Contacts of the strand formed by residues 75 - 82 (chain O) in PDB entry 3FKS
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 LYS 75 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10O THR* 3.6 35.2 - - + -
11O GLY 3.6 2.5 - - - +
12O LYS* 5.6 1.6 - - - -
38O GLU 3.7 7.6 - - - +
39O ILE* 3.9 13.9 - - - +
40O LYS* 3.5 43.1 + - - +
73O GLY 3.7 1.0 + - - -
74O GLU* 1.3 75.9 + - - +
76O VAL* 1.3 62.8 + - - +
77O LEU* 3.9 3.4 + - + +
177X ALA* 4.1 16.0 + - + -
178X HIS 4.0 6.2 + - - -
179X GLY* 3.7 31.5 - - - +
214X LYS* 5.1 4.6 - - - +
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Residues in contact with VAL 76 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O ILE 3.7 0.7 - - - +
10O THR* 3.4 5.9 - - - -
11O GLY* 2.7 39.9 + - - +
13O VAL* 3.6 32.1 - - + -
23O VAL* 3.7 21.5 - - + -
25O PHE* 4.4 3.4 - - + -
37O LEU* 3.6 42.6 - - + -
38O GLU 3.3 6.3 - - - +
39O ILE* 3.8 10.8 - - + -
48O LEU* 4.4 3.6 - - + -
74O GLU 3.9 0.4 - - - +
75O LYS* 1.3 76.0 - - - +
77O LEU* 1.3 63.6 + - - +
78O ASP 3.7 0.3 + - - -
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Residues in contact with LEU 77 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8O PRO* 4.2 22.2 - - + -
9O ILE 3.8 8.7 - - - +
10O THR* 5.0 8.1 - - + +
37O LEU* 3.3 8.2 - - - +
38O GLU* 2.8 65.0 + - + +
40O LYS* 6.4 1.8 - - + -
75O LYS* 3.9 5.9 + - + +
76O VAL* 1.3 73.7 - - - +
78O ASP* 1.3 74.6 + - - +
79O THR* 3.8 1.9 + - - +
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Residues in contact with ASP 78 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8O PRO* 5.6 1.2 - - - +
9O ILE* 3.0 47.8 + - + +
25O PHE* 4.9 1.8 - - + -
30O LEU 5.2 0.5 - - - -
31O PRO* 3.8 32.9 - - + +
35O ASN* 4.6 2.9 + - - +
36O ALA 3.5 8.0 - - - +
37O LEU* 3.7 11.1 - - + +
77O LEU* 1.3 84.1 - - - +
79O THR* 1.3 63.8 + - - +
80O GLY* 2.9 29.1 + - - -
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Residues in contact with THR 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O ALA* 3.2 29.8 + - + +
38O GLU* 3.8 26.7 + - - +
77O LEU* 3.8 3.0 + - - -
78O ASP* 1.3 73.5 + - - +
80O GLY* 1.3 59.1 + - - +
81O GLY* 3.2 18.3 + - - +
82O PRO 5.1 3.4 - - - +
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Residues in contact with GLY 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O ASN* 3.6 14.4 + - - -
78O ASP* 2.9 23.3 + - - -
79O THR* 1.3 77.7 - - - +
81O GLY* 1.3 56.0 + - - +
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Residues in contact with GLY 81 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O ASN* 3.6 10.2 - - - +
36O ALA* 2.7 33.0 + - - +
79O THR* 3.2 9.7 + - - -
80O GLY* 1.3 81.7 - - - +
82O PRO* 1.3 74.1 - - - +
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Residues in contact with PRO 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82L ARG* 4.3 24.0 - - - +
34O LEU* 3.1 32.8 - - + +
35O ASN* 3.8 4.7 - - - +
36O ALA* 3.9 3.9 - - - +
79O THR* 5.1 3.8 - - - +
81O GLY* 1.3 89.8 - - - +
83O ILE* 1.3 66.3 + - - +
84O SER* 3.1 13.0 + - - +
116O PRO* 4.1 24.9 - - + -
118O HIS* 4.5 15.5 - - + -
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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