Contacts of the helix formed by residues 130 - 144 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A LYS* 5.5 0.3 - - - -
129A ALA* 1.3 74.4 - - - +
131A PHE* 1.3 64.6 + - - +
132A ASP* 3.3 14.3 + - - +
133A MET* 3.0 37.9 + - - +
134A VAL* 3.1 23.6 + - - +
195A LYS* 3.6 50.1 + - + +
196A ALA 3.1 6.9 + - - +
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Residues in contact with PHE 131 (chain A).
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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107A MET* 5.8 9.9 - - + -
129A ALA 3.7 3.8 + - - -
130A ASP* 1.3 74.2 + - - +
132A ASP* 1.3 71.7 + - - +
134A VAL* 3.0 15.6 + - + +
135A ARG* 2.8 68.8 + - + +
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Residues in contact with ASP 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS* 6.2 1.3 - - - +
130A ASP* 3.3 12.0 + - - +
131A PHE* 1.3 94.2 - - - +
133A MET* 1.3 52.6 + - + +
135A ARG* 3.2 6.7 + - - +
136A ASN* 2.8 49.2 + - - +
195A LYS* 5.6 4.5 + - - +
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Residues in contact with MET 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS* 3.8 38.8 - - + +
85A ILE 3.7 13.9 - - - +
86A ILE* 3.4 36.3 - - + -
130A ASP* 3.0 25.0 + - + +
131A PHE 3.2 0.2 - - - -
132A ASP* 1.3 76.2 - - + +
134A VAL* 1.3 62.8 + - - +
136A ASN* 3.7 9.8 - - - +
137A ALA* 3.0 17.5 + - - +
195A LYS* 3.7 27.8 - - - -
196A ALA 3.9 9.9 - - - -
197A LEU* 3.4 28.1 - - + +
231A SER* 4.9 1.6 + - - -
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ILE* 4.2 8.2 - - + +
107A MET* 4.4 18.4 - - + -
129A ALA* 3.9 21.8 - - + -
130A ASP 3.1 17.4 + - - +
131A PHE* 3.0 18.5 + - + +
133A MET* 1.3 77.0 - - - +
135A ARG* 1.3 64.3 + - - +
137A ALA* 3.1 5.4 + - - +
138A VAL* 3.0 31.0 + - + +
150A VAL* 3.9 28.9 - - + -
197A LEU* 3.9 14.8 - - + -
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Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A PHE* 2.8 49.7 + - + +
132A ASP* 3.6 7.4 - - - +
134A VAL* 1.3 80.2 - - - +
136A ASN* 1.3 58.5 + - - +
138A VAL* 3.4 7.1 + - + +
139A ASP* 2.9 53.7 + - - +
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Residues in contact with ASN 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS* 4.5 7.1 - - - +
132A ASP* 2.8 39.7 + - - +
133A MET* 3.7 9.6 - - - +
135A ARG* 1.3 73.0 - - - +
137A ALA* 1.3 62.1 + - - +
139A ASP* 4.5 2.5 - - - +
140A ALA* 2.9 31.0 + - - +
231A SER* 3.3 25.2 + - - +
234A LEU* 3.6 17.5 - - + +
235A GLY* 3.1 32.5 + - - -
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Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ILE* 3.8 18.4 - - + -
133A MET 3.0 13.9 + - - +
134A VAL 3.1 8.9 + - - +
136A ASN* 1.3 76.8 - - - +
138A VAL* 1.3 57.3 + - - +
140A ALA* 3.3 2.1 + - - +
141A ALA* 2.9 30.7 + - - +
197A LEU* 3.8 17.3 - - + -
199A ILE* 4.0 15.0 - - + -
227A ILE* 3.7 7.0 - - + +
231A SER* 3.7 11.7 - - - -
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Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ILE* 3.8 10.5 - - + -
134A VAL* 3.0 22.4 + - + +
135A ARG* 3.6 10.5 - - + +
137A ALA* 1.3 77.0 - - - +
139A ASP* 1.3 66.6 + - - +
141A ALA* 3.4 5.4 + - - +
142A LYS* 3.1 25.2 + - + +
148A ALA* 5.2 7.6 - - + +
150A VAL* 3.5 32.8 - - + -
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Residues in contact with ASP 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ARG* 2.9 41.5 + - - +
136A ASN* 4.5 2.1 - - - +
138A VAL* 1.3 81.0 - - - +
140A ALA* 1.3 60.0 + - - +
142A LYS* 3.4 7.9 + - - +
143A ALA* 3.0 28.2 + - - +
234A LEU* 3.8 20.8 - - + +
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Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ASN 2.9 18.8 + - - +
137A ALA 3.7 3.1 - - - +
139A ASP* 1.3 74.0 - - - +
141A ALA* 1.3 67.3 + - - +
143A ALA* 3.4 6.6 + - - +
144A LEU* 3.1 29.2 + - - +
227A ILE* 3.6 26.2 - - - +
230A GLU* 3.9 13.6 - - + +
231A SER* 3.8 11.7 - - - +
234A LEU* 3.7 7.2 - - + +
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Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ILE* 5.5 0.2 - - + -
137A ALA 2.9 17.4 + - - +
138A VAL 3.7 4.9 - - - +
140A ALA* 1.3 75.8 - - - +
142A LYS* 1.3 63.6 + - - +
144A LEU* 2.9 11.2 + - - +
146A ILE* 2.9 37.2 + - + +
148A ALA* 4.1 18.8 - - + -
227A ILE* 4.0 30.0 - - + +
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Residues in contact with LYS 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A VAL* 3.1 17.0 + - + +
139A ASP* 3.4 12.1 - - - +
141A ALA* 1.3 76.8 - - - +
143A ALA* 1.3 54.9 + - - +
145A GLY* 2.6 27.1 + - - -
146A ILE 3.7 8.9 + - - +
147A ASP* 5.4 8.7 + - - +
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ASP 3.0 13.2 + - - +
140A ALA* 3.7 8.5 - - - +
141A ALA 3.3 0.2 - - - -
142A LYS* 1.3 79.3 - - - +
144A LEU* 1.3 63.0 + - + +
145A GLY 3.2 1.2 + - - -
234A LEU* 6.3 0.7 - - + -
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ALA 3.1 15.0 + - - +
141A ALA 2.9 9.1 + - - +
143A ALA* 1.3 81.0 - - + +
145A GLY* 1.3 65.4 + - - +
146A ILE* 3.2 19.2 + - + +
223A ASP* 4.5 1.1 - - - +
226A LYS* 3.6 41.7 - - + +
227A ILE* 3.7 30.3 - - + +
230A GLU* 4.8 9.9 - - + -
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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