Contacts of the strand formed by residues 93 - 98 (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 MET 93 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D SER* 4.8 9.9 - - - +
92D HIS* 5.2 12.3 - - + -
93D MET* 4.0 22.9 - - + +
119D MET* 6.2 1.1 - - - -
131D ILE* 3.6 38.6 - - + -
91E SER* 5.4 4.5 - - - +
92E HIS* 5.4 8.1 - - + -
93E MET* 3.6 34.5 - - + -
89F SER* 3.3 2.3 - - - -
90F ALA* 2.7 45.4 + - + +
91F SER* 5.4 3.4 - - - +
92F HIS* 1.3 86.3 - - + +
94F ILE* 1.3 66.4 + - - +
95F VAL* 5.6 0.9 - - + -
129F LEU* 4.2 10.8 - - + -
130F ILE 3.5 3.1 - - - +
131F ILE* 4.9 0.9 - - + -
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Residues in contact with ILE 94 (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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87F ILE* 4.0 22.9 - - + -
88F ASP 3.4 12.6 - - - +
89F SER* 4.1 5.8 - - - -
93F MET* 1.3 81.4 - - - +
95F VAL* 1.3 65.8 - - - +
96F LEU 4.6 0.4 - - - +
128F ILE 3.3 3.6 - - - +
129F LEU* 3.6 3.3 - - - +
130F ILE* 2.9 59.3 + - + +
132F CYS* 4.1 15.0 - - - -
138F THR* 3.4 37.0 - - + +
141F VAL* 4.1 9.9 - - + -
142F LYS* 4.1 17.7 - - + +
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Residues in contact with VAL 95 (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* 3.8 37.7 - - + +
120D GLY* 4.3 4.3 - - - +
131D ILE* 4.2 23.6 - - + -
87F ILE* 3.5 1.7 - - - -
88F ASP* 2.8 42.8 + - + +
89F SER* 4.8 0.2 - - - +
93F MET* 5.6 1.3 - - + -
94F ILE* 1.3 75.8 - - - +
96F LEU* 1.3 60.3 + - - +
97F LYS* 3.7 32.1 + - + +
127F THR* 4.2 11.2 - - - +
128F ILE 3.6 3.6 - - - +
129F LEU* 5.3 7.6 - - + -
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Residues in contact with LEU 96 (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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80F LEU* 3.8 22.2 - - + -
84F PHE* 3.8 20.6 - - + -
86F LYS 3.5 10.5 - - - +
87F ILE* 4.3 11.0 - - + +
94F ILE* 4.0 0.8 - - + -
95F VAL* 1.3 71.8 - - - +
97F LYS* 1.3 79.2 + - - +
98F THR* 3.3 21.6 + - + +
110F MET* 5.0 7.4 - - - -
126F ASP 3.9 0.2 - - - +
127F THR* 3.3 3.7 - - - -
128F ILE* 2.9 50.4 + - + +
130F ILE* 4.7 12.1 - - + -
145F LEU* 4.3 23.3 - - + -
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Residues in contact with LYS 97 (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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111D ASP* 5.3 7.9 + - - -
119D MET 2.9 28.4 + - - -
120D GLY* 4.2 6.4 - - - -
85F VAL* 3.1 28.2 + - + -
86F LYS* 3.0 36.5 + - + +
95F VAL* 3.7 13.9 + - + +
96F LEU* 1.3 77.7 - - - +
98F THR* 1.3 61.3 + - - +
126F ASP* 3.3 12.6 - - - +
127F THR* 3.5 35.0 - - + -
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Residues in contact with THR 98 (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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80F LEU* 5.0 0.2 - - + -
83F ALA* 3.2 22.9 - - - +
84F PHE* 4.6 0.9 - - - -
85F VAL* 3.4 9.6 - - - +
96F LEU* 3.3 25.1 - - + +
97F LYS* 1.3 78.9 - - - +
99F MET* 1.3 73.3 + - - +
100F PRO* 3.7 1.0 - - - +
102F ASN* 3.9 1.1 - - - +
103F ALA* 3.5 24.6 + - + +
106F ILE* 4.2 19.1 - - + -
126F ASP* 2.7 26.9 + - - +
128F ILE* 4.9 3.8 - - + -
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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