Contacts of the helix formed by residues 147 - 161 (chain A) in PDB entry 3PAR
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 THR 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A VAL* 5.4 0.2 - - - +
145A PRO 3.5 0.8 - - - -
146A ARG* 1.3 92.4 - - + +
148A PRO* 1.3 76.7 - - - +
149A GLU* 3.5 8.4 + - - +
150A GLU* 3.1 30.4 + - - +
151A ASN* 2.8 22.7 + - - +
188A TYR* 3.9 8.8 - - - -
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Residues in contact with PRO 148 (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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147A THR* 1.3 88.2 - - - +
149A GLU* 1.3 55.7 + - - +
151A ASN* 3.3 2.4 + - - +
152A GLU* 2.9 30.2 + - - +
188A TYR* 3.7 31.2 - - + +
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Residues in contact with GLU 149 (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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114A VAL* 3.4 27.0 - - + +
115A GLY* 4.9 4.0 + - - -
147A THR* 3.1 7.4 + - - +
148A PRO* 1.3 78.1 - - - +
150A GLU* 1.3 64.9 + - - +
152A GLU* 3.4 6.9 + - + +
153A ALA* 3.0 21.3 + - - +
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Residues in contact with GLU 150 (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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114A VAL* 4.1 22.8 - - + +
117A LYS* 2.8 43.7 + - + +
119A PHE* 4.0 14.7 - - + -
145A PRO* 3.5 11.4 - - + +
146A ARG* 2.7 27.9 + - - +
147A THR* 3.1 28.9 + - - +
149A GLU* 1.3 75.2 - - - +
151A ASN* 1.3 64.8 + - - +
153A ALA* 3.0 5.1 + - - +
154A ILE* 3.0 25.3 + - - +
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Residues in contact with ASN 151 (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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145A PRO* 3.1 26.9 - - + +
147A THR 2.8 10.1 + - - +
148A PRO 3.4 8.5 - - - +
149A GLU 3.2 0.2 - - - -
150A GLU* 1.3 77.9 - - - +
152A GLU* 1.3 58.6 + - - +
154A ILE 3.3 0.9 + - - -
155A ALA* 2.9 27.2 + - - +
188A TYR* 3.4 20.7 + - + +
190A ASN* 3.5 12.3 - - - +
207A MET* 3.2 8.8 - - - +
211A GLY* 3.2 26.1 + - - -
213A TRP* 2.9 26.8 + - - -
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Residues in contact with GLU 152 (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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148A PRO 2.9 17.0 + - - +
149A GLU* 3.7 6.5 - - - +
150A GLU 3.3 0.2 - - - -
151A ASN* 1.3 75.2 - - - +
153A ALA* 1.3 61.5 + - - +
155A ALA* 3.1 13.8 + - - +
156A SER* 2.8 37.0 + - - -
210A ASP 5.2 4.3 - - - +
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Residues in contact with ALA 153 (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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112A LEU* 3.5 18.3 - - + +
114A VAL* 3.5 31.9 - - + -
119A PHE* 4.0 10.8 - - + -
149A GLU 3.0 9.3 + - - +
150A GLU 3.0 10.3 + - - +
152A GLU* 1.3 76.8 - - - +
154A ILE* 1.3 60.3 + - - +
156A SER* 2.7 26.0 + - - -
157A ILE* 3.3 6.2 + - - +
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Residues in contact with ILE 154 (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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119A PHE* 3.9 24.5 - - + -
143A ALA* 3.9 19.3 - - + -
145A PRO* 3.5 44.0 - - + -
150A GLU 3.0 8.9 + - - +
151A ASN 3.7 5.6 - - - +
153A ALA* 1.3 72.2 - - - +
155A ALA* 1.3 60.8 + - - +
157A ILE* 3.0 11.0 + - - +
158A ALA* 2.9 25.8 + - - +
165A VAL* 4.2 26.2 - - + -
167A LEU* 4.4 4.3 - - + -
207A MET* 3.9 15.5 - - + -
225A VAL* 4.7 10.3 - - + -
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Residues in contact with ALA 155 (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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151A ASN 2.9 14.3 + - - +
152A GLU* 3.3 23.1 - - - +
154A ILE* 1.3 78.0 - - - +
156A SER* 1.3 56.5 + - - +
158A ALA* 3.1 5.5 + - - +
159A LYS* 2.8 31.0 + - - +
207A MET* 3.6 9.4 - - - -
209A THR 3.9 7.2 - - - +
210A ASP 4.6 1.1 - - - -
211A GLY* 3.7 30.1 - - - +
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Residues in contact with SER 156 (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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112A LEU* 3.4 16.8 - - - +
152A GLU* 2.8 20.6 + - - -
153A ALA* 2.7 21.0 + - - -
155A ALA* 1.3 74.8 - - - +
157A ILE* 1.3 58.6 + - - +
159A LYS* 3.6 11.4 - - - +
160A LYS* 2.8 31.6 + - - +
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Residues in contact with ILE 157 (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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112A LEU* 3.9 17.9 - - + -
119A PHE* 3.9 32.8 - - + +
120A SER* 4.6 4.3 - - - +
121A THR* 3.7 21.1 - - + -
153A ALA 3.5 13.7 - - - +
154A ILE* 3.0 9.9 + - - +
156A SER* 1.3 73.6 + - - +
158A ALA* 1.3 64.6 + - - +
160A LYS* 3.5 6.5 + - + -
161A TYR* 3.1 28.3 + - + -
223A LEU* 3.5 19.0 - - + +
225A VAL* 4.0 21.1 - - + -
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Residues in contact with ALA 158 (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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154A ILE 2.9 12.7 + - - +
155A ALA* 3.3 12.6 - - - +
157A ILE* 1.3 79.1 - - - +
159A LYS* 1.3 56.4 + - - +
161A TYR 3.5 0.5 + - - -
162A ASN* 3.0 22.5 + - - -
163A ASN 3.1 30.2 + - - +
165A VAL* 3.6 18.8 - - + +
207A MET* 4.8 5.8 - - - +
208A TYR 4.6 3.8 - - - +
209A THR* 3.7 15.3 - - - +
223A LEU* 4.2 1.8 - - - +
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Residues in contact with LYS 159 (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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155A ALA 2.8 17.7 + - - +
156A SER* 3.6 10.3 - - - +
158A ALA* 1.3 77.1 - - - +
160A LYS* 1.3 58.4 + - - +
162A ASN* 2.9 21.8 + - - +
209A THR* 4.1 25.7 - - - +
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Residues in contact with LYS 160 (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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109A GLY* 5.2 16.5 + - - +
156A SER 2.8 21.5 + - - +
157A ILE* 3.8 8.7 - - + +
159A LYS* 1.3 75.3 - - - +
161A TYR* 1.3 80.6 + - + +
162A ASN* 3.5 1.4 + - - +
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Residues in contact with TYR 161 (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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109A GLY 5.2 5.5 + - - -
121A THR* 3.7 27.0 + - + +
122A ASN 5.1 0.5 - - - -
123A GLY* 3.3 33.3 + - - -
157A ILE* 3.1 20.5 + - + -
158A ALA 4.4 0.2 - - - +
160A LYS* 1.3 97.7 - - + +
162A ASN* 1.3 71.4 + - - +
163A ASN* 3.1 7.8 + - + +
223A LEU* 3.6 29.4 - - + -
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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