Contacts of the strand formed by residues 47 - 52 (chain A) in PDB entry 2YSX
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 TYR 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ASN* 4.9 12.7 + - - -
15A GLY* 6.5 0.4 - - - -
37A VAL* 4.0 17.7 - - + -
38A ARG 3.6 18.8 - - - -
39A ALA* 4.3 11.0 - - + -
40A SER* 4.1 8.5 - - - +
44A SER 4.9 4.9 - - - -
45A ARG 4.7 2.2 - - - -
46A ALA* 1.3 80.9 - - - +
48A ALA* 1.3 62.6 + - - +
61A ARG* 3.6 4.9 - - - +
62A ILE* 3.0 44.7 + - + -
70A PHE* 3.6 34.7 - + - -
86A LEU* 3.3 33.8 - - + +
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 3.3 5.7 - - - -
38A ARG* 2.8 81.1 + - + +
40A SER* 4.7 6.7 - - - +
47A TYR* 1.3 77.2 - - - +
49A LEU* 1.3 60.0 + - - +
50A CYS* 3.9 1.8 + - - -
59A THR* 4.2 6.5 - - + -
60A TYR 3.4 5.6 - - - +
61A ARG* 5.4 1.1 - - - -
62A ILE* 4.1 1.6 - - - -
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 4.1 18.6 - - + -
36A LEU 3.1 22.0 - - - +
37A VAL* 4.1 12.3 - - + +
48A ALA* 1.3 72.0 - - - +
50A CYS* 1.3 66.6 + - - +
51A VAL* 4.1 7.4 - - + -
58A TYR 3.2 5.7 - - - +
60A TYR* 2.7 41.4 + - + +
62A ILE* 3.7 13.8 - - + +
72A VAL* 5.0 10.1 - - + -
89A LEU* 5.5 3.6 - - + -
90A ILE* 4.6 13.5 - - + -
93A TYR* 5.7 2.7 - - + -
100A LEU* 3.8 38.6 - - + -
104A LEU* 4.8 3.1 - - + -
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Residues in contact with CYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA* 3.6 27.4 - - - -
26A LEU* 4.0 15.6 - - + +
35A PHE* 3.2 5.7 - - - +
36A LEU* 2.9 51.0 + - + +
38A ARG* 3.7 20.4 - - - -
48A ALA 4.8 0.2 - - - -
49A LEU* 1.3 72.9 - - - +
51A VAL* 1.3 62.7 + - - +
57A VAL* 4.1 8.3 - - + -
58A TYR 3.6 3.1 - - - -
59A THR* 3.7 17.9 - - - -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 4.7 0.9 - - - -
34A SER 3.7 6.3 - - - +
35A PHE* 4.2 1.3 - - + -
49A LEU* 4.1 18.6 - - + -
50A CYS* 1.3 80.4 - - - +
52A LEU* 1.3 60.2 + - - +
56A CYS 3.2 3.8 - - - +
57A VAL* 4.5 1.1 - - - -
58A TYR* 2.9 43.3 + - + +
60A TYR* 4.7 3.4 - - + -
100A LEU* 4.2 20.4 - - + -
101A VAL* 3.4 15.7 - - + +
102A THR* 2.9 42.0 - - + +
104A LEU* 4.2 12.1 - - + -
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 3.7 47.2 - - + +
27A SER* 4.9 3.6 - - - +
30A GLY* 4.1 15.3 - - - -
31A LYS 3.6 22.0 - - - +
33A GLY 4.2 8.5 + - - -
34A SER* 3.2 14.5 + - - +
51A VAL* 1.3 70.3 - - - +
53A TYR* 1.3 65.7 - - - +
55A ASN* 4.7 9.4 - - - +
56A CYS 3.4 16.4 - - - +
57A VAL* 3.8 26.2 - - + -
102A THR* 3.3 16.5 - - - +
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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