Contacts of the helix formed by residues 90 - 100 (chain C) in PDB entry 2JIF
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 GLU 90 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79C LEU* 4.1 23.1 - - + -
82C THR* 5.2 6.9 - - + +
83C MET* 3.4 27.9 - - + +
88C LYS* 4.4 24.9 + - - +
89C MET* 1.3 74.7 - - - +
91C LYS* 1.3 69.7 + - - +
92C SER* 3.7 18.3 + - - +
93C VAL* 3.1 14.9 + - + +
94C ILE* 3.1 13.1 + - - +
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Residues in contact with LYS 91 (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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88C LYS* 6.2 0.6 - - - +
89C MET 3.7 2.8 + - - -
90C GLU* 1.3 76.8 + - - +
92C SER* 1.3 53.9 + - - +
94C ILE* 4.2 20.8 - - + +
95C GLN* 2.8 65.3 + - + +
169C GLU 5.6 3.8 + - - -
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Residues in contact with SER 92 (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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71C PHE* 5.3 0.9 - - - -
75C GLN* 4.7 17.8 + - - +
79C LEU* 3.6 24.4 - - - +
90C GLU* 3.7 7.7 + - - +
91C LYS* 1.3 77.9 - - - +
93C VAL* 1.3 58.7 + - - +
95C GLN* 4.4 2.6 - - - +
96C GLY* 3.0 25.5 + - - -
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Residues in contact with VAL 93 (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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71C PHE* 3.9 7.2 - - + -
75C GLN* 3.7 23.3 - - - +
76C ILE* 4.2 14.1 - - + -
79C LEU* 3.8 18.4 - - + -
83C MET* 4.1 17.5 - - + -
89C MET* 4.4 9.6 - - + -
90C GLU* 3.1 9.0 + - + +
92C SER* 1.3 72.6 + - - +
94C ILE* 1.3 61.1 + - - +
96C GLY* 3.2 1.7 + - - -
97C LEU* 2.9 30.2 + - + +
135C VAL* 3.8 39.9 - - + -
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Residues in contact with ILE 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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89C MET* 3.8 40.2 - - + +
90C GLU 3.1 18.1 + - - +
91C LYS* 3.7 21.8 - - + +
93C VAL* 1.3 75.2 - - - +
95C GLN* 1.3 67.5 + - - +
97C LEU* 3.2 14.7 + - - +
98C PHE* 3.2 32.5 + - + -
138C PHE* 3.8 32.5 - - + -
171C VAL* 4.8 4.5 - - + -
213C HIS* 5.8 9.0 - - + -
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Residues in contact with GLN 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 LYS* 2.8 49.1 + - + +
92C SER* 4.4 2.5 - - - +
94C ILE* 1.3 75.5 - - - +
96C GLY* 1.3 56.2 + - - +
98C PHE* 3.4 17.0 + - - +
99C GLN* 2.9 45.9 + - - +
168C THR 3.6 22.4 + - - -
169C GLU* 4.4 11.5 - - - +
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Residues in contact with GLY 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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71C PHE* 3.6 19.7 - - - -
92C SER 3.0 20.6 + - - -
93C VAL 3.2 2.2 + - - -
95C GLN* 1.3 75.7 - - - +
97C LEU* 1.3 56.4 - - - +
99C GLN* 3.4 13.6 + - - +
100C GLN* 2.9 36.1 + - - +
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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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71C PHE* 3.7 21.0 - - + -
93C VAL* 2.9 19.3 + - + +
94C ILE* 3.2 7.4 + - - +
96C GLY* 1.3 75.6 - - - +
98C PHE* 1.3 59.9 + - - +
100C GLN* 3.5 1.2 + - - -
101C GLY 3.4 2.4 + - - -
102C LEU* 2.9 50.9 + - + +
103C MET* 4.0 17.0 - - + -
128C LEU* 4.0 22.4 - - + -
135C VAL* 3.8 20.6 - - + +
138C PHE* 3.4 36.6 - - + -
139C CYS* 4.7 3.6 - - + -
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Residues in contact with PHE 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 ILE* 3.2 41.0 + - + -
95C GLN* 3.7 19.3 - - - +
96C GLY 3.4 0.2 - - - -
97C LEU* 1.3 77.2 - - - +
99C GLN* 1.3 64.3 + - - +
101C GLY* 3.0 15.4 + - - -
103C MET* 3.6 36.6 - - + -
142C GLN* 3.9 0.2 - - - -
166C LEU 3.3 22.7 - - - -
167C THR 3.7 14.6 - - - +
168C THR* 3.3 30.5 - - - +
169C GLU* 3.6 24.5 - - - -
170C LYS 3.6 18.8 - - - -
171C VAL* 4.0 7.2 - - + -
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Residues in contact with GLN 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 GLN* 2.9 29.0 + - - +
96C GLY* 3.5 14.9 + - - +
98C PHE* 1.3 75.9 - - - +
100C GLN* 1.3 64.7 + - + +
101C GLY 3.1 3.9 + - - -
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Residues in contact with GLN 100 (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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67C SER* 4.4 18.0 + - - -
68C VAL* 6.3 0.2 - - - +
71C PHE* 3.8 38.8 - - + +
96C GLY* 2.9 21.0 + - - +
97C LEU 4.0 0.2 - - - +
98C PHE 3.2 0.4 - - - -
99C GLN* 1.3 79.8 - - + +
101C GLY* 1.3 60.4 + - - +
102C LEU* 3.5 28.1 + - + +
114C THR* 5.1 0.5 + - - +
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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