Contacts of the strand formed by residues 40 - 45 (chain J) 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 ILE 40 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36J VAL* 3.2 6.5 - - - +
37J GLY 2.9 33.9 + - - +
38J ASP* 2.9 13.9 - - + +
39J GLY* 1.3 82.9 - - - +
41J ALA* 1.3 71.8 + - - +
42J ARG* 4.2 13.2 - - + +
74J GLY* 5.3 0.9 - - - -
75J ILE 3.6 9.2 - - - +
76J VAL* 4.7 10.1 - - + -
77J LEU* 4.4 1.1 - - - -
283J LEU* 4.7 3.8 - - + +
286J LEU* 3.1 49.4 - - + +
287J LEU* 3.8 25.8 - - + +
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Residues in contact with ALA 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J VAL* 5.3 1.1 - - + -
35J ALA 3.8 4.3 - - - +
36J VAL* 4.1 12.6 - - + -
40J ILE* 1.3 76.2 - - - +
42J ARG* 1.3 62.7 + - - +
43J VAL* 3.5 6.8 + - + +
57J PHE* 3.9 32.8 - - + -
73J VAL 3.5 2.3 - - - +
74J GLY 3.9 0.2 - - - -
75J ILE* 2.8 42.9 + - + +
77J LEU* 4.6 6.5 - - + -
84J VAL* 4.9 1.1 - - + -
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Residues in contact with ARG 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J VAL 3.9 0.3 - - - -
34J LEU* 2.8 44.4 + - + +
35J ALA* 2.9 40.5 + - - +
40J ILE* 4.2 12.3 - - + -
41J ALA* 1.3 71.7 - - - +
43J VAL* 1.3 62.3 + - - +
69J GLU* 6.1 0.7 - - - +
72J GLN* 2.9 37.0 + - - +
73J VAL 3.3 7.4 - - - +
74J GLY* 5.3 3.8 - - - -
287J LEU* 6.4 0.4 - - + -
54M LEU 4.7 4.8 + - - -
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Residues in contact with VAL 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J GLY* 3.7 10.1 - - - -
32J ARG 3.2 25.1 - - - +
33J VAL* 4.2 11.7 - - + -
34J LEU* 4.1 2.2 - - - +
41J ALA* 3.9 12.6 - - + +
42J ARG* 1.3 76.4 - - - +
44J PHE* 1.3 71.6 + - - +
46J LEU* 4.2 7.9 - - + -
57J PHE* 4.5 3.1 - - + -
72J GLN* 3.6 5.3 - - - -
73J VAL* 2.9 35.5 + - + +
75J ILE* 3.9 26.2 - - + -
90J VAL* 3.8 22.0 - - + -
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Residues in contact with PHE 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J LEU* 3.7 33.1 - - + +
31J GLY* 3.2 2.3 - - - -
32J ARG* 2.8 47.5 + - + +
34J LEU* 4.4 21.6 - - + +
42J ARG 4.3 0.4 + - - -
43J VAL* 1.3 73.5 - - - +
45J GLY* 1.3 64.6 + - - +
71J GLY* 3.3 25.6 - - - -
72J GLN* 5.0 0.2 - - - +
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Residues in contact with GLY 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J LEU* 3.6 22.2 - - - -
30J THR 3.8 4.0 - - - -
31J GLY* 4.2 0.2 - - - -
43J VAL 4.1 0.2 + - - -
44J PHE* 1.3 84.8 - - - +
46J LEU* 1.3 75.1 + - - +
47J ASN* 3.3 10.0 - - - +
71J GLY 5.0 1.4 + - - -
72J GLN* 5.9 0.2 - - - +
73J VAL* 3.7 7.2 - - - +
72N ARG* 3.3 12.6 + - - -
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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