Contacts of the strand formed by residues 93 - 98 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93D MET* 4.4 15.3 - - + -
129D LEU* 4.6 1.6 - - - -
89E SER* 3.4 0.3 - - - -
90E ALA* 2.8 34.8 + - - +
91E SER* 5.9 1.8 - - - +
92E HIS* 1.3 89.7 - - + +
94E ILE* 1.3 64.6 + - - +
129E LEU* 3.8 31.2 - - + -
130E ILE 3.3 4.3 - - - +
131E ILE* 4.5 6.5 - - + -
138E THR* 4.2 0.2 - - - +
93F MET* 3.6 40.2 - - + -
119F MET* 3.3 7.3 - - + +
129F LEU* 4.5 9.4 - - + -
131F ILE* 3.4 48.9 - - + -
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Residues in contact with ILE 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E ILE* 3.7 26.9 - - + -
88E ASP 3.4 12.3 - - - +
89E SER* 3.8 7.2 - - - -
93E MET* 1.3 73.9 - - - +
95E VAL* 1.3 66.8 + - - +
96E LEU* 4.8 0.4 - - + +
128E ILE 3.4 3.1 - - - +
129E LEU* 3.5 5.1 - - - +
130E ILE* 2.8 55.3 + - + +
132E CYS* 4.3 6.7 - - - -
138E THR* 3.5 41.5 - - + +
141E VAL* 4.1 16.6 - - + -
142E LYS* 4.0 17.3 - - + +
145E LEU* 5.1 0.9 - - + -
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Residues in contact with VAL 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E LYS* 4.2 0.5 + - - +
87E ILE* 3.5 4.0 - - - +
88E ASP* 2.7 36.2 + - + +
94E ILE* 1.3 75.0 - - - +
96E LEU* 1.3 62.2 + - - +
97E LYS* 4.2 17.3 + - + +
127E THR* 4.1 21.1 - - + -
128E ILE 3.6 3.4 - - - +
129E LEU* 5.1 3.1 - - + -
119F MET* 3.2 37.2 - - + +
120F GLY* 4.7 14.6 - - - -
121F THR 6.0 0.4 - - - +
122F ILE* 5.0 14.1 - - + -
131F ILE* 4.9 9.0 - - + -
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Residues in contact with LEU 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E LEU* 4.0 23.1 - - + -
84E PHE* 3.3 34.8 - - + -
86E LYS 3.3 11.9 - - - +
87E ILE* 3.6 15.7 - - + -
94E ILE* 4.1 0.6 - - + -
95E VAL* 1.3 74.9 - - - +
97E LYS* 1.3 67.8 + - - +
98E THR* 4.1 11.3 + - + +
106E ILE* 4.8 3.8 - - + -
110E MET* 5.0 2.7 - - - -
126E ASP 3.8 0.2 - - - +
127E THR* 3.4 4.0 - - - -
128E ILE* 2.9 58.7 + - + +
130E ILE* 4.8 18.8 - - + -
145E LEU* 5.0 8.3 - - + -
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Residues in contact with LYS 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E VAL* 3.2 26.0 + - + -
86E LYS* 2.9 47.5 + - + +
95E VAL* 4.3 14.0 - - + +
96E LEU* 1.3 76.2 - - - +
98E THR* 1.3 67.6 + - - +
126E ASP* 3.3 10.3 + - - +
127E THR* 2.6 41.0 + - + +
111F ASP* 4.8 11.8 + - - -
121F THR 5.6 3.0 + - - -
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Residues in contact with THR 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E LEU* 5.4 2.0 - - + -
83E ALA* 3.2 24.2 - - + +
84E PHE* 5.0 2.7 - - - +
85E VAL* 3.5 8.9 - - - +
96E LEU* 4.3 21.3 - - + +
97E LYS* 1.3 81.4 - - - +
99E MET* 1.3 73.6 + - - +
100E PRO* 3.4 3.3 - - - +
102E ASN* 3.8 1.7 - - - +
103E ALA* 3.6 17.8 + - - -
106E ILE* 4.6 10.3 - - + -
126E ASP* 2.9 25.0 + - - +
128E ILE* 4.4 16.6 - - + -
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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