Contacts of the helix formed by residues 142 - 156 (chain A) in PDB entry 4PYK
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 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A GLU* 3.1 20.0 + - - +
141A ILE* 1.3 80.4 - - + +
143A PRO* 1.3 59.1 - - - +
144A ASP* 2.9 25.0 + - - +
145A CYS* 3.0 21.6 + - + -
146A ALA* 2.8 34.6 + - - +
166A VAL* 4.6 0.9 - - - -
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Residues in contact with PRO 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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141A ILE 3.4 9.4 - - - +
142A ASN* 1.3 89.8 - - - +
144A ASP* 1.3 62.4 + - - +
146A ALA* 3.5 9.1 - - + +
147A ALA* 2.9 28.1 + - - +
166A VAL* 4.1 18.1 - - + -
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Residues in contact with ASP 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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142A ASN* 2.9 10.8 + - - +
143A PRO* 1.3 82.2 - - - +
145A CYS* 1.3 65.8 + - - +
147A ALA* 3.5 6.2 + - - +
148A ILE* 3.3 33.0 + - + +
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Residues in contact with CYS 145 (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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117A ALA 3.3 20.4 - - - +
118A TYR* 3.4 36.7 - - - +
140A GLU* 3.9 7.4 - - - +
142A ASN* 3.0 27.8 + - - +
144A ASP* 1.3 75.4 - - - +
146A ALA* 1.3 66.4 + - - +
148A ILE* 3.4 4.5 + - - +
149A THR* 3.0 29.3 + - - -
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Residues in contact with ALA 146 (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 GLU* 4.0 13.8 - - + +
142A ASN 2.8 16.8 + - - +
143A PRO* 3.5 7.0 - - + +
145A CYS* 1.3 76.7 - - - +
147A ALA* 1.3 60.9 + - - +
149A THR* 3.3 2.9 + - - -
150A GLN* 3.0 21.0 + - - +
164A LEU* 3.2 24.7 - - + +
166A VAL* 3.6 30.5 - - + -
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Residues in contact with ALA 147 (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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143A PRO 2.9 18.2 + - - +
144A ASP* 3.9 8.1 - - - +
145A CYS 3.3 0.2 - - - -
146A ALA* 1.3 76.9 - - - +
148A ILE* 1.3 61.8 + - + +
150A GLN* 3.5 5.6 + - - +
151A ARG* 3.1 31.4 + - - +
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Residues in contact with ILE 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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118A TYR 4.6 1.6 - - - +
119A CYS* 3.7 32.1 - - + +
144A ASP* 3.3 23.2 + - + +
145A CYS* 3.9 6.5 - - - +
147A ALA* 1.3 78.7 - - + +
149A THR* 1.3 52.8 + - - +
151A ARG* 3.2 15.9 + - - +
152A MET* 2.7 39.0 + - + +
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Residues in contact with THR 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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117A ALA* 3.6 23.9 - - + +
118A TYR 3.6 2.1 + - - -
119A CYS 3.5 8.8 - - - -
120A GLY* 3.2 29.3 + - - -
123A ALA* 4.4 6.7 - - + -
138A THR* 5.3 2.2 - - + -
145A CYS 3.0 18.0 + - - -
146A ALA* 3.6 5.2 - - - -
148A ILE* 1.3 76.7 - - - +
150A GLN* 1.3 51.7 + - - +
152A MET* 3.0 2.8 + - - +
153A VAL* 2.6 46.5 + - + +
162A VAL* 6.0 1.8 - - + -
164A LEU* 4.2 14.6 - - + -
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Residues in contact with GLN 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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146A ALA 3.0 16.7 + - - +
147A ALA* 3.8 6.7 - - - +
149A THR* 1.3 75.3 - - - +
151A ARG* 1.3 53.5 + - - +
153A VAL* 4.2 14.8 - - - +
154A ASP* 2.7 71.3 + - - +
159A LYS* 4.5 5.3 + - - +
162A VAL* 5.5 8.2 + - - +
164A LEU* 3.8 27.8 + - + +
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Residues in contact with ARG 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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147A ALA* 3.1 22.8 + - + +
148A ILE* 3.4 16.6 - - - +
150A GLN* 1.3 78.0 - - + +
152A MET* 1.3 56.6 + - - +
154A ASP* 3.7 7.7 - - - +
155A PHE* 2.9 32.1 + - - +
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Residues in contact with MET 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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119A CYS* 3.3 50.7 - - + +
120A GLY* 4.2 7.0 - - - +
121A TYR* 4.8 1.6 - - - +
124A VAL* 4.1 15.9 - - + -
148A ILE* 2.7 18.3 + - + +
149A THR* 3.3 6.5 - - - +
151A ARG* 1.3 72.5 - - - +
153A VAL* 1.3 58.8 + - - +
155A PHE* 3.4 10.1 + - - +
156A ALA* 2.9 32.2 + - + +
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Residues in contact with VAL 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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120A GLY 4.7 0.9 - - - +
123A ALA* 3.7 29.4 - - + -
124A VAL* 4.1 13.9 - - + -
149A THR* 2.6 28.7 + - + +
150A GLN* 3.7 12.8 - - - +
152A MET* 1.3 70.6 - - - +
154A ASP* 1.3 66.5 + - - +
156A ALA 3.4 0.9 + - - -
157A GLY 3.3 15.4 + - - -
158A VAL* 3.4 13.4 + - + +
159A LYS* 3.6 27.0 + - + +
162A VAL* 3.8 27.6 - - + -
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Residues in contact with ASP 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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150A GLN* 2.7 53.2 + - - +
151A ARG* 3.7 6.9 - - - +
153A VAL* 1.3 73.1 - - - +
155A PHE* 1.3 62.7 + - - +
157A GLY* 3.2 13.2 + - - -
159A LYS* 3.3 36.8 + - + +
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Residues in contact with PHE 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 ARG 2.9 19.0 + - - +
152A MET* 3.8 10.3 - - - +
154A ASP* 1.3 76.6 - - - +
156A ALA* 1.3 62.9 + - - +
157A GLY* 3.3 1.4 + - - -
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Residues in contact with ALA 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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124A VAL* 3.6 36.6 - - + -
152A MET* 2.9 19.0 + - + +
153A VAL 3.9 3.4 - - - +
154A ASP 3.2 0.6 - - - -
155A PHE* 1.3 80.1 - - + +
157A GLY* 1.3 60.0 + - - +
158A VAL* 3.4 9.2 + - + +
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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