Contacts of the strand formed by residues 38 - 44 (chain F) in PDB entry 2RHB
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 ILE 38 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73E ASN* 5.6 6.1 - - - +
87E ASP* 5.8 0.2 - - - +
90E ARG* 3.7 33.4 - - - +
93E PRO 4.9 0.9 - - - +
94E ALA 3.7 25.8 - - - +
95E HIS* 4.3 1.6 - - - -
96E VAL* 4.1 22.2 - - + +
271E MET* 4.3 24.0 - - + -
34F LYS* 3.8 2.0 - - - +
35F VAL* 2.9 37.9 + - - +
36F ASP* 4.2 12.8 - - + +
37F GLY* 1.3 85.8 - - - +
39F ASP* 1.3 66.9 + - - +
40F VAL* 3.6 3.0 + - + +
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Residues in contact with ASP 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E THR* 2.7 45.5 + - + +
90E ARG* 2.6 28.9 + - - +
92E ALA* 5.2 1.7 - - - +
25F SER* 4.4 10.9 + - - -
32F TYR* 4.1 13.9 - - + -
33F THR 3.5 8.4 - - - +
34F LYS* 3.2 36.3 + - - +
38F ILE* 1.3 73.4 - - - +
40F VAL* 1.3 58.5 + - - +
41F GLU 4.3 0.5 + - - -
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Residues in contact with VAL 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E ARG* 4.1 13.0 - - + +
269E ILE* 3.9 13.7 - - + -
270E PRO* 3.7 48.0 - - + +
271E MET* 4.0 21.8 - - + +
32F TYR* 3.9 3.1 - - - -
33F THR* 3.0 46.1 + - + +
35F VAL* 4.6 4.0 - - + -
38F ILE* 4.3 5.4 - - + +
39F ASP* 1.3 75.3 - - - +
41F GLU* 1.3 65.1 + - - +
42F ILE* 3.4 4.0 + - - +
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Residues in contact with GLU 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E LYS* 4.8 12.3 + - - +
90E ARG* 5.6 0.8 - - - +
270E PRO* 3.2 30.0 - - + +
30F ALA* 3.4 20.5 - - + +
31F VAL 3.7 8.1 - - - +
32F TYR* 3.4 33.0 + - + -
40F VAL* 1.3 71.9 - - - +
42F ILE* 1.3 62.0 + - - +
43F PHE 3.9 14.8 - - - +
44F GLU* 3.8 31.1 - - - +
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Residues in contact with ILE 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E PHE 3.8 22.2 - - - +
269E ILE* 4.2 11.0 - - + -
270E PRO* 4.7 0.9 - - + -
6F ALA* 4.3 9.4 - - + -
9F VAL* 4.3 12.1 - - + +
10F VAL* 4.3 15.0 - - + -
24F VAL* 4.8 0.2 - - + -
31F VAL* 2.9 31.3 + - + +
33F THR* 3.7 23.6 - - + +
40F VAL 3.6 10.8 - - - +
41F GLU* 1.3 78.4 - - - +
43F PHE* 1.3 61.8 + - - +
55F PHE* 3.7 26.5 - - + -
58F TRP* 3.6 23.0 - - - -
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Residues in contact with PHE 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ALA* 3.2 8.0 - - - +
31F VAL* 2.8 41.2 + - + +
41F GLU* 3.7 5.9 - - - +
42F ILE* 1.3 81.7 - - - +
44F GLU* 1.3 77.3 + - - +
45F ASN* 4.3 12.3 - - + -
46F LYS 5.6 0.2 - - - -
47F THR* 5.1 0.7 - - + -
51F VAL* 3.8 5.6 - - + -
54F ALA* 3.4 29.6 - - + -
55F PHE* 3.4 50.5 - + + -
58F TRP* 3.6 40.6 - + + -
86F TRP* 4.5 11.4 - + - -
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Residues in contact with GLU 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E LYS* 3.4 24.8 + - - -
28F ASN 5.6 1.8 - - - +
29F ASN 4.1 6.1 - - - +
30F ALA* 4.4 2.7 - - + -
41F GLU* 3.8 23.5 - - - +
43F PHE* 1.3 90.6 - - - +
45F ASN* 1.3 65.1 + - - +
46F LYS* 3.4 39.5 + - + +
91F GLU* 5.9 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