Contacts of the helix formed by residues 130 - 144 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B LYS* 5.6 0.2 - - - -
129B ALA* 1.3 72.7 - - - +
131B PHE* 1.3 66.8 + - - +
132B ASP* 3.2 13.9 + - - +
133B MET* 2.9 40.2 + - + +
134B VAL* 3.1 21.5 + - - +
195B LYS* 3.3 52.1 - - + +
196B ALA 3.1 7.9 + - - +
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Residues in contact with PHE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B MET* 6.2 4.3 - - + -
129B ALA 3.5 4.8 + - - -
130B ASP* 1.3 74.9 + - - +
132B ASP* 1.3 69.1 + - - +
134B VAL* 3.0 16.6 + - + +
135B ARG* 2.9 56.5 + - + +
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Residues in contact with ASP 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LYS* 6.2 1.1 - - - +
130B ASP* 3.2 11.2 + - - +
131B PHE* 1.3 89.7 - - - +
133B MET* 1.3 57.8 + - + +
135B ARG* 2.7 43.3 + - - +
136B ASN* 2.9 40.3 + - - +
195B LYS* 5.4 6.9 + - - +
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Residues in contact with MET 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LYS* 3.9 37.2 - - + +
85B ILE 3.8 10.3 - - - +
86B ILE* 3.4 37.9 - - + -
130B ASP* 2.9 26.0 + - + +
132B ASP* 1.3 77.0 - - + +
134B VAL* 1.3 62.3 + - - +
136B ASN* 3.4 8.7 + - - +
137B ALA* 3.0 18.2 + - - +
195B LYS* 3.6 36.1 - - - +
196B ALA 3.8 6.1 - - - -
197B LEU* 3.5 26.2 - - + +
231B SER* 4.9 1.9 + - - -
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ILE* 4.1 8.3 - - + -
107B MET* 4.4 13.5 - - + -
129B ALA* 3.7 12.3 - - + -
130B ASP 3.1 15.4 + - - +
131B PHE* 3.0 15.8 + - + +
133B MET* 1.3 77.4 - - - +
135B ARG* 1.3 58.4 + - - +
137B ALA* 3.2 4.5 + - - +
138B VAL* 3.0 32.5 + - + +
150B VAL* 4.0 26.9 - - + -
197B LEU* 3.6 26.5 - - + -
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Residues in contact with ARG 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B PHE* 2.9 35.1 + - + +
132B ASP* 2.7 52.6 + - - +
134B VAL* 1.3 74.0 - - - +
136B ASN* 1.3 96.5 + - - +
138B VAL* 3.3 8.5 + - - +
139B ASP* 2.9 38.1 + - - +
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Residues in contact with ASN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LYS* 4.2 9.7 - - - +
132B ASP* 2.9 30.1 + - - +
133B MET* 3.7 8.7 - - - +
135B ARG* 1.3 103.4 + - - +
137B ALA* 1.3 57.7 + - - +
139B ASP* 3.5 1.6 + - - +
140B ALA* 2.9 30.3 + - - +
231B SER* 3.2 25.9 + - - +
234B LEU* 3.6 20.3 - - + +
235B GLY* 3.4 28.5 + - - -
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ILE* 3.7 19.5 - - + -
133B MET 3.0 16.6 + - - +
134B VAL* 3.5 4.9 - - - +
136B ASN* 1.3 75.1 - - - +
138B VAL* 1.3 59.9 + - - +
140B ALA 3.4 0.2 + - - -
141B ALA* 3.0 30.7 + - - +
197B LEU* 3.8 17.3 - - + -
199B ILE* 4.3 11.0 - - + -
227B ILE* 3.5 7.5 - - + +
231B SER* 3.6 14.3 - - - -
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ILE* 4.1 10.1 - - + -
134B VAL* 3.0 26.2 + - + +
135B ARG* 3.7 8.3 - - + +
137B ALA* 1.3 74.8 - - - +
139B ASP* 1.3 64.4 + - - +
141B ALA* 3.5 5.2 + - - +
142B LYS* 3.1 37.5 + - - +
147B ASP* 6.0 1.8 - - - +
148B ALA* 5.7 5.2 - - + +
150B VAL* 3.6 31.4 - - + -
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Residues in contact with ASP 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ARG* 2.9 29.0 + - - +
136B ASN* 5.0 0.9 - - - +
138B VAL* 1.3 76.9 - - - +
140B ALA* 1.3 64.8 + - - +
142B LYS* 2.7 39.1 + - - +
143B ALA* 3.0 21.8 + - - +
234B LEU* 3.7 19.1 - - + +
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Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ASN 2.9 18.9 + - - +
137B ALA 3.4 3.6 + - - +
139B ASP* 1.3 76.0 - - - +
141B ALA* 1.3 63.0 + - - +
143B ALA* 3.1 18.3 + - - +
144B LEU* 3.2 18.7 + - - +
227B ILE* 3.6 25.6 - - + +
230B GLU* 4.0 12.7 - - + +
231B SER* 3.8 11.9 - - - +
234B LEU* 3.9 7.9 - - + +
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Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ALA 3.0 17.2 + - - +
138B VAL* 3.7 5.2 - - - +
140B ALA* 1.3 76.4 - - - +
142B LYS* 1.3 57.6 + - - +
144B LEU* 3.1 7.1 + - - +
146B ILE* 2.7 47.0 + - - +
148B ALA* 4.5 17.0 - - + +
227B ILE* 3.8 31.6 - - + +
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Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B VAL* 3.1 24.5 + - - +
139B ASP* 2.7 37.4 + - - +
141B ALA* 1.3 78.4 - - - +
143B ALA* 1.3 58.5 + - - +
145B GLY* 2.9 19.6 + - - +
146B ILE 4.1 5.4 - - - +
147B ASP* 5.8 7.4 - - - +
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ASP 3.0 12.2 + - - +
140B ALA* 3.1 12.3 + - - +
142B LYS* 1.3 76.3 - - - +
144B LEU* 1.3 61.2 + - + +
145B GLY 3.3 1.2 + - - -
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ALA 3.5 10.8 - - - +
141B ALA 3.1 7.1 + - - +
142B LYS 3.1 1.0 - - - -
143B ALA* 1.3 79.6 - - + +
145B GLY* 1.3 62.4 + - - +
146B ILE* 3.2 19.5 + - + +
223B ASP* 4.3 6.1 - - - +
226B LYS* 3.8 39.7 - - + +
227B ILE* 3.5 42.8 - - + +
230B GLU* 5.2 10.1 - - + -
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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