Contacts of the helix formed by residues 150 - 157 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27G ARG* 3.3 34.8 - - + +
32G ILE* 4.0 24.3 - - + +
71G GLN 4.4 12.2 + - - +
72G LEU* 3.7 29.1 - - - +
149G ILE* 1.3 86.5 + - - +
151G PHE* 1.3 68.8 + - - +
152G VAL* 3.2 3.6 - - + +
153G ASP* 2.9 25.9 + - - +
154G THR* 3.0 15.5 + - - -
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Residues in contact with PHE 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G ILE 5.4 4.9 + - - +
33G ASP* 6.2 1.8 - - - -
35G ALA* 4.0 27.6 - - + -
39G TYR* 4.5 11.7 - + - -
63G LEU* 3.5 25.6 - - + -
72G LEU* 3.9 29.3 + - + +
74G VAL* 3.7 31.9 - - + -
76G GLN* 4.7 6.3 - - + -
77G PRO 3.8 22.7 - - - -
78G ASP* 4.0 2.2 - - - -
150G GLN* 1.3 76.2 - - - +
152G VAL* 1.3 74.1 + - + +
154G THR* 3.3 6.3 + - - -
155G VAL* 3.1 49.5 + - + +
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Residues in contact with VAL 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G ARG* 3.8 24.0 - - + +
30G ILE* 3.5 27.5 - - + +
31G GLY 3.9 5.2 - - - +
32G ILE 3.8 21.5 + - - +
33G ASP 4.6 0.4 - - - -
34G ASN 3.3 37.2 - - - +
35G ALA* 4.2 3.4 - - - +
38G ALA* 3.4 18.7 - - + +
150G GLN* 3.2 2.1 - - + +
151G PHE* 1.3 84.1 - - + +
153G ASP* 1.3 63.9 + - - +
156G ALA* 3.3 22.2 + - - +
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Residues in contact with ASP 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G PRO* 3.8 5.1 - - - +
26G LEU* 2.8 34.8 + - - +
27G ARG* 2.9 44.0 + - - +
144G ILE* 3.6 18.3 - - + +
148G SER 4.6 0.4 - - - -
149G ILE* 3.6 15.9 - - + -
150G GLN* 2.9 19.8 + - - +
152G VAL* 1.3 76.7 - - - +
154G THR* 1.3 64.7 + - - +
156G ALA* 3.8 4.0 - - - +
157G ASP* 3.1 23.2 + - - +
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Residues in contact with THR 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G LEU* 5.0 5.7 - - + +
72G LEU* 4.7 4.2 - - - +
78G ASP* 4.2 13.0 - - - +
147G TRP* 5.7 0.9 - - + -
149G ILE* 3.8 19.8 - - + +
150G GLN 3.0 15.2 + - - -
151G PHE* 3.4 6.5 + - - -
153G ASP* 1.3 73.4 - - - +
155G VAL* 1.3 62.3 + - - +
157G ASP* 2.9 14.1 + - - +
159G ALA* 2.7 39.5 + - - +
160G SER* 2.6 31.0 - - - +
1263G PO4 4.7 6.7 - - - +
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Residues in contact with VAL 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G ALA* 3.7 9.2 - - + -
39G TYR* 3.4 57.2 - - + +
42G GLN* 3.2 20.2 + - - +
78G ASP* 3.2 24.0 - - - +
79G PHE 4.9 0.2 - - - +
151G PHE* 3.1 42.4 + - + +
154G THR* 1.3 77.8 - - - +
156G ALA* 1.3 64.7 + - - +
158G ASN 3.1 11.3 + - - -
159G ALA* 4.0 6.3 - - - +
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Residues in contact with ALA 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LEU* 3.6 12.0 - - - +
26G LEU* 4.1 18.6 - - + -
30G ILE* 5.0 1.3 - - + -
38G ALA* 3.4 19.0 + - - +
41G ILE* 3.9 23.8 - - + +
42G GLN* 3.8 14.9 + - - +
45G ASN* 4.8 3.8 + - - -
152G VAL 3.3 17.6 + - - +
153G ASP 3.8 4.0 - - - +
154G THR 3.2 0.4 - - - -
155G VAL* 1.3 78.1 - - - +
157G ASP* 1.3 57.7 + - - +
158G ASN* 3.0 5.6 + - - +
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Residues in contact with ASP 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LEU* 4.0 15.5 - - + +
141G GLY 4.3 0.9 - - - +
142G SER* 3.7 8.8 + - - -
143G ARG* 2.7 80.9 + - - +
144G ILE* 4.0 8.8 + - + +
149G ILE* 5.4 0.8 - - + +
153G ASP 3.1 17.7 + - - +
154G THR* 2.9 9.9 + - - +
156G ALA* 1.3 73.9 - - - +
158G ASN* 1.3 64.5 + - - +
160G SER* 3.1 7.7 + - - +
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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