Contacts of the strand formed by residues 74 - 79 (chain F) in PDB entry 5DK3
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 74 (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 3.7 3.4 - - - -
24F ARG* 3.2 42.0 + - + +
70F GLY* 3.5 12.0 - - - -
71F SER 3.4 14.9 + - - +
73F THR* 1.4 91.3 + - - +
75F PHE* 1.3 64.3 + - - +
76F THR* 5.5 0.2 - - - -
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Residues in contact with PHE 75 (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* 3.5 2.4 - - - -
23F CYS* 2.7 43.2 + - + +
25F ALA* 5.1 3.4 - - + -
29F VAL* 3.5 27.8 - - + -
35F SER* 3.7 10.5 - - - -
37F LEU* 3.8 31.0 - - + -
39F TRP* 3.9 7.4 - - + +
55F ALA* 3.6 28.3 - - + -
69F SER 3.6 3.1 - - - +
70F GLY* 3.4 28.5 - - - -
71F SER* 3.7 16.2 - - - -
72F GLY 3.4 23.8 - - - -
73F THR* 3.8 10.5 - - - -
74F ASP* 1.3 72.8 - - - +
76F THR* 1.3 66.0 + - - +
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Residues in contact with THR 76 (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 ARG* 5.9 0.4 - - - +
20F THR* 4.5 13.9 - - + -
21F LEU 3.3 11.4 + - - +
22F SER* 4.7 5.5 + - - -
39F TRP* 4.0 5.8 + - - -
68F GLY* 3.2 2.9 - - - -
69F SER* 2.8 50.1 + - - +
74F ASP 5.5 0.5 - - - -
75F PHE* 1.3 77.0 + - - +
77F LEU* 1.4 64.3 + - - +
78F THR* 3.7 21.2 + - - +
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Residues in contact with LEU 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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19F ALA 3.6 2.1 - - - +
20F THR* 3.6 0.9 - - - -
21F LEU* 2.9 45.1 + - + +
39F TRP* 3.5 47.2 - - + -
51F LEU* 4.1 12.1 - - + -
52F ILE* 3.8 24.9 - - + -
66F PHE* 4.9 4.0 - - + -
67F SER 3.5 16.4 - - - +
68F GLY* 4.3 0.7 - - - -
76F THR* 1.4 71.5 - - - +
78F THR* 1.3 65.9 + - - +
79F ILE* 5.0 6.0 - - + +
90F TYR* 3.8 31.2 - - + -
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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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18F ARG* 3.4 39.2 + - - +
19F ALA 3.3 6.1 - - - +
20F THR* 4.2 2.1 - - + +
66F PHE* 3.6 4.3 - - - -
67F SER* 2.7 48.8 + - - +
68F GLY* 5.8 0.3 - - - -
69F SER* 5.4 2.9 + - - -
76F THR* 3.7 17.2 + - - +
77F LEU* 1.3 77.6 - - - +
79F ILE* 1.3 67.5 + - - +
80F SER* 3.8 14.1 - - - +
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Residues in contact with ILE 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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17F GLU 3.9 0.9 - - - +
18F ARG* 3.5 1.6 - - - -
19F ALA* 2.9 43.9 + - + +
21F LEU* 5.4 2.7 - - + -
65F ARG* 3.4 14.4 - - - +
66F PHE* 3.7 20.2 - - + -
77F LEU* 5.0 7.6 - - + +
78F THR* 1.3 78.4 - - - +
80F SER* 1.4 66.4 + - - +
81F SER* 2.8 16.2 + - - +
82F LEU* 4.0 19.7 - - + -
86F ASP* 3.4 23.3 - - - +
90F TYR* 3.7 37.9 - - + +
108F VAL* 5.1 2.0 - - + -
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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