Contacts of the helix formed by residues 150 - 157 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27J ARG* 3.3 34.1 - - + +
32J ILE* 4.0 25.6 - - + +
71J GLN 4.4 12.6 + - - +
72J LEU* 3.8 28.7 - - - +
149J ILE* 1.3 86.9 + - - +
151J PHE* 1.3 69.4 + - - +
152J VAL 3.2 3.6 - - - +
153J ASP* 2.9 25.8 + - - +
154J THR* 3.1 14.0 + - - -
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Residues in contact with PHE 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32J ILE 5.4 4.9 - - - +
33J ASP* 6.2 1.6 - - + -
35J ALA* 4.0 27.8 - - + -
39J TYR* 4.4 11.7 - + - -
63J LEU* 3.5 26.0 - - + -
72J LEU* 3.9 26.9 + - + +
74J VAL* 3.7 32.3 - - + -
76J GLN* 4.6 6.3 - - + -
77J PRO 3.8 21.8 - - - -
78J ASP* 4.0 2.5 - - - -
150J GLN* 1.3 75.4 - - - +
152J VAL* 1.3 73.4 + - + +
154J THR* 3.3 6.6 + - - -
155J VAL* 3.1 50.0 + - + +
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Residues in contact with VAL 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J ARG* 3.8 24.2 - - + +
30J ILE* 3.5 28.3 - - + +
31J GLY 3.9 7.2 - - - +
32J ILE 3.8 19.5 + - - +
33J ASP 4.7 0.4 - - - -
34J ASN 3.3 35.0 - - - +
35J ALA* 4.2 3.6 - - - +
38J ALA* 3.4 19.0 - - + +
150J GLN* 3.2 2.6 - - + +
151J PHE* 1.3 84.1 - - + +
153J ASP* 1.3 64.0 + - - +
156J ALA* 3.3 22.3 + - - +
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Residues in contact with ASP 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J PRO* 3.8 5.1 - - - +
26J LEU* 2.8 34.8 + - - +
27J ARG* 2.9 43.9 + - - +
144J ILE* 3.7 18.2 - - + +
148J SER 4.7 0.2 - - - -
149J ILE* 3.6 16.2 - - + -
150J GLN* 2.9 20.1 + - - +
152J VAL* 1.3 76.1 - - - +
154J THR* 1.3 65.0 + - - +
156J ALA* 3.6 4.3 + - - +
157J ASP* 3.1 22.9 + - - +
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Residues in contact with THR 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63J LEU* 5.0 5.8 - - + +
72J LEU* 4.7 4.2 - - - +
78J ASP* 4.2 12.1 - - - +
147J TRP* 5.7 0.9 - - + -
149J ILE* 3.8 22.0 - - + +
150J GLN 3.1 14.1 + - - -
151J PHE* 3.4 7.0 + - - -
153J ASP* 1.3 73.4 - - - +
155J VAL* 1.3 61.6 + - - +
157J ASP* 2.9 14.0 + - - -
159J ALA* 2.7 41.7 + - - +
160J SER* 2.5 34.3 + - - +
1263J PO4 4.6 7.0 - - - +
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Residues in contact with VAL 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38J ALA* 3.7 9.0 - - + -
39J TYR* 3.4 56.8 - - + +
42J GLN* 3.1 21.1 + - - +
78J ASP* 3.2 24.9 - - - +
151J PHE* 3.1 41.8 + - + +
153J ASP 3.4 0.2 - - - -
154J THR* 1.3 78.6 - - - +
156J ALA* 1.3 63.4 + - - +
158J ASN 3.1 11.3 + - - -
159J ALA* 4.0 5.8 - - - +
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Residues in contact with ALA 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J LEU* 3.7 12.0 - - - +
26J LEU* 4.0 19.1 - - + -
30J ILE* 5.0 1.8 - - + -
38J ALA* 3.4 20.1 + - - +
41J ILE* 3.9 23.7 - - + +
42J GLN* 3.8 13.7 + - - +
45J ASN* 4.8 4.0 + - - +
152J VAL 3.3 15.9 + - - +
153J ASP 3.7 3.8 - - - +
154J THR 3.3 0.2 - - - -
155J VAL* 1.3 78.9 - - - +
157J ASP* 1.3 57.1 + - - +
158J ASN 3.0 5.9 + - - -
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Residues in contact with ASP 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J LEU* 4.0 15.0 - - + +
141J GLY 4.2 1.0 - - - +
142J SER* 3.7 8.8 + - - -
143J ARG* 2.7 78.7 + - - +
144J ILE* 4.1 9.0 + - + +
149J ILE* 5.4 1.0 - - + +
153J ASP 3.1 17.3 + - - +
154J THR* 2.9 10.1 + - - +
156J ALA* 1.3 73.2 - - - +
158J ASN* 1.3 65.5 + - - +
160J SER* 3.1 7.3 + - - +
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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