Contacts of the strand formed by residues 80 - 87 (chain J) in PDB entry 1FSK
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 80 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19J PHE* 4.3 0.7 - - - -
73J GLU* 4.4 6.5 - - - +
74J VAL* 3.7 0.9 - - - -
75J ASP* 2.8 45.2 + - + +
78J ASN* 3.1 7.5 + - + +
79J PHE* 1.3 77.1 - - - +
81J TYR* 1.3 66.0 + - - +
82J ASN* 3.7 17.0 - - - +
101J GLU* 2.9 44.5 + - + +
102J ILE 3.5 4.5 - - - +
103J LYS* 4.3 15.9 - - + +
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Residues in contact with TYR 81 (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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19J PHE* 4.1 7.4 - - + -
23J ILE* 3.5 49.4 - - + -
24J LEU* 5.7 0.4 - - + -
27J ASP* 4.6 13.2 + - - -
54J LYS* 5.5 2.8 + - - +
71J VAL* 4.0 30.3 - - + +
73J GLU 3.6 4.7 - - - -
74J VAL* 3.7 20.6 - - + -
80J LYS* 1.3 78.8 - - - +
82J ASN* 1.3 62.0 + - - +
83J TYR* 3.2 45.5 - + + +
101J GLU* 3.6 0.5 - - - -
102J ILE* 2.9 43.3 + - + +
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Residues in contact with ASN 82 (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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71J VAL* 3.9 3.5 - - - +
72J ASP* 3.0 26.4 + - + +
73J GLU* 2.9 45.2 + - + +
80J LYS* 3.7 11.9 - - - +
81J TYR* 1.3 82.6 - - - +
83J TYR* 1.3 65.4 + - - +
100J ASN 3.3 9.4 + - - +
101J GLU* 3.1 37.3 + - - +
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Residues in contact with TYR 83 (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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69J ASP* 3.3 37.9 - - + -
70J ARG 3.3 15.0 - - - +
71J VAL* 4.1 0.9 - - - -
72J ASP* 3.1 13.9 + - - -
81J TYR* 3.2 38.1 - + - +
82J ASN* 1.3 78.3 - - - +
84J SER* 1.3 61.7 + - - +
85J VAL* 4.4 3.5 - - + +
99J SER* 3.7 0.5 - - - -
100J ASN* 2.8 71.5 + - + +
102J ILE* 4.2 20.1 - - + +
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Residues in contact with SER 84 (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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69J ASP* 2.9 7.2 - - - -
70J ARG* 2.9 36.5 + - - -
72J ASP* 2.3 30.1 + - - -
83J TYR* 1.3 79.7 + - - +
85J VAL* 1.3 64.2 + - - +
86J ILE* 3.3 17.9 - - - +
97J LYS* 3.8 22.8 + - - -
98J ILE 3.2 10.1 - - - -
99J SER* 4.3 4.0 - - - -
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Residues in contact with VAL 85 (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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67J VAL* 3.3 31.4 - - + -
68J LYS 3.7 3.6 - - - -
69J ASP* 4.0 14.1 - - - +
83J TYR* 4.4 1.8 - - + +
84J SER* 1.3 73.1 - - - +
86J ILE* 1.3 65.3 + - - +
90J PRO* 4.3 9.4 - - + -
91J ILE* 3.6 20.2 - - + -
97J LYS* 3.4 6.1 - - - +
98J ILE* 2.7 45.8 + - + +
100J ASN* 3.7 20.6 - - - +
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Residues in contact with ILE 86 (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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53J ILE* 4.6 6.5 - - + -
68J LYS* 2.8 30.5 + - + +
69J ASP 4.4 4.0 - - - +
70J ARG* 3.9 34.3 - - + +
84J SER* 3.3 24.0 - - - +
85J VAL* 1.3 81.1 - - - +
87J GLU* 1.3 64.4 + - + +
91J ILE* 3.9 15.5 - - - +
96J GLU 4.5 1.9 - - - +
97J LYS* 4.6 12.5 - - + +
31L SER* 5.5 2.5 - - - +
52L PHE* 4.0 27.1 - - + -
54L SER* 5.9 1.8 - - - +
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Residues in contact with GLU 87 (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 TYR* 3.0 22.5 + - - +
67J VAL* 3.3 1.4 - - - +
68J LYS* 2.9 67.2 + - + +
86J ILE* 1.3 86.7 - - + +
88J GLY* 1.3 73.2 + - - +
91J ILE* 3.9 8.3 - - - +
28L THR* 5.5 0.5 - - - +
31L SER* 3.6 19.6 + - - -
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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