Contacts of the strand formed by residues 84 - 89 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B LEU* 2.7 41.8 + - + +
83B ALA* 1.3 71.2 - - - +
85B VAL* 1.3 60.7 + - - +
86B LYS* 3.8 13.0 - - - -
87B ILE* 3.5 41.3 - - + -
96B LEU* 3.3 30.1 - - + -
97B LYS 4.3 2.7 - - - -
98B THR* 4.8 4.4 - - - +
145B LEU* 5.8 5.6 - - + -
146B LEU* 4.1 13.0 - - + -
149B LEU* 3.7 27.4 - - + -
8E ILE* 4.6 14.1 - - + -
11E ARG* 2.8 46.1 + - - +
64E LEU* 3.3 6.6 - - - +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ALA 3.2 15.9 - - - +
84B PHE* 1.3 80.4 - - - +
86B LYS* 1.3 70.3 + - + +
97B LYS* 3.0 20.9 + - + +
98B THR 3.6 18.2 - - - +
99B MET* 3.7 18.8 - - - +
8E ILE* 4.6 3.3 - - - +
11E ARG* 3.9 23.6 - - - +
12E GLU* 4.2 6.8 + - + +
15E THR* 3.7 33.9 - - + +
64E LEU* 4.2 5.2 - - + -
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Residues in contact with LYS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PHE* 3.8 10.0 - - - -
85B VAL* 1.3 90.6 - - + +
87B ILE* 1.3 72.0 + - - +
88B ASP* 4.8 13.7 + - - -
95B VAL 4.0 0.8 - - - +
96B LEU* 3.3 5.2 - - - +
97B LYS* 2.7 45.7 + - + -
8E ILE* 6.2 0.9 - - - -
12E GLU* 4.3 28.1 + - + +
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Residues in contact with ILE 87 (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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84B PHE* 3.5 28.5 - - + -
86B LYS* 1.3 86.6 - - - +
88B ASP* 1.3 69.8 + - - +
94B ILE* 3.8 24.7 - - + -
95B VAL 3.5 6.3 - - - +
96B LEU* 4.2 7.2 - - + -
142B LYS* 3.8 35.2 - - + +
145B LEU* 4.3 21.1 - - + -
146B LEU* 4.2 15.9 - - + -
8E ILE* 6.4 1.1 - - + -
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Residues in contact with ASP 88 (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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86B LYS* 4.8 15.3 + - - -
87B ILE* 1.3 78.5 - - - +
89B SER* 1.3 76.9 + - - +
94B ILE* 3.3 7.1 - - - +
95B VAL* 2.9 35.2 + - + +
142B LYS* 4.9 2.9 - - - -
119C MET* 3.9 28.7 - - - +
133C ARG* 3.4 36.7 + - - -
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Residues in contact with SER 89 (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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88B ASP* 1.3 89.4 + - - +
90B ALA* 1.3 60.1 + - - +
93B MET 3.4 9.0 - - - -
94B ILE* 4.3 4.3 - - - -
138B THR* 4.1 17.0 - - - -
139B GLU* 4.0 10.8 + - - +
142B LYS* 3.2 38.2 + - - +
119C MET* 3.6 4.5 - - - -
133C ARG* 3.6 10.7 + - - -
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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