Contacts of the helix formed by residues 80 - 93 (chain C) in PDB entry 1RBO
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 PRO 80 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C ALA* 4.9 4.9 - - + +
30C VAL* 3.9 18.8 - - + +
31C ASP* 3.2 32.5 - - - +
34C LEU* 3.4 21.3 - - + -
78C THR 3.8 4.5 - - - +
79C ASP* 1.3 91.3 - - - +
81C ALA* 1.3 61.1 + - - +
83C VAL* 3.1 6.0 + - + +
84C LEU* 3.0 33.3 + - + +
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Residues in contact with ALA 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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79C ASP* 3.1 22.2 + - - +
80C PRO* 1.3 80.0 - - - +
82C GLN* 1.3 56.1 + - - +
84C LEU* 3.8 10.0 - - - +
85C ASN* 2.9 38.9 + - - +
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Residues in contact with GLN 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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74C MET* 3.8 15.1 - - + +
77C CYS* 3.6 22.2 - - - +
78C THR* 3.3 8.3 + - - -
79C ASP* 2.9 47.9 + - + +
81C ALA* 1.3 78.3 - - - +
83C VAL* 1.3 56.6 + - - +
85C ASN* 3.3 7.4 - - - +
86C GLU* 3.0 32.4 + - - +
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Residues in contact with VAL 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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30C VAL* 3.8 29.2 - - + -
34C LEU* 4.8 1.3 - - + -
40C PRO* 3.9 29.8 - - + -
42C LEU* 4.1 20.9 - - + +
74C MET* 4.2 10.5 - - - -
77C CYS* 4.0 14.1 - - - -
79C ASP 4.3 1.8 - - - +
80C PRO* 3.1 7.4 + - + +
82C GLN* 1.3 73.9 - - - +
84C LEU* 1.3 61.0 + - - +
86C GLU* 3.1 5.0 + - - +
87C LEU* 2.9 26.0 + - - +
101C ILE* 4.3 23.6 - - + -
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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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23C THR* 5.6 6.1 - - + +
26C LEU* 3.8 30.1 - - + -
27C ALA* 4.2 24.5 - - + +
30C VAL* 4.1 20.0 - - + -
80C PRO* 3.0 23.3 + - + +
81C ALA* 4.0 7.6 - - - +
83C VAL* 1.3 76.0 - - - +
85C ASN* 1.3 60.8 + - - +
87C LEU* 3.3 13.4 + - + +
88C GLU* 3.1 28.1 + - - +
101C ILE* 5.2 2.0 - - + -
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Residues in contact with ASN 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 ALA* 2.9 25.1 + - - +
82C GLN* 3.3 9.2 - - - +
84C LEU* 1.3 75.1 - - - +
86C GLU* 1.3 67.6 + - + +
88C GLU* 3.2 8.6 + - - +
89C GLU* 3.0 25.0 + - - +
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Residues in contact with GLU 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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42C LEU* 3.7 15.5 - - + -
70C TRP* 2.8 33.3 + - + +
71C LYS* 2.9 30.3 + - - +
74C MET* 3.8 22.2 - - + +
82C GLN 3.0 14.6 + - - +
83C VAL* 3.1 8.0 + - - +
85C ASN* 1.3 81.8 - - - +
87C LEU* 1.3 53.8 + - - +
89C GLU* 3.2 11.1 + - - +
90C CYS* 2.7 36.7 + - - +
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Residues in contact with LEU 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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26C LEU* 3.9 28.3 - - + -
42C LEU* 3.6 12.7 - - + +
83C VAL 2.9 12.5 + - - +
84C LEU* 3.4 15.7 - - + +
85C ASN 3.2 0.2 - - - -
86C GLU* 1.3 75.4 - - - +
88C GLU* 1.3 64.5 + - - +
90C CYS* 3.2 1.9 + - - +
91C LYS* 2.9 46.9 + - + +
99C ILE* 3.9 28.7 - - + -
101C ILE* 4.4 10.3 - - + -
117C ALA* 4.0 26.0 - - + +
118C TYR* 4.5 2.2 - - + -
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Residues in contact with GLU 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* 3.1 18.6 + - + +
85C ASN* 3.2 9.8 + - - +
87C LEU* 1.3 81.1 - - - +
89C GLU* 1.3 57.9 - - - +
91C LYS* 2.8 38.9 + - - +
92C LYS* 2.9 29.3 + - - +
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Residues in contact with GLU 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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70C TRP* 3.5 11.8 - - + -
71C LYS* 3.0 34.4 + - - -
85C ASN* 3.0 14.5 + - - +
86C GLU* 3.5 15.2 - - - +
88C GLU* 1.3 77.7 - - - +
90C CYS* 1.3 59.7 + - - +
92C LYS* 2.8 61.8 + - - +
93C GLU* 3.1 3.6 + - - +
1F MET 5.3 0.9 - - - +
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Residues in contact with CYS 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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42C LEU* 4.2 6.7 - - + -
44C PHE* 4.1 19.3 - - - -
70C TRP* 3.6 43.7 - - + -
86C GLU 2.7 20.9 + - - +
87C LEU* 3.7 4.0 - - - +
89C GLU* 1.3 71.8 - - - +
91C LYS* 1.3 53.5 + - - +
93C GLU* 3.2 2.9 + - - +
94C TYR* 2.7 36.5 + - - +
99C ILE* 3.7 29.8 - - + -
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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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87C LEU* 2.9 32.3 + - + +
88C GLU* 2.8 39.7 + - - +
90C CYS* 1.3 77.4 - - - +
92C LYS* 1.3 61.1 + - - +
94C TYR 4.4 2.2 - - - -
95C PRO* 3.1 28.6 - - - +
99C ILE* 3.7 12.1 - - + +
117C ALA 5.6 0.4 - - - +
118C TYR* 3.6 48.8 - - + -
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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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88C GLU 2.9 15.5 + - - +
89C GLU* 2.8 59.3 + - - +
91C LYS* 1.3 77.5 - - - +
93C GLU* 1.3 95.6 + - - +
95C PRO* 3.7 8.9 - - - +
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Residues in contact with GLU 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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70C TRP* 3.5 20.8 - - + -
89C GLU* 3.1 10.7 + - - +
90C CYS 3.8 3.4 - - - +
92C LYS* 1.3 105.4 + - - +
94C TYR* 1.3 85.6 + - + +
95C PRO* 3.5 6.5 - - - +
96C ASN* 5.1 0.2 - - - +
3F VAL* 4.3 16.8 + - - +
5F PRO* 6.0 1.2 - - - +
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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