Contacts of the helix formed by residues 90 - 100 (chain C) in PDB entry 5DO7
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 SER 90 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C ILE* 4.6 10.2 - - - +
87C SER 2.8 11.0 + - - -
88C SER 2.8 18.4 + - - -
89C GLY* 1.3 66.5 - - - -
91C GLY* 1.3 57.9 + - - +
92C LYS* 3.8 8.7 - - - +
93C THR* 2.1 33.7 + - - +
94C THR* 2.7 26.2 + - - -
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Residues in contact with GLY 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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68C ILE* 4.9 2.7 - - - +
69C LEU* 4.2 6.0 - - - +
86C GLY* 5.8 0.4 - - - -
87C SER 4.9 0.2 + - - -
89C GLY 2.4 19.1 + - - -
90C SER* 1.3 68.8 - - - +
92C LYS* 1.3 66.4 + - - +
94C THR* 2.8 14.2 + - - -
95C LEU* 2.9 15.1 + - - +
266C LEU* 3.7 21.8 - - - +
269C GLY* 4.1 17.2 - - - +
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Residues in contact with LYS 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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84C ILE* 4.0 16.4 - - + +
85C LEU 4.5 0.4 - - - -
86C GLY* 3.4 48.6 - - - +
87C SER 4.7 2.0 - - - -
88C SER* 5.7 3.6 - - - +
90C SER* 4.5 5.3 - - - +
91C GLY* 1.3 77.0 - - - +
93C THR* 1.3 90.3 + - + +
95C LEU* 3.6 3.6 + - - +
96C LEU* 3.4 21.5 + - - +
218C GLU* 2.7 34.8 + - - +
248C THR* 3.6 30.3 - - + +
249C ILE 4.6 0.7 - - - +
250C HIS* 4.7 22.9 - - - +
266C LEU* 3.8 12.6 - - - +
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Residues in contact with THR 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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90C SER* 2.1 38.5 + - - +
92C LYS* 1.3 107.9 - - + +
94C THR* 1.3 58.8 + - - +
96C LEU* 3.8 2.1 - - - +
97C ASP* 2.4 36.7 + - - +
134C GLN* 5.5 3.8 - - - +
217C ASP* 4.4 15.3 - - - +
218C GLU* 4.3 14.6 - - - +
248C THR* 4.8 1.1 - - - -
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Residues in contact with THR 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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45C TYR* 4.5 15.3 - - + -
68C ILE* 3.8 36.1 - - + +
69C LEU* 5.3 3.6 - - + -
90C SER* 2.7 29.5 + - - -
91C GLY* 2.8 7.2 + - - -
93C THR* 1.3 74.9 + - - +
95C LEU* 1.3 66.6 + - - +
97C ASP* 3.5 6.7 + - - +
98C ALA* 2.9 23.1 + - + +
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Residues in contact with LEU 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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40C ILE* 5.3 6.7 - - + -
69C LEU* 3.3 30.4 - - + +
72C VAL* 5.1 11.9 - - + -
84C ILE* 5.0 17.3 - - + -
91C GLY 2.9 10.5 + - - +
92C LYS* 4.1 6.7 - - - +
94C THR* 1.3 73.8 - - - +
96C LEU* 1.3 74.7 + - + +
98C ALA* 2.8 6.9 + - - +
99C MET* 2.8 56.6 + - + +
246C VAL* 6.2 0.2 - - + -
266C LEU* 3.5 33.7 - - + -
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Residues in contact with LEU 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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84C ILE* 5.2 1.1 - - + -
92C LYS 3.4 15.1 + - - +
93C THR 3.8 2.2 - - - +
94C THR 3.3 0.6 - - - -
95C LEU* 1.3 89.9 - - + +
97C ASP* 1.3 67.3 + - - +
99C MET* 3.4 12.2 + - + +
100C SER* 3.4 15.9 + - - -
131C TYR* 4.2 7.9 - - + -
215C LEU* 3.7 35.8 - - + +
216C PHE 3.6 26.9 - - - +
217C ASP* 4.0 11.9 - - + -
246C VAL* 4.2 13.9 - - + +
247C LEU 4.9 0.2 - - - -
248C THR* 3.5 28.5 - - + +
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Residues in contact with ASP 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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93C THR* 2.4 31.5 + - - +
94C THR* 3.6 8.2 - - - +
96C LEU* 1.3 77.5 - - - +
98C ALA* 1.3 66.2 - - - +
100C SER* 2.6 26.1 + - - -
101C GLY 3.5 1.9 + - - -
102C ARG* 3.1 44.5 + - + -
103C LEU 6.0 0.2 - - - +
131C TYR* 2.6 26.6 + - - -
134C GLN* 5.0 2.7 - - - +
217C ASP* 3.7 12.2 - - - +
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Residues in contact with ALA 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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45C TYR* 4.9 22.0 - - + -
69C LEU* 5.5 2.5 - - + -
94C THR* 2.9 16.6 + - + +
95C LEU* 2.8 19.0 + - - +
97C ASP* 1.3 71.0 - - - +
99C MET* 1.3 53.7 + - + +
101C GLY* 2.8 29.1 + - - -
103C LEU 4.0 18.8 - - - +
109C PHE* 5.6 9.6 - - + -
122C ARG* 4.9 4.3 + - - -
125C PHE* 5.1 4.1 - - - -
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Residues in contact with MET 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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38C LEU* 6.3 2.2 - - + -
40C ILE* 4.1 23.1 - - + -
95C LEU* 2.8 38.6 + - + +
96C LEU* 3.6 18.8 - - + +
98C ALA* 1.3 73.9 - - + +
100C SER* 1.3 57.0 + - - +
101C GLY 3.0 0.6 + - - -
109C PHE* 6.1 5.6 - - + -
113C VAL* 5.4 9.9 - - + -
125C PHE* 2.7 42.5 - - + -
129C PHE* 3.6 18.3 - - + -
215C LEU* 3.8 31.9 - - + -
246C VAL* 5.2 5.6 - - + -
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Residues in contact with SER 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C LEU 3.4 4.1 + - - -
97C ASP* 2.6 26.2 + - - -
99C MET* 1.3 73.5 - - - +
101C GLY* 1.3 57.6 + - - +
102C ARG* 3.3 8.3 + - - +
125C PHE* 4.3 4.0 - - - -
126C GLN* 4.2 21.4 - - - +
129C PHE* 4.7 8.7 - - - +
131C TYR* 3.7 37.2 - - - -
215C LEU* 3.9 21.1 - - - +
454C GLN 5.7 0.9 - - - +
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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