Contacts of the helix formed by residues 153 - 158 (chain B) in PDB entry 2QFI
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 HIS 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B ASP* 4.4 3.5 + - - -
48B VAL* 6.0 3.1 - - + -
49B ASP* 3.3 15.5 + - - -
52B ALA* 5.1 8.7 - - + +
86B GLN* 5.8 5.0 - - + +
90B ILE 4.8 10.6 + - - -
91B SER* 4.3 22.9 - - - +
150B ASP* 2.4 38.3 + - + +
151B MET 2.6 0.4 + - - +
152B LEU 1.3 65.7 - - - +
154B TYR* 1.3 64.0 + + + +
156B SER 3.3 1.9 + - - -
157B ASP* 2.4 66.7 + - + +
189B TYR* 3.6 6.8 + - - -
192B TYR* 2.6 12.0 + - + +
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Residues in contact with TYR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B MET* 3.1 25.1 - - + -
22B LEU* 4.5 4.7 - - + -
23B LEU* 2.6 47.9 - - + +
26B ILE* 6.5 0.7 - - + -
27B LYS* 6.2 1.1 - - + -
49B ASP* 3.9 27.2 + - + -
52B ALA* 3.3 16.7 - - + +
128B THR* 5.5 7.6 - - + -
132B VAL* 3.3 20.2 - - + -
135B GLN* 3.8 4.3 - - - -
150B ASP* 4.3 2.7 - - - -
151B MET* 2.3 37.4 + - - +
153B HIS* 1.3 74.2 - + + +
155B GLN* 1.3 50.9 + - - +
156B SER 2.4 18.5 + - - -
157B ASP* 3.4 13.9 - - + -
158B VAL* 2.5 34.5 + - + +
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Residues in contact with GLN 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ILE* 5.4 5.8 - - + -
132B VAL* 3.8 16.4 - - + +
136B ARG* 4.8 11.0 + - - +
151B MET* 3.1 24.2 + - + +
152B LEU* 2.9 49.5 + - + +
154B TYR* 1.3 72.4 - - - +
156B SER* 1.3 65.0 + - - +
158B VAL* 4.4 2.9 - - - -
159B MET* 3.4 24.3 - - + +
188B ILE* 5.8 0.3 - - - +
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Residues in contact with SER 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU* 3.2 12.4 + - - +
154B TYR 2.4 10.9 + - - -
155B GLN* 1.3 82.6 + - - +
157B ASP* 1.3 55.0 + - - +
158B VAL 3.0 5.4 - - - +
159B MET* 3.2 30.8 + - - +
184B LEU* 5.3 0.9 - - - +
188B ILE* 3.3 25.4 + - - +
189B TYR* 2.8 41.5 + - - -
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Residues in contact with ASP 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ASP* 2.6 31.0 - - - +
49B ASP* 2.9 13.0 - - - +
153B HIS* 2.4 57.9 + - + +
154B TYR* 2.8 12.2 + - + -
156B SER* 1.3 70.9 - - - +
158B VAL* 1.3 61.7 + - - +
159B MET 3.5 1.1 - - - -
160B MET* 4.2 15.2 - - - +
189B TYR* 4.5 1.3 - - - -
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LEU* 6.1 2.2 - - + -
126B ILE* 4.0 33.0 - - + +
128B THR* 4.0 26.0 - - + -
129B ILE* 3.6 41.2 - - + +
132B VAL* 5.4 1.6 - - + -
154B TYR* 2.5 34.6 + - + +
155B GLN 4.6 0.5 - - - +
157B ASP* 1.3 76.2 - - - +
159B MET* 1.3 71.3 + - - +
160B MET* 3.5 6.9 + - - -
161B ASN* 4.9 0.2 + - - -
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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