Contacts of the strand formed by residues 27 - 34 (chain C) in PDB entry 2WJX
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 ILE 27 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ASN* 4.1 11.2 - - + +
26C SER* 1.3 77.4 - - - +
28C GLN* 1.3 64.1 + - - +
29C ILE* 3.4 4.0 + - + +
56C PHE* 6.0 0.7 - - + -
57C ARG 3.0 12.7 + - - +
58C LEU* 3.5 18.3 - - + -
59C THR 2.8 24.5 + - - -
86C TYR* 3.3 35.0 - - + -
311C PHE* 3.8 42.4 - - + -
315C ARG* 4.8 12.8 - - + +
321C ILE* 4.5 12.1 - - + -
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Residues in contact with GLN 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C SER* 3.5 27.3 + - - +
27C ILE* 1.3 72.0 - - - +
29C ILE* 1.3 62.0 + - - +
59C THR* 3.4 17.4 - - - +
61C HIS* 3.2 29.0 + - + -
83C ARG 6.1 0.9 - - - +
84C GLY 4.4 8.5 - - - +
85C VAL* 4.2 14.1 - - + -
86C TYR* 2.8 40.9 + - + +
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Residues in contact with ILE 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ILE* 4.1 15.0 - - + +
28C GLN* 1.3 79.7 - - - +
30C GLY* 1.3 66.7 + - - +
44C PHE* 5.0 7.2 - - + -
48C MET* 5.5 0.2 - - - -
58C LEU* 3.5 26.2 - - + -
59C THR 3.1 38.9 + - - +
60C PRO* 3.2 14.8 - - + +
61C HIS* 2.8 29.1 + - - -
85C VAL* 3.8 7.2 - - - -
87C ALA* 3.4 20.0 - - + +
307C MET* 4.8 14.1 - - + -
311C PHE* 4.5 10.8 - - + -
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Residues in contact with GLY 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ILE* 1.3 81.8 - - - +
31C GLY* 1.3 59.5 + - - -
44C PHE* 5.4 0.5 - - - -
60C PRO* 5.4 0.9 - - - -
61C HIS 3.5 2.9 - - - -
80C GLN* 3.2 25.4 - - - -
85C VAL* 3.7 3.6 - - - +
87C ALA 3.0 12.6 + - - -
88C ILE* 4.2 8.1 - - - -
89C PHE* 2.8 28.4 + - - +
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Residues in contact with GLY 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLY* 1.3 74.6 - - - -
32C LEU* 1.3 63.8 + - - +
33C PHE* 3.9 12.3 + - - -
44C PHE* 5.3 2.7 - - - -
61C HIS 2.9 11.5 + - - +
62C ILE* 3.4 17.5 - - - +
63C ASP 2.8 29.1 + - - +
80C GLN* 4.0 0.8 - - - +
89C PHE* 3.1 8.7 - - - -
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C GLY* 1.3 78.4 - - - +
33C PHE* 1.3 62.2 + - - +
34C PRO* 4.0 0.5 - - - +
63C ASP* 3.6 23.8 - - + +
65C LEU* 4.1 17.3 - - + -
67C VAL* 5.0 0.3 - - - +
73C VAL* 4.6 14.6 - - + +
76C ALA* 4.0 21.8 - - + -
77C PHE* 4.4 14.4 - - + +
80C GLN* 3.9 17.9 - - + +
88C ILE* 4.2 11.4 - - + -
89C PHE 2.8 10.1 + - - +
90C GLY* 3.3 11.6 - - - -
91C PHE* 3.1 33.5 + - - +
100C ILE* 6.0 0.2 - - + -
111C PHE* 4.5 15.9 - - + -
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Residues in contact with PHE 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C GLY* 4.0 11.0 - - - -
32C LEU* 1.3 76.4 - - - +
34C PRO* 1.3 71.6 - - + +
37C ALA* 4.4 9.9 - - + -
40C GLU* 4.0 5.6 - - + -
41C TYR* 3.7 46.9 - + + -
44C PHE* 3.7 23.1 - + - -
62C ILE* 4.1 24.5 - - + -
63C ASP 2.9 7.5 + - - -
64C ASN* 3.3 20.1 - - - +
65C LEU* 3.0 26.0 + - - +
89C PHE* 3.6 28.5 - + - -
91C PHE* 3.8 20.6 - + - -
300C THR* 4.6 0.2 - - + -
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Residues in contact with PRO 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU 4.0 0.2 - - - +
33C PHE* 1.3 90.1 - - + +
35C ARG* 1.3 69.6 + - - +
36C GLY 3.3 0.3 + - - -
37C ALA* 3.2 30.1 + - + +
64C ASN* 4.9 2.0 - - - +
65C LEU 3.4 9.2 - - - +
67C VAL* 4.0 21.5 - - + -
91C PHE* 3.4 43.5 - - + -
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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