Contacts of the strand formed by residues 62 - 68 (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 LYS 62 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54J LEU* 5.2 15.1 - - + +
55J VAL 3.2 11.4 - - - +
56J GLU* 3.7 35.7 - - + +
57J PHE* 4.4 3.1 - - - -
60J GLY 3.6 6.9 + - - +
61J VAL* 1.3 84.0 - - - +
63J GLY* 1.3 60.6 + - - +
77J LEU* 4.2 3.5 - - - +
78J PHE* 3.4 33.2 + - + +
93J THR* 5.0 8.3 - - + -
113J LEU* 4.3 21.4 - - - +
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Residues in contact with GLY 63 (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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54J LEU* 3.0 2.4 - - - -
55J VAL* 2.5 41.4 + - - +
57J PHE* 4.8 0.4 - - - -
62J LYS* 1.3 78.5 - - - +
64J MET* 1.3 57.6 + - - -
75J ILE* 3.8 11.9 - - - -
76J VAL 3.5 11.2 - - - -
77J LEU* 4.7 0.2 - - - -
78J PHE* 3.3 19.4 - - - -
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Residues in contact with MET 64 (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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52J GLU* 4.0 27.1 - - + +
53J GLU 3.5 15.5 - - - +
54J LEU* 4.2 6.7 - - + -
63J GLY* 1.3 75.1 - - - +
65J ALA* 1.3 58.4 + - - +
66J LEU* 3.6 30.3 - - + -
75J ILE* 3.1 4.5 - - - -
76J VAL* 2.8 47.7 + - + +
78J PHE* 3.5 28.0 - - + -
97J VAL* 4.0 20.4 - - + -
243J PRO* 5.4 1.1 - - - -
246J TYR* 4.9 7.2 - - + -
247J LEU* 4.3 15.7 - - + -
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Residues in contact with ALA 65 (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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49J ILE* 4.7 10.1 - - + -
50J GLN 4.9 0.9 - - - +
51J ALA* 4.4 2.1 - - - -
52J GLU* 2.9 30.2 + - - -
53J GLU 3.2 13.5 + - - +
55J VAL* 5.7 0.4 - - + -
64J MET* 1.3 72.8 - - - +
66J LEU* 1.3 61.6 - - - +
68J LEU* 4.2 10.2 - - + +
73J VAL* 3.5 31.2 - - + -
74J GLY 3.2 4.9 - - - +
75J ILE* 3.7 10.7 - - + +
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Residues in contact with LEU 66 (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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51J ALA* 5.9 2.5 - - - +
52J GLU* 4.0 18.4 - - + +
64J MET* 3.6 29.8 + - + -
65J ALA* 1.3 75.9 - - - +
67J ASN* 1.3 61.4 + - - +
68J LEU* 3.8 4.1 + - - +
74J GLY 2.8 5.4 + - - +
76J VAL* 3.7 34.1 - - + -
246J TYR* 5.1 13.5 - - + +
280J TYR* 5.8 7.4 - - + -
283J LEU* 4.2 17.0 - - + -
287J LEU* 4.0 14.4 - - + -
289J ARG* 3.0 31.3 + - - +
16N VAL* 4.1 6.4 - - - +
18N GLY 4.3 4.5 + - - -
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Residues in contact with ASN 67 (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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66J LEU* 1.3 75.3 - - - +
68J LEU* 1.3 63.8 + - - +
69J GLU* 3.4 26.0 + - - +
73J VAL* 3.5 0.9 - - - -
74J GLY* 2.6 41.4 + - - -
287J LEU* 3.3 40.6 + - + +
289J ARG* 2.8 41.9 + - - +
17N ILE* 3.3 24.3 - - + +
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Residues in contact with LEU 68 (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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49J ILE* 3.6 30.3 - - + +
50J GLN 4.1 4.3 - - - +
51J ALA* 3.7 18.6 - - + +
65J ALA* 4.2 13.7 - - + +
66J LEU 3.8 1.8 + - - +
67J ASN* 1.3 70.0 - - - +
69J GLU* 1.3 63.1 + - - +
72J GLN 4.5 1.1 - - - -
73J VAL* 3.7 20.4 - - + -
15N ALA* 3.0 5.4 - - - +
16N VAL* 2.8 63.1 + - + +
17N ILE* 4.6 0.5 - - - +
70N LEU 3.4 25.6 - - - +
72N ARG* 4.2 19.3 - - + +
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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