Contacts of the helix formed by residues 80 - 91 (chain C) in PDB entry 3OP5
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 LEU 80 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73C GLU* 4.9 17.7 - - + -
81C PHE* 1.4 58.4 + - - +
82C THR* 3.4 5.5 - - - +
83C GLU* 3.9 11.5 - - - +
84C LEU* 2.8 35.8 + - - +
127C ARG* 5.2 11.7 - - + -
129C MET* 3.5 24.2 - - + +
199C GLY* 5.1 7.5 + - - -
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Residues in contact with PHE 81 (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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80C LEU* 1.4 76.4 - - - +
82C THR* 1.4 61.2 + - - +
84C LEU* 3.5 11.6 + - + +
85C LYS* 3.0 32.5 + - + +
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Residues in contact with THR 82 (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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80C LEU 4.4 2.0 - - - +
81C PHE* 1.4 78.3 - - - +
83C GLU* 1.4 57.3 + - - +
85C LYS* 3.4 6.8 + - - +
86C PHE* 3.1 26.5 + - - +
173C TYR* 5.1 4.7 + - + -
198C TYR 3.7 6.3 - - - +
199C GLY 3.4 25.8 + - - +
200C LEU* 4.6 0.9 - - - -
201C ALA* 3.5 25.6 - - + +
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Residues in contact with GLU 83 (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 LYS* 4.5 13.7 - - - +
80C LEU* 3.5 12.7 + - - +
81C PHE 3.4 0.2 - - - -
82C THR* 1.4 75.6 - - - +
84C LEU* 1.3 64.8 + - - +
86C PHE* 3.3 2.9 + - - +
87C TYR* 3.1 54.1 + - + -
129C MET* 3.6 20.7 - - + +
197C ASP* 3.4 14.3 + - - -
198C TYR* 2.9 44.5 + - + +
199C GLY* 3.8 9.9 - - - +
365C REB 4.9 5.0 + - - -
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Residues in contact with LEU 84 (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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80C LEU 2.8 22.2 + - - +
81C PHE* 3.8 11.4 - - + +
83C GLU* 1.3 72.0 - - - +
85C LYS* 1.4 56.7 + - - +
87C TYR* 3.4 2.1 + - - -
88C GLN* 2.9 50.9 + - - +
113C TYR* 3.2 44.2 - - + +
116C SER* 3.6 20.9 - - - +
129C MET* 4.1 12.7 - - + -
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Residues in contact with LYS 85 (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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81C PHE* 3.0 26.6 + - + +
82C THR* 3.7 7.2 - - - +
83C GLU 3.3 0.2 - - - -
84C LEU* 1.4 76.1 - - - +
86C PHE* 1.4 55.5 + - - +
88C GLN* 3.9 9.5 - - - +
89C ARG* 3.0 34.1 + - - +
173C TYR* 3.8 10.3 - - - +
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Residues in contact with PHE 86 (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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82C THR 3.1 13.5 + - - +
83C GLU 3.3 6.7 + - - +
85C LYS* 1.4 76.2 - - - +
87C TYR* 1.3 75.0 + + - +
89C ARG 3.3 0.5 + - - -
90C ALA* 2.8 52.8 + - + +
91C ALA* 4.3 4.7 - - + -
110C VAL* 4.4 9.2 - - + -
168C ILE* 3.7 26.2 - - + -
173C TYR* 3.6 48.2 + + + -
198C TYR* 3.4 62.1 - + + -
201C ALA* 4.7 2.7 - - + -
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Residues in contact with TYR 87 (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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83C GLU* 3.1 46.8 + - + +
84C LEU 3.9 3.6 - - - +
86C PHE* 1.3 90.0 - + - +
88C GLN* 1.3 59.3 + - - +
91C ALA* 3.0 48.6 + - + +
92C LYS* 3.7 1.2 + - - +
111C PRO* 3.3 43.2 - - + +
113C TYR* 3.6 33.3 - - + -
129C MET* 4.7 0.7 - - - -
131C MET* 3.7 26.0 - - + -
196C VAL* 4.7 0.9 - - - -
198C TYR* 3.4 27.9 - + - -
365C REB 3.8 11.9 + + - -
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Residues in contact with GLN 88 (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 LEU* 2.9 36.7 + - + +
85C LYS* 3.9 8.4 - - - +
87C TYR* 1.3 76.3 - - - +
89C ARG* 1.4 52.0 + - + +
92C LYS* 2.8 37.9 + - - +
113C TYR* 3.7 35.7 + - + -
116C SER* 4.9 1.0 + - - -
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Residues in contact with ARG 89 (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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85C LYS* 3.0 18.8 + - - +
86C PHE 4.1 1.3 - - - +
88C GLN* 1.4 78.0 - - - +
90C ALA* 1.4 57.4 + - - +
92C LYS* 3.3 9.7 + - - +
95C GLN* 3.0 18.7 + - - -
171C HIS* 5.0 1.9 - - - +
172C GLU* 4.4 3.4 + - - -
173C TYR* 4.3 18.6 - - + -
203C ARG* 3.1 47.8 - - - +
207C GLU* 5.6 3.0 - - - +
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Residues in contact with ALA 90 (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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86C PHE* 2.8 40.7 + - + +
89C ARG* 1.4 73.3 - - - +
91C ALA* 1.3 55.3 + - - +
95C GLN* 3.3 13.0 - - - +
167C TYR* 2.5 36.7 + - + -
168C ILE* 5.7 0.2 - - - -
171C HIS* 3.8 25.8 - - + +
173C TYR* 4.3 7.6 - - + -
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Residues in contact with ALA 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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86C PHE* 3.7 3.3 + - + -
87C TYR* 3.0 46.5 + - + +
90C ALA* 1.3 79.5 - - - +
92C LYS* 1.4 62.6 + - - +
93C PRO* 3.6 4.9 - - - +
96C ILE* 3.7 18.6 - - + +
110C VAL* 4.0 9.4 - - + -
111C PRO 3.7 10.8 - - - +
112C LYS* 4.6 0.9 - - - -
113C TYR* 4.2 14.6 + - - +
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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