Contacts of the strand formed by residues 84 - 89 (chain F) in PDB entry 1F9N
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 PHE 84 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ILE* 4.4 17.0 - - + -
11A ARG* 3.6 35.5 + - - +
64A LEU* 3.2 18.0 - - - +
80F LEU* 2.9 41.9 + - + +
82F ASP 3.9 0.6 - - - -
83F ALA* 1.3 78.3 - - - +
85F VAL* 1.3 62.6 + - - +
86F LYS* 3.4 39.5 - - - -
87F ILE* 3.6 26.9 - - + -
96F LEU* 3.8 20.6 - - + -
97F LYS 4.2 2.7 - - - -
98F THR* 4.6 2.2 - - - +
145F LEU* 6.1 1.3 - - + -
146F LEU* 3.9 14.6 - - + -
149F LEU* 3.7 13.9 - - + -
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Residues in contact with VAL 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 4.7 7.6 - - - +
11A ARG* 4.4 17.3 - - - +
12A GLU* 4.8 7.5 + - + +
15A THR* 3.9 31.6 - - + +
64A LEU* 4.7 0.7 - - + -
83F ALA 3.3 14.6 - - - +
84F PHE* 1.3 82.7 - - - +
86F LYS* 1.3 70.0 + - + +
97F LYS* 3.1 19.5 + - + +
98F THR 3.4 20.6 - - - +
99F MET* 3.5 18.4 - - - +
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Residues in contact with LYS 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 5.6 3.4 - - + -
12A GLU* 5.5 12.1 - - + +
119D MET* 6.2 0.8 - - - +
133D ARG* 4.3 7.9 - - - +
84F PHE* 3.4 11.7 - - - -
85F VAL* 1.3 87.8 - - + +
87F ILE* 1.3 83.1 + - - +
88F ASP* 3.1 31.4 + - + +
95F VAL 4.8 0.2 - - - -
96F LEU* 3.5 6.4 - - - +
97F LYS* 3.0 38.6 + - + +
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Residues in contact with ILE 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F PHE* 3.6 12.6 - - + -
86F LYS* 1.3 90.9 - - - +
88F ASP* 1.3 66.9 + - - +
94F ILE* 4.0 23.6 - - + -
95F VAL 3.5 7.2 - - - +
96F LEU* 4.4 9.4 - - + -
142F LYS* 4.0 42.0 - - + +
145F LEU* 4.6 15.3 - - + -
146F LEU* 3.6 34.1 - - + -
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Residues in contact with ASP 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D MET* 3.3 24.9 - - + +
133D ARG* 2.6 34.5 + - - -
86F LYS* 3.1 22.3 + - + +
87F ILE* 1.3 76.9 - - - +
89F SER* 1.3 81.6 + - - +
94F ILE* 3.4 8.0 - - - +
95F VAL* 2.8 37.4 + - + +
142F LYS* 4.7 3.8 - - - +
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Residues in contact with SER 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D MET* 4.0 6.4 - - - +
133D ARG* 5.2 3.3 - - - +
88F ASP* 1.3 93.4 + - - +
90F ALA* 1.3 63.1 + - - +
93F MET 3.3 10.1 - - - -
94F ILE* 4.1 9.9 - - - +
138F THR* 4.3 7.9 - - - -
142F LYS* 2.7 42.8 + - - +
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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