - + +
145C GLY 3.3 0.2 - - - -
234C LEU* 6.2 0.9 - - + -
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Residues in contact with LEU 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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140C ALA 3.0 14.3 + - - +
141C ALA 2.7 8.0 + - - +
143C ALA* 1.3 80.0 - - + +
145C GLY* 1.3 63.6 + - - +
146C ILE* 3.4 24.8 + - + +
226C LYS* 3.5 42.2 - - + +
227C ILE* 3.7 18.2 - - + +
230C GLU* 4.3 15.9 - - + -
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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