Contacts of the strand formed by residues 76 - 81 (chain F) in PDB entry 3Q3G
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 ASP 76 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23F CYS 3.9 2.9 - - - -
24F LYS* 3.3 36.9 - - + +
72F GLY* 3.4 19.4 - - - -
73F SER 3.5 8.2 + - - +
75F THR* 1.3 96.0 - - - +
77F PHE* 1.3 60.3 + - - +
78F THR* 5.1 2.6 - - + +
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Residues in contact with PHE 77 (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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22F SER* 3.6 3.6 + - - -
23F CYS* 2.8 45.1 + - + +
24F LYS* 5.0 0.4 - - - +
25F SER* 4.6 0.9 - - - -
29F LEU* 3.7 22.0 - - + -
37F ASN* 3.7 29.8 - - + -
39F LEU* 3.6 32.3 - - + -
41F TRP* 4.4 3.1 - - + -
57F ALA* 3.7 16.8 - - + -
71F THR 3.5 4.9 - - - +
72F GLY* 3.7 14.4 - - - -
73F SER 3.7 12.8 - - - -
74F GLY 3.5 36.8 - - - -
75F THR 3.4 18.2 - - - -
76F ASP* 1.3 70.7 - - - +
78F THR* 1.3 63.6 + - - +
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Residues in contact with THR 78 (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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20F THR* 4.6 9.2 - - - +
21F MET 3.2 11.9 + - - -
22F SER* 4.8 2.7 - - - -
41F TRP* 3.9 5.7 + - - -
69F THR 3.8 0.9 - - - +
70F GLY* 3.6 2.4 - - - -
71F THR* 2.9 53.8 + - - +
72F GLY* 5.0 1.3 - - - +
76F ASP 5.1 2.5 - - - +
77F PHE* 1.3 79.4 - - - +
79F LEU* 1.3 59.9 + - - +
80F THR* 3.6 15.0 + - - -
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Residues in contact with LEU 79 (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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20F THR* 3.4 3.3 - - - -
21F MET* 2.8 57.2 + - + +
41F TRP* 3.6 52.4 - - + -
53F LEU* 3.9 23.8 - - + -
54F ILE* 3.5 29.2 - - + -
68F PHE* 5.1 4.0 - - + -
69F THR 3.7 3.8 - - - +
70F GLY* 4.0 11.0 - - - -
78F THR* 1.3 71.0 + - - +
80F THR* 1.3 66.3 + - - +
81F ILE* 5.1 0.7 - - + -
92F TYR* 3.9 11.0 - - + -
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Residues in contact with THR 80 (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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18F LYS* 4.0 21.3 - - + -
19F VAL 3.3 9.9 - - - +
20F THR* 3.8 18.0 - - + +
67F ARG 3.1 4.2 - - - +
68F PHE* 3.4 2.4 - - - -
69F THR* 2.7 53.5 + - - +
71F THR* 4.7 4.3 + - - +
78F THR* 3.6 13.7 + - - -
79F LEU* 1.3 76.4 + - - +
81F ILE* 1.3 67.0 + - - +
82F SER* 3.7 5.2 - - - +
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Residues in contact with ILE 81 (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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17F GLU 3.5 1.0 - - - +
19F VAL* 2.9 41.7 + - + +
21F MET* 3.7 26.2 - - + -
67F ARG* 3.2 21.1 - - + -
68F PHE* 3.6 18.8 - - + -
79F LEU* 5.1 1.6 - - + -
80F THR* 1.3 72.6 - - - +
82F SER* 1.3 65.0 + - - +
83F SER 3.5 2.6 + - - -
84F VAL* 3.8 13.0 - - + -
88F ASP* 3.5 23.8 - - + +
92F TYR* 3.7 30.1 - - + +
110F LEU* 3.8 16.8 - - + -
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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