Contacts of the strand formed by residues 52 - 58 (chain I) in PDB entry 5EEZ
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 THR 52 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101H TRP* 2.7 39.2 + - + +
23I GLY* 4.0 8.5 - - - -
24I LEU 3.4 3.1 - - - +
26I ARG* 3.5 1.4 + - - -
33I HIS* 2.8 19.6 + - - -
47I GLN 4.6 1.8 - - - +
48I PHE* 3.6 5.8 - - + -
49I THR* 2.8 35.2 + - - +
51I HIS* 1.3 78.1 - - - +
53I SER* 1.3 59.4 + - - +
54I ALA 3.7 18.4 - - - +
55I ILE* 3.8 19.7 - - + -
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Residues in contact with SER 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I LEU 3.1 5.3 + - - -
25I THR 3.7 0.9 + - - -
26I ARG* 3.4 34.1 - - - +
48I PHE* 3.9 6.3 - - - -
52I THR* 1.3 74.1 - - - +
54I ALA* 1.3 59.5 + - - +
101I TRP* 2.9 38.5 + - - +
47J GLN* 3.0 35.9 + - - +
49J THR* 3.7 10.8 - - - -
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Residues in contact with ALA 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I LEU* 2.9 52.4 + - + -
48I PHE* 3.8 1.7 - - - -
52I THR* 3.6 2.1 - - - +
53I SER* 1.3 82.4 + - - +
55I ILE* 1.3 67.1 + - - +
101I TRP* 4.0 15.0 - - + +
44J LEU* 4.4 5.2 - - + -
45J ILE 3.1 13.0 - - - +
46J ALA* 4.0 12.6 - - + -
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Residues in contact with ILE 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H TRP* 3.8 27.1 - - + -
10I VAL* 3.9 26.0 - - + -
21I VAL* 3.8 28.0 - - + -
22I ILE 3.3 6.1 - - - +
24I LEU* 4.4 0.4 - - - -
46I ALA* 4.4 3.8 - - + +
47I GLN 4.3 9.9 - - - +
48I PHE* 3.8 22.2 - - + -
52I THR* 3.8 5.6 - - + -
54I ALA* 1.3 79.6 - - - +
56I LYS* 1.3 66.3 + - - +
57I VAL* 4.5 3.4 - - + -
44J LEU* 3.4 5.8 - - - +
45J ILE* 2.7 53.2 + - + +
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Residues in contact with LYS 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I ASN 3.6 2.4 - - - +
21I VAL* 3.6 2.1 - - - -
22I ILE* 2.8 49.0 + - + +
24I LEU* 4.1 14.1 - - + +
32I PHE* 4.0 20.7 - - + -
55I ILE* 1.3 76.2 - - - +
57I VAL* 1.3 72.5 + - - +
58I ARG* 5.2 2.7 - - + +
36J GLU* 3.2 24.0 + - - +
37J LYS 3.2 18.2 + - - -
38J LEU* 3.8 14.8 - - + -
42J GLU* 3.4 28.2 + - + -
43J VAL 3.3 11.4 - - - +
44J LEU* 4.2 6.3 - - + -
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Residues in contact with VAL 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I ILE* 4.0 27.8 - - + -
19I VAL* 4.1 14.1 - - + -
20I ASN 3.4 2.9 - - - +
21I VAL* 4.6 4.0 - - + -
55I ILE* 4.5 12.1 - - + -
56I LYS* 1.3 80.9 - - - +
58I ARG* 1.3 63.1 + - - +
59I GLY 4.4 0.2 - - - +
61I ALA* 4.1 16.2 - - + -
63I ILE* 4.0 16.4 - - + -
72I SER* 3.4 25.1 - - - +
42J GLU* 3.7 7.6 - - - +
43J VAL* 2.9 29.2 + - + +
45J ILE* 4.6 9.2 - - + -
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Residues in contact with ARG 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I GLY 4.5 1.0 - - - +
19I VAL* 3.5 3.6 - - - +
20I ASN* 2.9 57.4 + - + +
22I ILE* 4.7 14.8 - - + -
56I LYS* 4.2 3.6 - - + -
57I VAL* 1.3 75.0 - - - +
59I GLY* 1.4 64.3 + - - +
42J GLU* 3.4 33.8 + - + +
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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