Contacts of the helix formed by residues 72 - 81 (chain B) in PDB entry 1FSJ
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 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B ASN 3.7 2.6 + - - -
71B LEU* 1.3 76.6 - - - +
73B PRO* 1.3 77.2 - - + +
74B SER* 3.3 10.8 + - - -
75B ASN* 2.8 48.7 + - - +
76B LYS* 2.8 21.5 + - - +
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Residues in contact with PRO 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU 4.7 0.2 - - - +
72B ASN* 1.3 88.8 - - + +
74B SER* 1.3 62.7 + - - +
76B LYS* 3.3 10.6 + - + +
77B SER* 3.0 23.0 + - - -
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Residues in contact with SER 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ASN* 3.3 10.1 + - - -
73B PRO* 1.3 79.5 - - - +
75B ASN* 1.3 61.8 + - - +
77B SER* 3.2 8.9 + - - -
78B SER* 3.0 31.1 + - - -
86B PHE* 5.4 9.1 - - - -
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Residues in contact with ASN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU* 4.2 19.2 - - + +
72B ASN* 2.8 31.1 + - - +
74B SER* 1.3 77.5 + - - +
76B LYS* 1.3 64.3 + - - +
78B SER* 3.3 9.3 + - - -
79B VAL* 3.0 28.6 + - - +
85B PRO* 3.5 18.8 - - + +
86B PHE* 3.0 55.7 + - - +
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Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B SER* 4.7 1.2 - - - -
68B SER* 3.2 29.9 + - - +
69B LYS* 3.4 13.6 + - - +
71B LEU* 2.9 36.1 + - + +
72B ASN 2.8 20.0 + - - +
73B PRO* 3.7 8.1 - - + +
75B ASN* 1.3 76.5 - - - +
77B SER* 1.3 62.5 + - - +
79B VAL* 3.4 11.4 - - - +
80B SER* 3.2 23.7 + - - -
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Residues in contact with SER 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B PRO 3.0 13.5 + - - -
74B SER* 3.5 11.2 - - - -
75B ASN 3.2 0.2 - - - -
76B LYS* 1.3 76.8 - - - +
78B SER* 1.3 62.3 + - - +
80B SER* 2.9 21.4 + - - -
81B LYS* 3.0 39.7 + - - -
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B SER* 3.0 19.9 + - - -
75B ASN* 3.5 17.0 + - - -
77B SER* 1.3 78.0 - - - +
79B VAL* 1.3 63.8 + - - +
81B LYS* 3.1 12.5 + - - +
83B TYR* 3.0 47.8 + - - +
84B SER 4.6 7.5 + - - -
85B PRO* 4.8 1.6 - - - -
86B PHE* 6.0 1.9 - - - -
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B TRP* 3.2 42.0 - - + +
59B GLU* 3.5 3.3 - - - -
61B VAL* 4.9 0.9 - - + -
62B SER* 3.6 20.6 - - - +
68B SER* 5.3 0.7 - - - -
71B LEU* 3.8 20.9 - - + -
75B ASN 3.0 19.7 + - - +
76B LYS* 3.4 16.2 - - - +
78B SER* 1.3 76.5 - - - +
80B SER* 1.3 62.8 + - - +
82B GLY 3.0 9.9 + - - +
83B TYR 3.5 17.7 - - - +
85B PRO* 3.7 25.4 - - + -
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Residues in contact with SER 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLU* 4.0 11.1 - - - +
62B SER* 3.5 19.0 + - - -
76B LYS 3.2 14.0 + - - -
77B SER* 2.9 20.0 + - - -
79B VAL* 1.3 77.5 - - - +
81B LYS* 1.3 68.7 + - - +
82B GLY 3.8 0.2 + - - -
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LYS* 4.0 14.6 - - - -
59B GLU* 4.3 5.2 - - - -
77B SER* 3.0 39.7 + - - +
78B SER* 3.1 9.2 + - - +
80B SER* 1.3 85.5 + - - +
82B GLY* 1.3 58.1 + - - +
83B TYR* 3.3 29.9 + - + -
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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