Contacts of the strand formed by residues 57 - 64 (chain F) in PDB entry 5X6E
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 57 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E ILE* 5.0 1.9 - - - +
47F LYS* 6.1 1.3 - - - +
49F THR* 4.6 8.7 - - + -
50F SER 3.5 6.3 - - - +
51F ILE* 3.7 33.0 - - + +
55F GLY 3.1 14.8 + - - +
56F THR* 1.3 81.8 + - - +
58F MET* 1.3 65.3 + - - +
59F ASN* 3.7 14.4 - - - +
176F TYR* 3.5 60.0 - - + +
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Residues in contact with MET 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E PHE* 3.7 25.4 - - + +
132E ASN* 3.8 22.7 - - - +
135E SER* 3.5 31.2 - - - +
136E ILE* 4.3 14.6 - - + -
49F THR* 3.2 21.9 - - - -
50F SER 3.0 12.5 + - - +
56F THR 5.4 0.4 - - - +
57F ILE* 1.3 79.3 - - - +
59F ASN* 1.3 65.7 + - - +
60F LEU* 3.2 24.4 + - + +
176F TYR* 3.1 27.4 - - - +
177F SER 4.1 1.1 - - - +
179F GLY* 3.6 21.8 - - - +
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Residues in contact with ASN 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F LYS* 3.7 12.3 + - + +
48F LEU 3.9 4.7 - - - -
49F THR* 3.2 20.6 - - - +
57F ILE* 3.7 10.2 - - - +
58F MET* 1.3 70.3 - - - +
60F LEU* 1.3 65.7 + - - +
61F GLN 3.3 2.0 - - - +
62F TYR* 3.9 15.2 + - + -
173F GLU* 2.9 37.0 + - - +
176F TYR* 3.1 26.1 + - - +
177F SER* 3.2 42.3 + - - +
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Residues in contact with LEU 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E LEU* 4.2 30.7 - - + +
131E PHE* 3.4 23.0 - - + -
132E ASN* 3.8 23.8 - - + +
48F LEU* 3.0 27.3 + - + +
50F SER 4.8 2.2 - - - +
58F MET* 3.2 27.4 + - + +
59F ASN* 1.3 72.6 - - - +
61F GLN* 1.3 61.8 + - + +
83F TYR* 3.5 37.5 - - + -
130F LYS* 2.7 30.4 + - - +
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Residues in contact with GLN 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E LEU* 4.1 8.3 - - + +
47F LYS* 3.4 1.7 - - - +
48F LEU* 2.7 35.9 + - + +
59F ASN* 3.3 3.1 - - - +
60F LEU* 1.3 87.5 - - + +
62F TYR* 1.3 75.1 + - - +
63F TYR* 3.1 18.5 + - + -
123F GLN* 2.8 41.5 + - - -
126F TYR* 3.5 17.5 - - + -
130F LYS* 4.2 2.0 - - - +
146F GLN* 6.0 1.3 - - - +
177F SER* 5.9 0.6 + - - -
301F GSH 3.1 44.4 - - - +
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Residues in contact with TYR 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F ILE* 5.1 1.3 - - + -
46F THR 3.2 7.2 - - - +
47F LYS* 3.4 28.7 - - + -
59F ASN* 3.9 15.3 + - + -
61F GLN* 1.3 90.0 - - - +
63F TYR* 1.3 75.4 + - - +
88F ILE* 4.1 16.6 - - + +
146F GLN* 4.7 4.0 - - - +
150F LEU* 4.1 17.5 - - + -
154F TYR* 3.0 35.2 - + - +
166F LEU* 4.8 9.9 - - + -
169F LEU* 4.6 10.5 - - + +
173F GLU* 3.8 26.2 + - - +
174F LEU* 5.8 0.5 - - - -
177F SER* 4.0 13.6 + - - -
301F GSH 3.2 29.1 + - - +
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Residues in contact with TYR 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E LEU* 5.4 1.4 - - - +
41F LEU* 3.8 6.6 - - + +
44F GLY 3.7 0.7 - - - +
45F ILE* 3.3 5.9 - - - +
46F THR* 2.5 51.6 + - + -
48F LEU* 4.0 32.7 - - + +
61F GLN* 3.1 33.7 + - - -
62F TYR* 1.3 89.0 - - - +
64F LYS* 1.3 60.8 + - - +
67F PHE* 3.7 37.2 - + + -
68F VAL 4.6 0.7 - - - -
69F ILE* 3.6 38.0 - - + +
85F LEU* 4.2 13.5 - - + -
123F GLN* 3.5 11.1 + - - -
154F TYR* 4.7 2.5 - - - -
301F GSH 3.8 6.1 - - - -
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Residues in contact with LYS 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F LEU* 4.2 0.2 - - - -
43F ASP* 5.9 2.2 + - - -
44F GLY 3.4 7.8 + - - +
45F ILE* 4.3 21.8 - - + +
63F TYR* 1.3 74.8 - - - +
65F GLY* 1.3 78.3 + - - +
66F ALA 4.1 1.9 - - - +
67F PHE* 4.4 2.1 - - - +
153F VAL* 4.0 23.8 - - + -
154F TYR* 3.4 43.1 - - + +
166F LEU* 6.5 0.2 - - - -
301F GSH 3.2 33.6 + - + +
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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