Contacts of the helix formed by residues 23 - 35 (chain F) 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 THR 23 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22F THR* 1.3 75.1 - - - +
24F ASP* 1.3 65.6 + - - +
26F LEU* 3.3 11.3 + - + +
27F ALA* 3.0 28.2 + - + +
84F LEU* 5.6 5.4 - - + +
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Residues in contact with ASP 24 (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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22F THR* 3.2 7.6 + - - +
23F THR* 1.3 86.4 - - - +
25F GLN* 1.3 61.5 + - + +
27F ALA* 3.4 8.0 + - - +
28F ARG* 3.0 34.5 + - + +
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Residues in contact with GLN 25 (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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429E GLN* 3.8 17.9 + - - +
433E GLU* 3.9 21.0 - - - +
19F PRO* 4.9 2.0 + - - +
20F PRO 3.6 7.1 + - - -
21F LEU* 3.3 24.7 - - + +
22F THR* 2.9 43.1 + - - +
24F ASP* 1.3 74.3 - - + +
26F LEU* 1.3 65.6 - - - +
28F ARG* 3.3 5.4 + - - +
29F GLN* 3.2 26.8 + - - +
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Residues in contact with LEU 26 (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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21F LEU* 4.1 20.4 - - + +
22F THR 2.9 12.4 + - - +
23F THR* 3.5 13.2 - - + +
25F GLN* 1.3 76.7 - - - +
27F ALA* 1.3 63.0 + - - +
29F GLN* 3.0 16.0 + - - +
30F VAL* 3.1 16.0 + - + +
84F LEU* 3.8 25.6 - - + -
87F LEU* 3.9 18.2 - - + -
101F ILE* 4.6 2.2 - - + -
115F PHE* 3.4 32.3 - - + -
117F ALA* 4.2 18.8 - - + +
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Residues in contact with ALA 27 (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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23F THR* 3.0 19.5 + - + +
24F ASP* 3.7 9.4 - - - +
26F LEU* 1.3 75.7 - - - +
28F ARG* 1.3 57.5 + - - +
30F VAL* 3.2 7.0 + - - +
31F ASP* 2.9 33.7 + - - +
80F PRO* 4.9 5.2 - - + +
84F LEU* 4.2 25.4 - - + -
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Residues in contact with ARG 28 (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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432E ASN 4.2 4.5 - - - +
433E GLU* 3.1 58.6 + - + +
24F ASP* 3.0 22.9 + - + +
25F GLN* 3.5 8.5 - - - +
27F ALA* 1.3 77.5 - - + +
29F GLN* 1.3 58.6 + - - +
31F ASP* 3.3 15.6 + - - +
32F TYR* 3.0 27.7 + - - +
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Residues in contact with GLN 29 (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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429E GLN* 3.9 24.6 + - - +
432E ASN* 3.0 40.2 + - - +
433E GLU* 4.3 6.4 - - - +
15F LEU* 4.0 29.4 - - + +
21F LEU* 4.5 8.3 - - + -
25F GLN 3.2 13.4 + - - +
26F LEU 3.0 8.8 + - - +
28F ARG* 1.3 76.8 - - - +
30F VAL* 1.3 62.0 + - - +
32F TYR* 3.2 10.9 + - - +
33F LEU* 3.1 22.2 + - - +
113F ILE* 5.5 3.8 - - - +
115F PHE* 3.7 27.8 - - + -
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Residues in contact with VAL 30 (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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26F LEU* 3.1 14.8 + - + +
27F ALA* 3.2 7.8 + - - +
29F GLN* 1.3 72.1 - - - +
31F ASP* 1.3 65.7 + - - +
33F LEU* 3.2 13.9 + - + +
34F LEU* 3.0 25.3 + - + +
80F PRO* 3.9 20.2 - - + +
83F VAL* 3.8 34.8 - - + -
84F LEU* 4.1 20.9 - - + -
101F ILE* 4.3 22.7 - - + -
115F PHE* 4.6 4.7 - - + -
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Residues in contact with ASP 31 (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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27F ALA* 2.9 19.2 + - - +
28F ARG* 3.5 20.5 - - - +
29F GLN 3.3 0.2 - - - -
30F VAL* 1.3 76.9 - - - +
32F TYR* 1.3 53.1 + - - +
34F LEU* 3.3 2.6 + - - +
35F ASN* 2.8 53.6 + - - +
80F PRO* 3.2 26.4 - - - +
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Residues in contact with TYR 32 (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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396E ASP* 4.4 4.5 + - - -
431E ARG* 3.6 21.7 + - + -
432E ASN* 3.2 67.4 + - + +
28F ARG 3.0 8.3 + - - +
29F GLN* 3.4 11.2 - - - +
31F ASP* 1.3 76.9 - - - +
33F LEU* 1.3 60.0 + - - +
35F ASN* 3.4 7.8 + - + +
36F ASN* 2.7 55.6 + - - -
38F TRP* 3.6 16.2 - + - -
113F ILE* 3.3 34.7 - - + +
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Residues in contact with LEU 33 (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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29F GLN 3.1 9.1 + - - +
30F VAL* 3.2 14.6 + - + +
32F TYR* 1.3 81.8 - - - +
34F LEU* 1.3 63.9 + - + +
36F ASN* 3.3 7.1 + - - -
38F TRP* 3.1 69.5 + - + +
40F PRO* 3.9 20.4 - - + -
101F ILE* 4.2 15.3 - - + -
102F ILE 3.8 9.4 - - - +
103F GLY* 3.8 21.8 - - - +
113F ILE* 4.0 24.2 - - + -
115F PHE* 5.5 0.7 - - + -
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Residues in contact with LEU 34 (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 VAL* 3.0 21.7 + - + +
31F ASP* 3.9 4.5 - - - +
33F LEU* 1.3 74.9 - - + +
35F ASN* 1.3 64.6 + - - +
37F LYS* 2.9 25.5 + - - +
38F TRP 4.3 5.4 - - - +
40F PRO* 3.9 31.2 - - + -
77F CYS* 3.7 26.5 - - - +
78F THR* 4.1 9.9 - - - +
79F ASP 3.8 6.1 - - - +
80F PRO* 3.4 49.1 - - + -
83F VAL* 4.9 0.2 - - + -
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Residues in contact with ASN 35 (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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31F ASP* 2.8 41.6 + - - +
32F TYR* 3.8 8.4 - - + +
33F LEU 3.3 0.2 - - - -
34F LEU* 1.3 74.8 - - - +
36F ASN* 1.3 62.8 + - - +
37F LYS* 3.1 13.1 + - - +
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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