Contacts of the strand formed by residues 25 - 31 (chain C) in PDB entry 2UX2
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 ALA 25 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C LEU* 3.3 13.6 - - - +
3C CYS* 3.6 7.3 - - - -
23C PHE* 3.7 1.9 - - - +
24C ASP* 1.3 89.6 - - - +
26C CYS* 1.3 60.2 + - - +
39C CYS* 3.9 0.3 - - - -
40C TRP* 2.8 36.9 + - + +
41C LYS 4.6 0.2 - - - -
42C PHE* 4.1 19.5 - - + +
45C CYS* 4.7 5.6 - - - -
64C CYS 3.4 10.8 - - - +
65C LYS* 4.2 7.0 - - + -
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Residues in contact with CYS 26 (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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1C LEU* 3.8 10.8 - - - -
2C GLN 3.5 13.7 - - - -
3C CYS* 2.0 47.1 - - - -
25C ALA* 1.3 72.9 - - - +
27C LEU* 1.3 60.0 + - - +
38C LYS 3.6 1.8 - - - -
40C TRP* 4.3 1.3 - - - -
62C TYR 3.8 0.7 - - - +
63C CYS* 3.3 7.3 - - - +
64C CYS* 2.8 30.6 + - - -
66C LYS 4.0 0.7 - - - -
68C LEU 4.6 0.2 - - - -
69C CYS* 3.7 22.4 - - - -
70C ASN* 3.6 22.4 - - + -
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Residues in contact with LEU 27 (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 CYS* 1.3 74.3 - - - +
28C ILE* 1.3 64.3 + - - +
29C THR* 3.6 25.4 - - - +
36C TYR* 5.4 1.1 - - + +
37C ASN* 3.3 1.7 - - - -
38C LYS* 2.9 33.9 + - + +
40C TRP* 3.6 54.5 - - + +
50C VAL* 4.2 10.1 - - + -
54C LEU* 4.4 10.5 - - + -
61C TYR* 4.0 13.2 - - + -
62C TYR 3.5 10.3 - - - +
63C CYS* 3.8 16.6 - - - -
70C ASN* 3.0 19.0 + - - -
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Residues in contact with ILE 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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27C LEU* 1.3 73.6 - - - +
29C THR* 1.3 65.5 + - - +
30C LYS* 4.0 14.4 - - + -
35C VAL* 4.3 2.2 - - + -
36C TYR 3.3 5.2 - - - +
37C ASN* 3.3 22.7 - - - +
61C TYR* 3.3 2.4 - - - +
62C TYR* 2.9 54.0 + - + +
70C ASN* 3.5 22.9 - - - +
71C PHE 3.7 15.0 - - - +
72C ASN* 3.7 25.8 - - - +
74C GLN* 4.3 5.6 - - + -
75C LEU* 3.6 19.1 - - + +
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Residues in contact with THR 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 LEU* 3.6 14.6 - - - +
28C ILE* 1.3 77.3 + - - +
30C LYS* 1.3 68.1 + - - +
31C ALA* 4.8 0.7 - - + +
34C GLN 3.9 0.7 - - - +
35C VAL* 3.3 7.4 - - - +
36C TYR* 2.9 43.0 + - + -
50C VAL* 3.8 1.0 - - - +
54C LEU* 3.7 30.1 - - + +
56C GLU* 5.8 0.2 - - + -
59C LEU* 3.9 27.1 - - + -
60C THR 3.3 13.5 - - - +
61C TYR* 3.5 12.0 - - - +
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Residues in contact with LYS 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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28C ILE* 4.0 8.7 - - + -
29C THR* 1.3 78.8 - - - +
31C ALA* 1.3 60.8 + - - +
32C GLY 3.8 5.8 - - - +
34C GLN 3.7 2.9 - - - -
35C VAL* 4.3 16.6 - - + -
59C LEU* 3.3 4.2 - - - +
60C THR* 3.0 36.1 + - - +
72C ASN* 3.0 40.3 + - - +
73C GLU* 4.8 1.4 - - - +
75C LEU* 2.8 41.7 + - + +
76C GLU 4.3 12.4 - - - +
77C ASN* 4.6 7.7 - - - +
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Residues in contact with ALA 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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29C THR* 5.2 0.9 - - + -
30C LYS* 1.3 73.4 - - - +
32C GLY* 1.3 64.1 + - - +
33C LEU 3.3 0.7 + - - -
34C GLN* 2.8 31.3 + - + +
36C TYR* 5.1 2.5 - - + -
56C GLU* 3.7 28.7 - - + +
58C GLU 3.5 24.2 - - - +
59C LEU* 4.1 7.0 - - + +
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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