Contacts of the helix formed by residues 147 - 162 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144S ASP* 3.5 18.5 + - - +
145S PRO 3.4 4.5 - - - +
146S SER* 1.3 80.0 - - - +
148S ARG* 1.3 64.2 + - - +
149S GLU* 3.1 4.4 + - - +
150S GLY* 3.4 6.3 + - - +
151S HIS* 3.1 22.3 + - - +
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Residues in contact with ARG 148 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136S LEU* 3.9 34.1 - - + +
139S GLY 5.2 2.7 - - - +
140S LEU* 4.9 13.0 - - + +
144S ASP* 5.7 1.6 - - - +
146S SER* 3.2 12.6 - - - -
147S ASN* 1.3 76.3 - - - +
149S GLU* 1.3 57.6 + - - +
151S HIS* 3.9 7.9 - - - +
152S SER* 2.9 29.5 + - - -
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Residues in contact with GLU 149 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110S ILE* 5.2 15.0 - - + -
114S ILE* 6.2 2.7 - - - -
144S ASP* 6.3 2.9 - - + +
147S ASN* 3.1 1.7 - - - -
148S ARG* 1.3 76.9 - - - +
150S GLY* 1.3 60.4 + - - +
152S SER* 3.2 5.9 + - - -
153S ALA* 2.9 28.6 + - - +
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Residues in contact with GLY 150 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147S ASN* 3.4 10.5 + - - +
149S GLU* 1.3 78.0 - - - +
151S HIS* 1.3 57.3 + - - +
153S ALA* 3.3 7.0 + - - +
154S ARG* 2.9 29.7 + - - +
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Residues in contact with HIS 151 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136S LEU* 6.1 1.8 - - + -
146S SER 5.5 1.8 - - - +
147S ASN 3.1 17.0 + - - +
148S ARG* 4.0 8.1 - - - +
150S GLY* 1.3 74.8 - - - +
152S SER* 1.3 60.0 + - - +
154S ARG* 3.9 5.8 - - - +
155S ILE* 2.9 32.4 + - - +
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Residues in contact with SER 152 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114S ILE* 4.9 17.0 - - - -
117S GLN* 5.7 5.5 - - - +
133S ILE* 5.2 15.0 - - - +
136S LEU* 4.9 11.4 - - - +
148S ARG 2.9 20.5 + - - -
149S GLU* 3.2 7.8 + - - -
151S HIS* 1.3 76.1 - - - +
153S ALA* 1.3 57.8 + - - +
155S ILE* 3.9 3.4 - - - +
156S TYR* 2.9 30.7 + - - +
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Residues in contact with ALA 153 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149S GLU 2.9 15.6 + - - +
150S GLY* 3.7 8.5 - - - +
152S SER* 1.3 75.8 - - - +
154S ARG* 1.3 59.8 + - - +
156S TYR* 3.6 4.6 - - - +
157S PHE* 2.9 32.9 + - - +
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Residues in contact with ARG 154 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150S GLY 2.9 16.8 + - - +
151S HIS* 3.9 6.7 - - - +
153S ALA* 1.3 75.8 - - - +
155S ILE* 1.3 57.5 + - - +
157S PHE* 4.5 2.1 - - - +
158S ASN* 2.9 34.5 + - - +
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Residues in contact with ILE 155 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129S LYS* 5.8 0.3 - - - +
132S SER* 6.4 1.8 - - - -
133S ILE* 6.5 0.7 - - + -
151S HIS 2.9 18.1 + - - +
152S SER* 4.3 3.8 - - - +
154S ARG* 1.3 75.8 - - - +
156S TYR* 1.3 60.3 + - - +
158S ASN* 4.4 4.0 - - - -
159S THR* 2.9 32.2 + - - -
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Residues in contact with TYR 156 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117S GLN* 5.2 13.9 - - + -
152S SER 2.9 21.8 + - - +
153S ALA* 3.2 6.9 + - - +
155S ILE* 1.3 77.9 - - - +
157S PHE* 1.3 57.9 + - - +
159S THR* 3.9 2.8 - - - -
160S LEU* 2.9 31.2 + - - +
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Residues in contact with PHE 157 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153S ALA 2.9 16.0 + - - +
154S ARG* 4.5 2.0 - - - +
156S TYR* 1.3 76.1 - - - +
158S ASN* 1.3 57.8 + - - +
160S LEU* 4.5 4.5 - - - +
161S PHE* 2.9 35.5 + - + +
162S GLY 4.1 0.7 - - - +
165S PHE* 4.6 4.2 - - + +
166S THR* 6.0 3.4 - - - -
167S ARG* 5.8 10.5 - - + +
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Residues in contact with ASN 158 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154S ARG 2.9 23.1 + - - +
155S ILE* 4.3 3.6 - - - +
157S PHE* 1.3 76.5 - - - +
159S THR* 1.3 57.4 + - - +
162S GLY* 3.0 38.6 + - - +
163S ASN* 3.4 12.3 + - + +
165S PHE 4.9 8.1 - - - +
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Residues in contact with THR 159 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129S LYS* 4.6 20.4 - - - -
155S ILE 2.9 22.1 + - - -
156S TYR* 3.9 3.1 - - - -
158S ASN* 1.3 77.7 - - - +
160S LEU* 1.3 66.1 + - - +
162S GLY* 4.2 2.9 + - - -
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Residues in contact with LEU 160 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156S TYR 2.9 19.0 + - - +
157S PHE* 4.1 4.0 - - - +
159S THR* 1.3 80.3 - - - +
161S PHE* 1.3 62.1 + - + +
162S GLY 3.7 0.3 + - - -
231S TYR* 5.5 11.4 - - + -
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Residues in contact with PHE 161 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157S PHE* 2.9 18.8 + - + +
160S LEU* 1.3 74.3 - - + +
162S GLY* 1.3 58.9 + - - +
165S PHE* 3.6 21.5 + - + +
173S ILE* 6.2 4.7 - - + -
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Residues in contact with GLY 162 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158S ASN* 3.0 24.0 + - - +
159S THR 4.2 2.3 + - - -
160S LEU 3.4 3.2 + - - -
161S PHE* 1.3 78.7 - - - +
163S ASN* 1.3 65.8 + - - -
164S ASP* 3.2 3.4 - - - -
165S PHE* 3.1 17.0 + - - +
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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