Contacts of the helix formed by residues 150 - 157 (chain R) in PDB entry 2WQT
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 GLN 150 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27R ARG* 3.4 34.1 - - + +
32R ILE* 4.0 24.6 - - + +
71R GLN 4.4 12.8 + - - +
72R LEU* 3.8 27.8 - - - +
149R ILE* 1.3 86.5 + - - +
151R PHE* 1.3 69.3 + - - +
152R VAL* 3.2 4.7 - - + +
153R ASP* 2.9 27.0 + - - +
154R THR* 3.1 14.0 + - - -
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Residues in contact with PHE 151 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32R ILE 5.4 5.2 - - - +
33R ASP* 6.2 1.8 - - + -
35R ALA* 3.9 27.6 - - + -
39R TYR* 4.4 11.7 - + - -
63R LEU* 3.4 26.5 - - + -
72R LEU* 3.9 28.8 + - + +
74R VAL* 3.7 33.0 - - + -
76R GLN* 4.6 5.8 - - + -
77R PRO 3.8 22.2 - - - -
78R ASP* 3.9 7.9 - - - -
150R GLN* 1.3 75.9 - - - +
152R VAL* 1.3 73.8 + - + +
154R THR* 3.2 6.4 + - - -
155R VAL* 3.1 43.9 + - + +
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Residues in contact with VAL 152 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27R ARG* 3.8 23.6 - - + -
30R ILE* 3.4 28.1 - - + +
31R GLY 3.9 4.9 - - - +
32R ILE 3.8 20.6 + - - +
33R ASP 4.6 0.2 - - - -
34R ASN 3.3 37.2 - - - +
35R ALA* 4.2 4.0 - - - +
38R ALA* 3.4 19.2 - - + +
150R GLN* 3.2 1.5 - - + +
151R PHE* 1.3 84.4 - - + +
153R ASP* 1.3 63.3 + - - +
156R ALA* 3.3 21.5 + - - +
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Residues in contact with ASP 153 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25R PRO* 3.8 5.2 - - - +
26R LEU* 2.8 35.4 + - - +
27R ARG* 2.9 43.6 + - - +
144R ILE* 3.7 17.7 - - + +
148R SER 4.7 0.7 - - - -
149R ILE* 3.6 16.4 - - + -
150R GLN* 2.9 19.2 + - - +
152R VAL* 1.3 75.2 - - - +
154R THR* 1.3 64.3 + - - +
156R ALA* 3.6 4.4 + - - +
157R ASP* 3.1 23.6 + - - +
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Residues in contact with THR 154 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63R LEU* 5.1 6.9 - - + +
72R LEU* 4.7 4.0 - - - +
78R ASP* 4.2 12.6 - - - +
147R TRP* 5.7 1.3 - - + -
149R ILE* 3.8 21.1 - - + +
150R GLN 3.1 14.8 + - - -
151R PHE* 3.4 6.6 + - - -
153R ASP* 1.3 73.7 - - - +
155R VAL* 1.3 62.0 + - - +
157R ASP* 2.9 15.1 + - - +
159R ALA* 2.8 42.0 + - - +
160R SER* 2.6 31.4 + - - +
1262R PO4 5.2 6.3 - - - +
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Residues in contact with VAL 155 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38R ALA* 3.7 9.0 - - + -
39R TYR* 3.4 57.7 - - + +
42R GLN* 3.2 20.7 + - - +
78R ASP* 3.1 24.2 - - - +
151R PHE* 3.1 42.9 + - + +
154R THR* 1.3 78.2 - - - +
156R ALA* 1.3 63.8 + - - +
158R ASN 3.0 10.9 + - - -
159R ALA* 4.0 6.5 - - - +
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Residues in contact with ALA 156 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13R LEU* 3.7 12.4 - - - +
26R LEU* 4.1 18.4 - - + -
30R ILE* 5.0 1.6 - - + -
38R ALA* 3.4 19.9 + - - +
41R ILE* 3.9 24.9 - - + +
42R GLN* 3.8 14.4 + - - +
45R ASN* 4.8 3.8 + - - -
152R VAL 3.3 16.5 + - - +
153R ASP 3.8 4.5 - - - +
154R THR 3.3 0.4 - - - -
155R VAL* 1.3 79.1 - - - +
157R ASP* 1.3 56.2 + - - +
158R ASN 3.0 5.5 + - - -
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Residues in contact with ASP 157 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13R LEU* 4.0 15.1 - - + +
141R GLY 4.2 0.7 - - - +
142R SER* 3.7 8.7 + - - -
143R ARG* 2.7 80.0 + - - +
144R ILE* 4.1 9.9 + - + +
149R ILE* 5.4 1.0 - - + +
153R ASP 3.1 17.7 + - - +
154R THR* 2.9 11.2 + - - +
156R ALA* 1.3 73.5 - - - +
158R ASN* 1.3 65.5 + - - +
160R SER* 3.1 6.8 + - - +
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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