Contacts of the helix formed by residues 147 - 162 (chain y) 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 y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144y ASP* 3.6 18.3 + - - +
145y PRO 3.4 4.4 - - - +
146y SER* 1.3 80.6 - - - +
148y ARG* 1.3 63.8 + - - +
149y GLU* 3.2 4.4 + - - +
150y GLY* 3.4 6.7 + - - +
151y HIS* 3.2 20.3 + - - +
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Residues in contact with ARG 148 (chain y).
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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136y LEU* 3.7 37.3 - - + +
139y GLY 5.2 1.6 - - - -
140y LEU* 4.9 12.3 - - + +
146y SER* 3.2 13.1 - - - -
147y ASN* 1.3 74.4 - - - +
149y GLU* 1.3 59.4 + - - +
151y HIS* 3.7 9.4 - - - +
152y SER* 2.9 28.9 + - - -
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Residues in contact with GLU 149 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110y ILE* 5.2 15.3 - - + +
114y ILE* 6.0 5.6 - - + -
147y ASN* 3.2 1.5 - - - +
148y ARG* 1.3 76.2 - - - +
150y GLY* 1.3 61.9 + - - +
152y SER* 3.2 6.0 + - - -
153y ALA* 2.9 27.6 + - - +
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Residues in contact with GLY 150 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147y ASN* 3.4 9.6 + - - +
149y GLU* 1.3 79.3 - - - +
151y HIS* 1.3 60.1 + - - +
153y ALA* 3.5 18.3 - - - +
154y ARG* 3.8 7.6 + - - +
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Residues in contact with HIS 151 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146y SER 5.6 0.9 - - - +
147y ASN 3.2 16.6 + - - +
148y ARG* 3.8 9.2 - - - +
149y GLU 3.2 0.6 - - - -
150y GLY* 1.3 75.9 - - - +
152y SER* 1.3 61.4 + - - +
154y ARG* 3.9 5.3 + - - +
155y ILE* 3.7 16.6 + - - +
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Residues in contact with SER 152 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114y ILE* 5.1 15.0 - - - -
133y ILE* 4.6 20.2 - - - +
136y LEU* 4.7 11.0 - - - +
148y ARG 2.9 17.5 + - - -
149y GLU* 3.2 6.5 + - - -
151y HIS* 1.3 74.1 - - - +
153y ALA* 1.3 60.8 + - - +
155y ILE* 3.4 8.1 + - - +
156y TYR* 2.9 31.5 + - - +
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Residues in contact with ALA 153 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149y GLU 2.9 13.2 + - - +
150y GLY* 3.5 15.7 - - - +
151y HIS 3.3 0.2 - - - -
152y SER* 1.3 76.5 - - - +
154y ARG* 1.3 64.6 + - - +
156y TYR* 2.9 7.4 + - - +
157y PHE* 2.9 26.1 + - - +
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Residues in contact with ARG 154 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150y GLY 3.8 8.2 + - - +
151y HIS* 3.9 6.3 + - - +
152y SER 3.5 0.2 - - - -
153y ALA* 1.3 79.5 - - - +
155y ILE* 1.3 56.9 + - - +
157y PHE* 4.7 3.8 - - - +
158y ASN* 2.8 34.4 + - - +
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Residues in contact with ILE 155 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129y LYS* 4.8 17.7 - - + +
132y SER* 5.8 5.8 - - - -
133y ILE* 5.6 5.8 - - + +
151y HIS 3.7 12.4 + - - +
152y SER* 3.4 10.3 + - - +
153y ALA 3.1 0.6 - - - -
154y ARG* 1.3 77.7 - - - +
156y TYR* 1.3 60.1 + - - +
158y ASN* 4.1 3.0 - - - +
159y THR* 2.9 31.4 + - - -
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Residues in contact with TYR 156 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117y GLN* 4.6 21.8 - - + +
152y SER 2.9 17.9 + - - +
153y ALA* 3.5 5.2 - - - +
155y ILE* 1.3 78.4 - - - +
157y PHE* 1.3 57.3 + - - +
159y THR* 3.3 4.7 + - - -
160y LEU* 2.9 30.2 + - - +
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Residues in contact with PHE 157 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153y ALA 2.9 14.6 + - - +
154y ARG* 4.5 3.4 - - - +
156y TYR* 1.3 77.1 - - - +
158y ASN* 1.3 58.8 + - - +
160y LEU* 4.4 5.4 - - - -
161y PHE* 2.9 32.1 + - + +
162y GLY 3.7 4.0 + - - +
165y PHE* 4.9 9.9 - - + +
166y THR* 5.7 6.3 - - - -
167y ARG* 5.8 4.5 - - + +
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Residues in contact with ASN 158 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154y ARG* 2.8 23.3 + - + +
155y ILE* 4.1 3.4 - - - +
157y PHE* 1.3 77.2 - - - +
159y THR* 1.3 62.3 + - - +
162y GLY* 3.1 35.2 - - - +
163y ASN* 3.6 15.2 + - + +
165y PHE 5.0 4.2 + - - +
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Residues in contact with THR 159 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121y LEU* 5.5 7.6 - - - -
126y PHE* 5.5 6.7 - - - -
129y LYS* 4.3 20.0 - - - -
155y ILE 2.9 20.7 + - - -
156y TYR* 3.6 5.8 - - - -
158y ASN* 1.3 78.1 - - - +
160y LEU* 1.3 66.7 + - - +
162y GLY* 4.2 1.6 + - - -
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Residues in contact with LEU 160 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156y TYR 2.9 16.4 + - - +
157y PHE* 3.8 6.3 - - - +
159y THR* 1.3 81.1 - - - +
161y PHE* 1.3 62.9 + - + +
162y GLY 3.7 0.2 + - - -
227y ASP* 5.4 6.5 - - + +
231y TYR* 4.7 23.9 - - + +
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Residues in contact with PHE 161 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157y PHE* 2.9 10.1 + - + +
160y LEU* 1.3 78.2 - - + +
162y GLY* 1.3 58.4 + - - +
164y ASP* 6.2 0.2 - - - +
165y PHE* 3.6 26.5 + - + +
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Residues in contact with GLY 162 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158y ASN* 3.1 28.7 + - - -
159y THR 4.2 1.7 + - - -
160y LEU 3.4 2.4 + - - -
161y PHE* 1.3 79.9 - - - +
163y ASN* 1.3 65.7 + - - -
164y ASP* 3.2 3.8 - - - -
165y PHE* 3.2 14.4 + - - +
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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