Contacts of the strand formed by residues 39 - 45 (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 VAL 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C LYS 4.9 4.0 - - - +
38C TRP* 1.3 73.0 - - - +
40C PRO* 1.3 68.2 - - - +
73C PRO* 3.8 28.3 - - + -
74C MET 3.8 13.5 - - - -
75C PHE* 3.8 32.1 - - + -
76C GLY 5.6 1.3 - - - +
103C GLY* 3.2 3.4 - - - -
104C PHE* 2.8 51.9 + - + +
106C SER* 5.5 10.1 - - - +
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Residues in contact with PRO 40 (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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33C LEU* 3.9 16.6 - - + -
34C LEU* 3.9 15.9 - - + -
38C TRP 3.4 9.9 - - - +
39C VAL* 1.3 84.3 - - - +
41C CYS* 1.3 61.7 + - - +
73C PRO* 3.5 1.2 - - - +
74C MET* 2.8 58.6 + - + +
77C CYS* 4.1 4.5 - - + +
83C VAL* 3.9 34.5 - - + -
101C ILE* 5.2 1.1 - - + -
102C ILE 3.4 8.1 - - - +
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Residues in contact with CYS 41 (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 PRO* 1.3 77.4 - - - +
42C LEU* 1.3 79.6 + - - +
43C GLU* 4.9 1.8 - - - -
69C MET* 4.0 25.8 - - - -
70C TRP 4.9 0.7 - - - -
72C LEU 4.5 3.6 - - - -
73C PRO* 4.0 24.0 - - + -
74C MET* 4.9 2.5 - - - +
101C ILE* 3.6 4.1 - - - +
102C ILE* 2.9 44.3 + - + +
104C PHE* 3.8 23.1 - - + -
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Residues in contact with LEU 42 (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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41C CYS* 1.3 89.7 - - - +
43C GLU* 1.3 65.8 + - - +
69C MET 3.8 0.2 - - - -
70C TRP* 2.9 46.5 + - + +
74C MET* 4.9 6.5 - - - -
83C VAL* 4.1 27.1 - - + +
86C GLU* 3.7 16.6 - - + +
87C LEU* 3.6 36.6 - - + +
90C CYS* 4.2 8.1 - - + -
99C ILE* 4.5 9.9 - - + -
100C ARG 3.4 9.2 - - - +
101C ILE* 4.4 13.5 - - + -
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Residues in contact with GLU 43 (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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41C CYS* 4.9 3.5 - - - -
42C LEU* 1.3 79.0 - - - +
44C PHE* 1.3 62.5 + - - +
66C TYR* 6.1 0.3 - - - -
67C TRP* 3.9 21.2 + - + +
68C THR 3.1 13.0 - - - +
69C MET* 4.7 7.9 + - + +
70C TRP 4.4 0.4 - - - +
99C ILE* 3.4 6.0 - - - +
100C ARG* 2.9 70.4 + - + -
102C ILE* 3.6 26.4 - - + +
111C GLN* 5.2 1.7 + - - -
187E ARG* 2.8 32.7 + - - -
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Residues in contact with PHE 44 (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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43C GLU* 1.3 77.1 - - - +
45C GLU* 1.3 65.7 + - - +
46C THR* 4.8 2.0 - - + -
67C TRP* 4.0 3.1 - - - -
68C THR* 2.8 65.9 + - + +
69C MET 3.7 17.0 - - - -
70C TRP* 3.9 25.8 - + + -
90C CYS* 4.1 11.7 - - - -
94C TYR* 3.6 48.2 - + - -
97C ALA* 4.2 6.7 - - + -
98C PHE 3.2 12.1 - - - +
99C ILE* 4.1 13.9 - - + -
3F VAL* 4.0 10.8 - - + -
6F ILE* 4.3 11.2 - - + -
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Residues in contact with GLU 45 (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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44C PHE* 1.3 78.7 - - - +
46C THR* 1.3 63.6 + - - +
47C ASP* 3.2 12.8 + - - +
48C HIS* 2.9 53.5 + - - +
49C GLY* 4.2 1.6 - - - +
67C TRP* 3.4 36.9 - - + +
68C THR* 4.3 6.1 - - - +
97C ALA* 3.3 0.6 - - - -
98C PHE* 2.8 37.2 + - + -
227E LYS* 2.9 30.7 + - - -
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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