Contacts of the helix formed by residues 147 - 162 (chain p) 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 p).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144p ASP* 3.6 17.9 + - - +
145p PRO 3.4 4.7 - - - +
146p SER* 1.3 80.4 - - - +
148p ARG* 1.3 58.8 + - - +
149p GLU* 3.1 4.9 + - - +
150p GLY* 3.3 6.6 + - - +
151p HIS* 3.0 26.9 + - - +
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Residues in contact with ARG 148 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136p LEU* 3.9 34.8 - - + +
139p GLY 5.2 2.5 - - - +
140p LEU* 5.0 13.0 - - + +
144p ASP* 5.7 1.6 - - - +
146p SER* 3.2 12.1 - - - +
147p ASN* 1.3 77.1 - - - +
149p GLU* 1.3 57.1 + - - +
151p HIS* 3.9 8.4 - - - +
152p SER* 2.9 29.3 + - - -
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Residues in contact with GLU 149 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110p ILE* 5.2 15.3 - - + -
114p ILE* 6.2 2.5 - - - -
144p ASP* 6.3 2.7 - - + +
147p ASN* 3.1 2.1 - - - +
148p ARG* 1.3 76.4 - - - +
150p GLY* 1.3 60.8 + - - +
152p SER* 3.2 6.3 + - - -
153p ALA* 2.9 28.6 + - - +
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Residues in contact with GLY 150 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147p ASN* 3.3 10.7 + - - +
149p GLU* 1.3 78.9 - - - +
151p HIS* 1.3 57.3 + - - +
153p ALA* 3.3 7.6 + - - +
154p ARG* 2.9 29.2 + - - +
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Residues in contact with HIS 151 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136p LEU* 6.1 1.8 - - + -
146p SER 5.4 1.3 - - - +
147p ASN 3.0 16.8 + - - +
148p ARG* 4.0 7.9 - - - +
150p GLY* 1.3 73.9 - - - +
152p SER* 1.3 60.4 - - - +
154p ARG* 3.9 5.5 - - - +
155p ILE* 2.9 32.7 + - - +
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Residues in contact with SER 152 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114p ILE* 4.9 17.3 - - - -
117p GLN* 5.7 5.0 - - - +
133p ILE* 5.2 15.4 - - - +
136p LEU* 4.9 11.8 - - - +
148p ARG 2.9 20.3 + - - -
149p GLU* 3.2 7.4 + - - -
151p HIS* 1.3 76.7 - - - +
153p ALA* 1.3 57.6 + - - +
155p ILE* 4.3 3.9 - - - +
156p TYR* 2.9 30.3 + - - +
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Residues in contact with ALA 153 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149p GLU 2.9 16.5 + - - +
150p GLY* 3.7 7.6 - - - +
151p HIS 3.2 0.2 - - - -
152p SER* 1.3 76.1 - - - +
154p ARG* 1.3 60.0 + - - +
156p TYR* 3.2 5.1 + - - +
157p PHE* 2.9 32.9 + - - +
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Residues in contact with ARG 154 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150p GLY 2.9 16.8 + - - +
151p HIS* 3.9 6.1 - - - +
153p ALA* 1.3 76.0 - - - +
155p ILE* 1.3 58.9 + - - +
157p PHE* 4.5 2.1 - - - +
158p ASN* 2.9 34.2 + - - +
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Residues in contact with ILE 155 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129p LYS* 5.8 0.2 - - - +
132p SER* 6.4 2.0 - - - -
133p ILE* 6.5 0.7 - - + -
151p HIS 2.9 18.1 + - - +
152p SER* 4.3 4.0 - - - +
154p ARG* 1.3 74.3 - - - +
156p TYR* 1.3 59.6 + - - +
158p ASN* 4.4 4.5 - - - -
159p THR* 2.9 33.3 + - - -
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Residues in contact with TYR 156 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117p GLN* 5.2 13.7 - - + -
152p SER 2.9 21.3 + - - +
153p ALA* 3.2 6.9 + - - +
155p ILE* 1.3 78.1 - - - +
157p PHE* 1.3 58.6 + - - +
159p THR* 3.8 2.6 - - - -
160p LEU* 2.9 31.1 + - - +
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Residues in contact with PHE 157 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153p ALA 2.9 14.7 + - - +
154p ARG* 4.5 2.5 - - - +
156p TYR* 1.3 77.4 - - - +
158p ASN* 1.3 58.0 + - - +
160p LEU* 4.5 4.3 - - - +
161p PHE* 2.9 36.2 + - + +
162p GLY 4.1 0.5 - - - +
165p PHE* 4.6 4.0 - - + +
166p THR* 6.0 3.8 - - - -
167p ARG* 5.8 10.5 - - + +
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Residues in contact with ASN 158 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154p ARG 2.9 22.0 + - - +
155p ILE* 4.2 4.0 - - - +
157p PHE* 1.3 78.0 - - - +
159p THR* 1.3 58.7 + - - +
162p GLY* 2.9 39.6 + - - +
163p ASN* 3.4 11.7 + - + +
165p PHE 4.9 8.1 - - - +
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Residues in contact with THR 159 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129p LYS* 4.6 20.2 - - - -
155p ILE 2.9 20.8 + - - -
156p TYR* 3.9 3.4 - - - -
158p ASN* 1.3 77.7 - - - +
160p LEU* 1.3 65.4 + - - +
162p GLY* 4.2 2.6 + - - -
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Residues in contact with LEU 160 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156p TYR 2.9 18.8 + - - +
157p PHE* 4.1 4.0 - - - +
159p THR* 1.3 80.0 - - - +
161p PHE* 1.3 62.5 + - + +
162p GLY 3.7 0.2 + - - -
231p TYR* 5.5 11.2 - - + -
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Residues in contact with PHE 161 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157p PHE* 2.9 19.6 + - + +
160p LEU* 1.3 73.7 - - + +
162p GLY* 1.3 59.7 + - - +
165p PHE* 3.6 20.9 + - + +
173p ILE* 6.2 4.3 - - + -
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Residues in contact with GLY 162 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158p ASN* 2.9 23.3 + - - +
159p THR 4.2 2.8 + - - -
160p LEU 3.4 3.0 + - - -
161p PHE* 1.3 78.3 - - - +
163p ASN* 1.3 66.9 + - - -
164p ASP 3.2 2.9 - - - -
165p PHE* 3.1 17.7 + - - +
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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