Contacts of the helix formed by residues 143 - 155 (chain d) 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 THR 143 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33c LYS* 5.2 10.1 - - - -
141d SER 3.7 2.6 + - - -
142d CYS* 1.3 75.9 - - - +
144d VAL* 1.3 55.0 + - - +
145d PHE* 3.2 8.1 - - - -
146d GLU* 3.1 12.2 + - - +
147d LYS* 2.8 34.1 + - - +
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Residues in contact with VAL 144 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29c ALA* 5.0 16.5 + - + +
32c VAL* 6.4 2.0 - - + -
33c LYS* 5.4 5.7 - - + +
65d ILE* 5.2 12.6 - - + +
66d LEU* 6.3 4.7 - - + -
142d CYS 4.1 0.2 + - - -
143d THR* 1.3 73.6 - - - +
145d PHE* 1.3 58.2 + - - +
147d LYS* 3.2 8.4 + - - +
148d ILE* 2.9 30.1 + - - +
172d TYR* 4.9 17.5 - - + -
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Residues in contact with PHE 145 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143d THR* 3.2 6.3 - - - -
144d VAL* 1.3 79.0 - - - +
146d GLU* 1.3 57.9 + - - +
148d ILE* 3.4 5.1 + - - +
149d PHE* 2.9 29.5 + - - +
173d PHE* 5.8 4.9 - - + -
177d GLU* 5.1 15.5 - - + -
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Residues in contact with GLU 146 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142d CYS* 4.3 11.2 - - + +
143d THR* 3.1 21.2 + - - +
145d PHE* 1.3 78.5 - - - +
147d LYS* 1.3 57.2 + - - +
149d PHE* 3.7 7.9 - - - +
150d GLU* 2.9 29.1 + - - +
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Residues in contact with LYS 147 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65d ILE* 4.8 19.1 - - + +
66d LEU* 5.5 4.5 - - + -
139d THR* 5.9 6.7 - - - -
142d CYS* 4.6 10.0 - - + +
143d THR 2.8 13.2 + - - +
144d VAL* 3.4 13.5 - - - +
145d PHE 3.2 0.2 - - - -
146d GLU* 1.3 74.9 - - - +
148d ILE* 1.3 60.3 + - - +
150d GLU* 3.2 6.5 + - - +
151d ILE* 2.9 27.9 + - - +
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Residues in contact with ILE 148 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65d ILE* 5.6 8.4 - - + +
144d VAL 2.9 15.4 + - - +
145d PHE* 3.9 4.7 - - - +
147d LYS* 1.3 76.5 - - - +
149d PHE* 1.3 58.2 + - - +
151d ILE* 3.2 9.5 + - - +
152d LEU* 2.9 28.1 + - - +
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Residues in contact with PHE 149 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145d PHE 2.9 17.4 + - - +
146d GLU* 3.7 9.2 - - - +
148d ILE* 1.3 77.4 - - - +
150d GLU* 1.3 57.8 + - - +
152d LEU* 3.2 8.7 + - - +
153d GLN* 2.9 26.5 + - - +
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Residues in contact with GLU 150 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117a LEU* 6.2 3.1 - - + +
118a ASP* 6.0 7.9 - - + +
70d ILE* 5.9 8.7 - - + +
137d ILE* 5.9 7.2 - - + -
146d GLU 2.9 18.7 + - - +
147d LYS* 3.6 6.5 - - - +
149d PHE* 1.3 75.9 - - - +
151d ILE* 1.3 57.6 + - - +
153d GLN* 3.2 8.8 + - - +
154d ILE* 2.9 30.1 + - - +
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Residues in contact with ILE 151 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70d ILE* 6.1 4.7 - - + -
147d LYS 2.9 13.6 + - - +
148d ILE* 3.5 12.3 - - - +
149d PHE 3.2 0.2 - - - -
150d GLU* 1.3 78.1 - - - +
152d LEU* 1.3 57.1 + - - +
154d ILE* 3.4 4.1 + - - -
155d PHE* 3.0 30.0 + - - +
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Residues in contact with LEU 152 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148d ILE 2.9 13.4 + - - +
149d PHE* 3.2 10.5 + - - +
151d ILE* 1.3 76.7 - - - +
153d GLN* 1.3 60.9 + - - +
155d PHE* 3.8 14.6 + - - +
156d LYS* 4.4 3.8 + - - +
184d TYR* 6.3 4.0 - - + -
185d THR* 6.3 3.8 - - - -
188d SER* 4.8 16.0 - - - -
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Residues in contact with GLN 153 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116a GLU* 5.8 3.1 - - + +
117a LEU* 4.7 21.8 - - + +
149d PHE 2.9 15.5 + - - +
150d GLU* 3.6 9.4 - - - +
151d ILE 3.2 0.2 - - - -
152d LEU* 1.3 79.1 - - - +
154d ILE* 1.3 59.8 + - - +
155d PHE 3.6 0.2 + - - -
156d LYS* 3.9 13.7 + - - +
157d TYR* 4.4 1.9 + - - +
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Residues in contact with ILE 154 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70d ILE* 5.4 13.5 - - + +
75d VAL* 5.5 7.7 - - + +
150d GLU 2.9 15.9 + - - +
151d ILE* 3.8 4.5 - - - +
153d GLN* 1.3 73.0 - - - +
155d PHE* 1.3 61.1 + - - +
156d LYS 3.2 2.5 - - - -
157d TYR* 3.0 27.5 + - + +
158d LEU* 3.1 12.3 + - - +
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Residues in contact with PHE 155 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151d ILE 3.0 17.5 + - - +
152d LEU* 3.9 11.2 - - - +
153d GLN 3.3 1.2 - - - -
154d ILE* 1.3 77.5 - - - +
156d LYS* 1.3 60.7 + - - +
158d LEU* 3.3 24.6 + - - +
161d LYS* 5.3 3.2 - - - +
164d LEU* 5.3 13.2 - - + -
190d ALA* 5.0 14.1 - - + -
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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