Contacts of the helix formed by residues 147 - 162 (chain U) in PDB entry 6QY3
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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144U ASP* 3.6 18.9 + - - +
145U PRO 3.4 4.0 - - - +
146U SER* 1.3 80.4 - - - +
148U ARG* 1.3 65.0 + - - +
149U GLU* 3.2 4.6 + - - +
150U GLY* 3.4 6.8 + - - +
151U HIS* 3.2 19.9 + - - +
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Residues in contact with ARG 148 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136U LEU* 3.7 37.1 - - + +
139U GLY 5.2 1.6 - - - -
140U LEU* 4.9 12.6 - - + +
146U SER* 3.2 13.1 - - - -
147U ASN* 1.3 74.1 - - - +
149U GLU* 1.3 60.3 + - - +
151U HIS* 3.7 9.2 - - - +
152U SER* 2.9 29.1 + - - -
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Residues in contact with GLU 149 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110U ILE* 5.2 15.9 - - + +
114U ILE* 6.0 5.2 - - + -
147U ASN* 3.2 1.5 - - - -
148U ARG* 1.3 76.0 - - - +
150U GLY* 1.3 60.7 + - - +
152U SER* 3.2 6.5 + - - -
153U ALA* 2.9 27.9 + - - +
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Residues in contact with GLY 150 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147U ASN* 3.4 10.1 + - - +
149U GLU* 1.3 78.7 - - - +
151U HIS* 1.3 60.6 + - - +
153U ALA* 3.5 18.4 - - - +
154U ARG* 3.8 8.0 + - - +
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Residues in contact with HIS 151 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136U LEU* 5.9 2.2 - - + -
146U SER 5.6 1.1 - - - +
147U ASN 3.2 16.4 + - - +
148U ARG* 3.8 9.6 - - - +
149U GLU 3.2 0.6 - - - -
150U GLY* 1.3 77.1 - - - +
152U SER* 1.3 61.7 + - - +
153U ALA 3.6 0.3 + - - -
154U ARG* 3.9 4.9 + - - +
155U ILE* 3.7 16.1 + - - +
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Residues in contact with SER 152 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114U ILE* 5.1 14.8 - - - -
133U ILE* 4.6 20.4 - - - +
136U LEU* 4.7 11.4 - - - +
148U ARG 2.9 19.1 + - - -
149U GLU* 3.2 6.3 + - - -
151U HIS* 1.3 74.0 - - - +
153U ALA* 1.3 60.0 + - - +
154U ARG 3.5 0.2 - - - -
155U ILE* 3.4 8.3 + - - +
156U TYR* 2.9 30.9 + - - +
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Residues in contact with ALA 153 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149U GLU 2.9 12.6 + - - +
150U GLY* 3.5 15.5 - - - +
151U HIS 3.3 0.2 - - - -
152U SER* 1.3 76.7 - - - +
154U ARG* 1.3 63.7 + - - +
156U TYR* 2.9 8.0 + - - +
157U PHE* 2.9 25.9 + - - +
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Residues in contact with ARG 154 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150U GLY 3.8 7.3 + - - +
151U HIS* 3.9 6.9 + - - +
152U SER 3.5 0.4 - - - -
153U ALA* 1.3 80.0 - - - +
155U ILE* 1.3 57.6 + - - +
157U PHE* 4.7 3.6 - - - +
158U ASN* 2.8 34.9 + - - +
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Residues in contact with ILE 155 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129U LYS* 4.8 17.6 - - + +
132U SER* 5.8 6.1 - - - -
133U ILE* 5.6 5.6 - - + +
151U HIS 3.7 11.8 + - - +
152U SER* 3.4 10.7 + - - +
153U ALA 3.1 1.0 - - - -
154U ARG* 1.3 75.5 - - - +
156U TYR* 1.3 59.2 + - - +
158U ASN* 3.9 3.3 - - - +
159U THR* 2.9 31.7 + - - -
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Residues in contact with TYR 156 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117U GLN* 4.6 21.1 - - + +
152U SER 2.9 18.1 + - - +
153U ALA* 3.5 5.4 - - - +
155U ILE* 1.3 77.7 - - - +
157U PHE* 1.3 58.1 + - - +
159U THR* 3.3 5.0 + - - -
160U LEU* 2.9 30.5 + - - +
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Residues in contact with PHE 157 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153U ALA 2.9 14.7 + - - +
154U ARG* 4.5 3.1 - - - +
156U TYR* 1.3 76.5 - - - +
158U ASN* 1.3 59.4 + - - +
160U LEU* 4.4 5.2 - - - -
161U PHE* 2.9 33.1 + - + +
162U GLY 3.7 3.6 + - - +
165U PHE* 4.9 9.5 - - + +
166U THR* 5.7 6.3 - - - -
167U ARG* 5.8 4.5 - - + +
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Residues in contact with ASN 158 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154U ARG* 2.8 23.1 + - + +
155U ILE* 4.1 3.1 - - - +
157U PHE* 1.3 77.7 - - - +
159U THR* 1.3 61.3 + - - +
162U GLY* 3.1 35.4 + - - +
163U ASN* 3.6 14.6 + - + +
165U PHE 5.0 4.0 + - - +
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Residues in contact with THR 159 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121U LEU* 5.6 7.2 - - - -
126U PHE* 5.5 7.0 - - - -
129U LYS* 4.3 20.2 - - - -
155U ILE 2.9 20.1 + - - -
156U TYR* 3.6 5.4 - - - -
157U PHE 3.2 0.2 - - - -
158U ASN* 1.3 77.8 - - - +
160U LEU* 1.3 67.7 + - - +
162U GLY* 4.2 2.1 + - - -
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Residues in contact with LEU 160 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156U TYR 2.9 17.5 + - - +
157U PHE* 3.8 5.6 - - - +
159U THR* 1.3 80.2 - - - +
161U PHE* 1.3 63.0 + - + +
162U GLY 3.6 0.2 + - - -
227U ASP* 5.4 7.2 - - + +
231U TYR* 4.7 22.5 - - + +
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Residues in contact with PHE 161 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157U PHE* 2.9 9.4 + - + +
160U LEU* 1.3 77.3 - - + +
162U GLY* 1.3 59.2 + - - +
165U PHE* 3.6 26.8 + - + +
173U ILE* 5.8 8.1 - - + -
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Residues in contact with GLY 162 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158U ASN* 3.1 29.5 + - - -
159U THR 4.2 1.5 + - - -
160U LEU 3.4 2.8 + - - -
161U PHE* 1.3 79.6 - - - +
163U ASN* 1.3 64.7 + - - -
164U ASP* 3.2 3.6 - - - -
165U PHE* 3.2 13.9 + - - +
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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