Contacts of the strand formed by residues 36 - 43 (chain a) in PDB entry 5OA3
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 36 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18642 U 3.3 34.5 - - + +
18672 U 5.9 9.9 - - + +
34a LYS 3.6 7.4 - - - +
35a ALA* 1.3 70.9 - - - +
37a LYS* 1.3 67.6 + - - +
38a LYS* 4.0 1.3 + - + -
71a LEU 3.5 0.9 - - - +
72a HIS* 3.4 3.1 - - - -
73a TYR* 2.8 61.7 + - + +
75a VAL* 4.0 22.0 - - + +
78a ALA* 4.6 15.7 - - + -
83a VAL* 5.0 11.2 - - + -
84a VAL* 4.9 15.3 - - + -
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Residues in contact with LYS 37 (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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9902 A 3.2 39.0 + - - +
9912 G 5.7 1.4 + - - -
18672 U 3.4 24.6 + - - +
18682 U 3.0 14.5 + - - +
116B LYS* 4.7 7.9 - - - +
32a LYS* 3.9 16.4 + - + +
33a ASP* 4.6 5.1 + - - +
35a ALA* 3.2 22.7 + - + +
36a ILE* 1.3 77.9 - - - +
38a LYS* 1.3 59.8 + - - +
70a LYS* 3.2 35.9 - - + +
71a LEU 3.1 5.2 - - - +
72a HIS* 3.8 15.5 - - + -
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Residues in contact with LYS 38 (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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18672 U 3.8 15.7 - - + +
18682 U 3.4 5.2 - - - +
36a ILE* 4.0 2.4 + - + -
37a LYS* 1.3 76.5 - - - +
39a PHE* 1.3 68.8 + - - +
40a VAL* 3.9 16.8 + - + +
70a LYS* 5.6 0.9 - - - -
71a LEU* 2.9 45.6 + - + +
73a TYR* 4.8 14.1 - - + -
83a VAL* 4.0 33.3 - - + +
100a ARG* 5.4 9.6 - - - +
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Residues in contact with PHE 39 (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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9872 A 5.1 11.4 - - - -
9882 C 5.2 4.7 - - - -
18682 U 3.3 36.6 + - - +
18692 A 3.4 39.3 - + - -
38a LYS* 1.3 79.3 - - - +
40a VAL* 1.3 73.6 + - - +
41a ILE* 3.6 29.1 + - + -
68a TYR* 4.3 16.4 - + + -
69a VAL 3.8 2.7 - - - -
70a LYS* 4.0 39.3 - - + +
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Residues in contact with VAL 40 (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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38a LYS* 4.2 17.7 - - - +
39a PHE* 1.3 80.1 - - - +
41a ILE* 1.3 69.8 + - - +
42a ARG* 4.4 31.4 - - + +
67a LEU 3.3 5.5 - - - +
68a TYR* 3.3 2.3 - - - -
69a VAL* 2.9 47.6 + - + +
71a LEU* 4.0 27.1 - - + -
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Residues in contact with ILE 41 (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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18692 A 3.5 52.5 - - + +
39a PHE* 3.6 15.3 + - + -
40a VAL* 1.3 72.3 - - - +
42a ARG* 1.3 65.1 + - - +
66a LYS* 4.3 20.4 - - + +
67a LEU 3.5 2.9 - - - +
68a TYR* 3.5 30.5 - - + -
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Residues in contact with ARG 42 (chain a).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3333 C 5.7 9.6 - - - +
107O THR* 3.7 28.3 - - - +
108O PRO* 4.4 9.3 + - - +
40a VAL* 4.4 23.7 - - + +
41a ILE* 1.3 76.4 - - - +
43a ASN* 1.3 77.1 + - - +
46a GLU* 3.5 29.4 + - - -
66a LYS* 3.2 11.8 - - - +
67a LEU* 2.9 45.6 + - + +
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Residues in contact with ASN 43 (chain a).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42a ARG* 1.3 99.1 + - - +
44a ILE* 1.3 66.0 + - - +
45a VAL 3.3 20.9 - - - +
46a GLU* 4.5 7.0 + - - +
50a VAL* 5.4 6.7 - - + +
64a LEU* 4.9 16.0 + - + +
65a PRO 4.0 7.4 - - - +
66a LYS* 4.3 21.6 - - - +
67a LEU 4.6 0.7 - - - -
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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