Contacts of the helix formed by residues 93 - 99 (chain C) in PDB entry 1FBA
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 93 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C ARG* 3.3 33.7 - - + -
59C ARG* 4.0 8.1 - - + -
60C GLN* 3.7 27.1 - - + -
63C PHE* 3.6 23.3 - + + -
78C LEU* 6.1 2.2 - - + -
82C THR* 3.7 22.7 - - + +
85C GLN* 3.1 53.4 + - + +
86C LYS 3.9 3.1 - - - -
87C ALA* 3.9 23.3 - - + -
91C THR 3.3 1.6 + - - -
92C PRO* 1.3 71.4 - - - +
94C ALA* 1.3 62.9 - - - +
96C ILE* 3.2 17.9 + - + +
97C LEU* 3.0 28.9 + - + +
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Residues in contact with ALA 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C LEU* 5.6 2.0 - - - -
83C LEU* 4.2 25.7 + - + +
92C PRO* 3.1 6.0 - - + +
93C PHE* 1.3 78.3 - - - +
95C GLU* 1.3 57.1 + - - +
97C LEU* 3.7 3.0 + - - +
98C LYS* 3.0 38.1 + - + +
104C LEU* 3.7 26.4 - - + +
140C ASP 4.7 7.0 - - - +
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Residues in contact with GLU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C THR* 3.3 21.7 - - + +
92C PRO* 2.8 31.2 + - + +
94C ALA* 1.3 77.8 - - - +
96C ILE* 1.3 65.5 + - - +
98C LYS* 3.4 4.6 + - - +
99C LYS* 3.1 57.2 + - + +
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Residues in contact with ILE 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C GLN* 6.0 1.8 - - + -
63C PHE* 3.3 33.2 - - + +
64C SER* 4.9 8.3 - - - -
87C ALA* 3.8 18.6 - - + -
91C THR* 3.5 34.1 - - + +
92C PRO 3.0 12.2 + - - +
93C PHE* 3.2 22.0 + - + +
95C GLU* 1.3 78.9 - - - +
97C LEU* 1.3 65.3 + - - +
99C LYS* 3.4 11.4 + - - +
100C LYS* 3.5 25.9 + - - +
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Residues in contact with LEU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C PHE* 3.9 61.7 - - + +
69C LEU* 6.0 2.5 - - + -
76C VAL* 4.3 17.3 - - + -
78C LEU* 4.5 6.7 - - + -
93C PHE 3.0 19.4 + - - +
94C ALA 4.1 0.4 - - - +
96C ILE* 1.3 75.0 - - - +
98C LYS* 1.3 61.4 + - - +
100C LYS* 3.1 15.2 + - + +
101C GLY 3.4 0.2 + - - -
102C ILE* 3.0 48.0 + - + +
104C LEU* 3.8 29.4 - - + -
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Residues in contact with LYS 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ALA* 3.0 26.6 + - + +
95C GLU* 4.0 4.9 - - - +
96C ILE 3.3 0.2 - - - -
97C LEU* 1.3 73.9 - - - +
99C LYS* 1.3 60.3 + - - +
101C GLY* 2.9 19.4 + - - -
102C ILE 3.7 12.1 - - - +
103C ILE* 5.9 1.1 - - - +
104C LEU* 4.1 19.5 - - + +
141C GLY* 3.0 42.9 + - - -
143C ASP* 4.4 10.9 + - - -
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Residues in contact with LYS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C GLU* 3.1 50.2 + - + +
96C ILE* 3.7 7.0 - - - +
97C LEU 3.3 0.2 - - - -
98C LYS* 1.3 78.3 - - - +
100C LYS* 1.3 59.6 + - + +
101C GLY* 3.1 2.8 + - - -
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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