Contacts of the strand formed by residues 35 - 40 (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 ASN 35 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82L ARG* 5.4 2.9 + - - -
31O PRO* 4.4 15.3 - - + +
32O ALA* 2.9 43.9 + - - +
33O ILE 2.9 9.4 - - - +
34O LEU* 1.3 81.4 - - - +
36O ALA* 1.3 62.7 + - - +
49O GLU* 3.3 3.3 - - - -
50O VAL* 3.0 26.4 + - + +
78O ASP* 4.6 1.5 + - - +
80O GLY* 3.6 26.9 + - - -
81O GLY* 3.5 16.6 - - - +
82O PRO* 4.7 4.5 - - - +
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Residues in contact with ALA 36 (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* 1.3 73.9 - - - +
37O LEU* 1.3 76.5 + - - +
38O GLU* 6.0 0.2 - - + -
47O VAL* 5.7 2.5 - - + -
48O LEU 3.4 5.4 - - - +
78O ASP* 3.5 3.3 - - - +
79O THR* 3.2 30.9 + - + +
81O GLY 2.7 19.0 + - - +
82O PRO 4.1 6.1 - - - +
83O ILE* 3.6 30.7 - - + -
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Residues in contact with LEU 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O VAL* 4.5 9.9 - - + -
25O PHE* 4.4 9.2 - - + -
31O PRO* 4.0 15.7 - - + -
35O ASN 5.0 0.7 - - - +
36O ALA* 1.3 83.6 - - - +
38O GLU* 1.3 65.5 + - - +
46O LEU 4.2 0.4 - - - -
47O VAL* 3.3 6.6 - - - +
48O LEU* 2.7 49.8 + - + -
50O VAL* 4.0 11.9 - - + -
59O VAL* 4.8 1.1 - - + -
61O THR* 3.5 30.3 - - + -
76O VAL* 3.6 24.5 - - + -
77O LEU 3.3 13.2 - - - +
78O ASP* 3.7 17.3 - - + +
79O THR* 4.5 0.4 - - - -
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Residues in contact with GLU 38 (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* 6.0 0.4 - - + -
37O LEU* 1.3 78.3 - - - +
39O ILE* 1.3 65.1 + - - +
40O LYS* 6.1 0.2 - - - -
45O LYS* 3.8 36.0 + - + +
46O LEU 3.3 3.8 - - - +
47O VAL* 4.6 12.5 - - + +
75O LYS 3.7 0.5 - - - +
76O VAL* 3.3 7.6 - - - -
77O LEU* 2.8 64.0 + - + +
79O THR* 3.8 22.1 + - - +
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Residues in contact with ILE 39 (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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13O VAL* 3.9 16.2 - - + -
21O VAL* 5.4 0.7 - - + -
38O GLU* 1.3 82.0 - - - +
40O LYS* 1.3 69.5 + - - +
41O THR* 3.1 5.8 + - - +
45O LYS* 3.4 5.4 - - - -
46O LEU* 3.0 61.2 + - + +
48O LEU* 4.1 14.1 - - + -
70O LEU* 4.3 21.8 - - + -
74O GLU* 3.9 22.0 - - + +
75O LYS 3.9 7.0 - - - +
76O VAL* 3.8 26.0 - - + -
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Residues in contact with LYS 40 (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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38O GLU 6.1 0.4 - - - -
39O ILE* 1.3 72.7 - - - +
41O THR* 1.3 59.6 + - - +
42O PRO* 4.6 1.2 - - - +
44O GLY 4.6 3.6 - - - -
45O LYS* 5.1 1.6 - - - +
74O GLU* 4.0 14.9 + - - +
75O LYS* 3.5 50.8 + - - +
77O LEU* 6.4 2.0 - - + -
176X LYS 4.4 5.3 + - - -
177X ALA* 4.1 20.0 - - - +
214X LYS* 5.7 5.2 - - - +
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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