Contacts of the strand formed by residues 73 - 77 (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 VAL 73 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J ALA 3.5 1.4 - - - +
42J ARG* 3.3 8.9 - - - +
43J VAL* 2.9 36.3 + - + +
45J GLY 3.7 12.8 - - - +
46J LEU* 4.4 9.0 - - + +
49J ILE* 4.8 3.4 - - + -
65J ALA* 3.5 18.6 - - + -
67J ASN 3.5 3.1 - - - -
68J LEU* 3.7 14.6 - - + -
69J GLU* 4.6 1.3 - - - +
72J GLN* 1.3 75.2 - - - +
74J GLY* 1.3 64.8 + - - +
75J ILE* 3.5 23.1 - - + -
72N ARG* 3.3 39.7 - - - +
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Residues in contact with GLY 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40J ILE* 5.3 0.9 - - - -
41J ALA 3.9 3.4 - - - -
42J ARG* 5.0 5.2 - - - -
65J ALA* 3.2 1.5 - - - -
66J LEU* 2.8 29.5 + - - +
67J ASN* 2.6 30.8 + - - -
69J GLU* 5.6 1.6 - - - -
73J VAL* 1.3 73.1 - - - +
75J ILE* 1.3 64.4 + - - -
76J VAL* 4.0 0.5 + - - +
287J LEU* 4.6 12.5 - - - +
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Residues in contact with ILE 75 (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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40J ILE* 3.6 3.3 - - - +
41J ALA* 2.8 45.6 + - + +
43J VAL* 3.9 25.1 - - + -
46J LEU* 4.4 9.6 - - + -
55J VAL* 3.7 22.4 - - + -
57J PHE* 3.9 16.4 - - + -
63J GLY* 3.8 8.1 - - - -
64J MET 3.1 21.5 - - - +
65J ALA* 3.7 15.5 - - + -
73J VAL* 3.5 29.6 - - + +
74J GLY* 1.3 73.8 - - - -
76J VAL* 1.3 68.5 + - - +
77J LEU 4.7 0.7 - - - +
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Residues in contact with VAL 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J GLY 3.7 4.3 - - - +
40J ILE* 4.7 9.4 - - + -
63J GLY* 3.5 3.1 - - - -
64J MET* 2.8 47.4 + - + +
66J LEU* 3.7 30.1 - - + -
74J GLY 5.1 0.9 - - - +
75J ILE* 1.3 76.3 - - - +
77J LEU* 1.3 63.2 + - - +
78J PHE* 3.6 1.0 + - - -
243J PRO* 3.8 24.5 - - + +
283J LEU* 3.8 20.4 - - + -
287J LEU* 4.2 20.2 - - + -
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Residues in contact with LEU 77 (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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36J VAL* 4.3 8.5 - - + -
39J GLY* 2.8 29.2 + - - +
40J ILE 4.2 8.5 - - - +
41J ALA* 4.6 6.7 - - + -
57J PHE* 3.5 38.8 - - + -
61J VAL* 4.4 11.9 - - + -
62J LYS 4.2 1.8 - - - +
76J VAL* 1.3 72.1 - - - +
78J PHE* 1.3 60.8 + - - +
79J GLY 3.2 16.8 + - - +
80J SER 4.9 0.2 - - - +
81J ASP* 3.5 39.5 - - + -
84J VAL* 3.9 14.1 - - + -
241J ALA* 3.6 7.6 - - - +
243J PRO* 3.5 16.1 - - - +
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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