Contacts of the helix formed by residues 147 - 162 (chain J) in PDB entry 6QXT
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 147 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144J ASP* 3.6 18.5 + - - +
145J PRO 3.4 3.7 - - - +
146J SER* 1.3 81.3 - - - +
148J ARG* 1.3 60.4 + - - +
149J GLU* 3.1 4.2 + - - +
150J GLY* 3.3 6.9 + - - +
151J HIS* 3.0 26.5 + - - +
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Residues in contact with ARG 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J LEU* 3.9 34.3 - - + +
139J GLY 5.2 2.7 - - - +
140J LEU* 5.0 13.0 - - + +
144J ASP* 5.7 1.4 - - - +
146J SER* 3.2 11.9 - - - +
147J ASN* 1.3 76.4 - - - +
149J GLU* 1.3 57.2 + - - +
151J HIS* 3.9 8.6 - - - +
152J SER* 2.9 29.5 + - - -
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Residues in contact with GLU 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J ILE* 5.2 15.0 - - + +
114J ILE* 6.2 2.0 - - - -
144J ASP* 6.3 2.7 - - + +
147J ASN* 3.1 2.1 - - - +
148J ARG* 1.3 76.2 - - - +
150J GLY* 1.3 61.1 + - - +
152J SER* 3.2 6.8 + - - -
153J ALA* 2.9 27.9 + - - +
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Residues in contact with GLY 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147J ASN* 3.3 9.6 + - - +
149J GLU* 1.3 79.1 - - - +
151J HIS* 1.3 56.7 + - - +
153J ALA* 3.3 7.8 + - - +
154J ARG* 2.9 29.1 + - - +
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Residues in contact with HIS 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J LEU* 6.1 2.0 - - + -
146J SER 5.4 1.6 - - - +
147J ASN* 3.0 17.2 + - - +
148J ARG* 4.0 8.1 - - - +
150J GLY* 1.3 73.4 - - - +
152J SER* 1.3 61.0 + - - +
154J ARG* 3.9 5.2 - - - +
155J ILE* 2.9 32.4 + - - +
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Residues in contact with SER 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J ILE* 4.9 17.5 - - - -
117J GLN* 5.7 4.5 - - - +
133J ILE* 5.2 14.3 - - - +
136J LEU* 4.9 12.1 - - - +
148J ARG 2.9 21.6 + - - -
149J GLU* 3.2 7.6 + - - -
151J HIS* 1.3 75.7 - - - +
153J ALA* 1.3 57.9 + - - +
155J ILE* 3.9 3.7 - - - +
156J TYR* 2.9 30.4 + - - +
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Residues in contact with ALA 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149J GLU 2.9 16.2 + - - +
150J GLY* 3.7 8.3 - - - +
152J SER* 1.3 75.9 - - - +
154J ARG* 1.3 59.6 + - - +
156J TYR* 3.5 4.8 - - - +
157J PHE* 2.9 32.7 + - - +
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Residues in contact with ARG 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150J GLY 2.9 17.8 + - - +
151J HIS* 3.9 6.3 - - - +
153J ALA* 1.3 75.4 - - - +
155J ILE* 1.3 57.9 + - - +
157J PHE* 4.5 1.7 - - - +
158J ASN* 2.9 34.0 + - - +
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Residues in contact with ILE 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J LYS* 5.8 0.3 - - - +
132J SER* 6.4 2.0 - - - -
133J ILE* 6.5 0.7 - - + -
151J HIS 2.9 18.1 + - - +
152J SER* 4.3 4.5 - - - +
154J ARG* 1.3 74.3 - - - +
156J TYR* 1.3 60.7 + - - +
158J ASN* 4.4 3.8 - - - -
159J THR* 2.9 32.4 + - - -
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Residues in contact with TYR 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J GLN* 5.2 13.9 - - + -
152J SER 2.9 22.2 + - - +
153J ALA* 3.2 7.4 + - - +
155J ILE* 1.3 78.6 - - - +
157J PHE* 1.3 58.9 + - - +
159J THR* 3.8 2.3 - - - -
160J LEU* 2.9 30.9 + - - +
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Residues in contact with PHE 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153J ALA 2.9 15.6 + - - +
154J ARG* 4.5 2.2 - - - +
156J TYR* 1.3 75.9 - - - +
158J ASN* 1.3 58.5 + - - +
160J LEU* 4.5 4.9 - - - +
161J PHE* 2.9 36.2 + - + +
162J GLY 4.1 0.5 - - - +
165J PHE* 4.6 4.9 - - + +
166J THR* 6.0 3.8 - - - -
167J ARG* 5.8 10.3 - - + +
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Residues in contact with ASN 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J ARG 2.9 22.0 + - - +
155J ILE* 4.2 4.0 - - - +
157J PHE* 1.3 77.1 - - - +
159J THR* 1.3 59.6 + - - +
162J GLY* 2.9 38.4 + - - +
163J ASN* 3.4 11.3 + - + +
165J PHE 4.9 8.1 - - - +
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Residues in contact with THR 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J LYS* 4.6 20.9 - - - -
155J ILE 2.9 20.9 + - - -
156J TYR* 3.9 3.1 - - - -
158J ASN* 1.3 78.3 - - - +
160J LEU* 1.3 65.3 + - - +
162J GLY* 4.2 2.6 + - - -
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Residues in contact with LEU 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156J TYR 2.9 18.8 + - - +
157J PHE* 4.1 4.3 - - - +
159J THR* 1.3 81.0 - - - +
161J PHE* 1.3 60.8 + - + +
162J GLY 3.7 0.3 + - - -
231J TYR* 5.5 11.0 - - + -
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Residues in contact with PHE 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J PHE* 2.9 19.0 + - + +
160J LEU* 1.3 75.8 - - + +
162J GLY* 1.3 59.6 + - - +
165J PHE* 3.6 21.4 + - + +
173J ILE* 6.2 3.8 - - + -
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Residues in contact with GLY 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J ASN* 2.9 24.2 + - - +
159J THR 4.2 2.1 + - - -
160J LEU 3.4 3.2 + - - -
161J PHE* 1.3 79.2 - - - +
163J ASN* 1.3 66.3 + - - -
164J ASP* 3.2 3.6 - - - -
165J PHE* 3.1 17.4 + - - +
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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