Contacts of the helix formed by residues 80 - 93 (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 PRO 80 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27F ALA* 4.9 4.7 - - + +
30F VAL* 3.9 19.2 - - + +
31F ASP* 3.2 32.8 - - - +
34F LEU* 3.4 21.7 - - + -
78F THR 3.8 4.5 - - - +
79F ASP* 1.3 92.3 - - - +
81F ALA* 1.3 60.8 + - - +
83F VAL* 3.1 6.2 + - + +
84F LEU* 3.0 32.1 + - + +
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Residues in contact with ALA 81 (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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79F ASP* 3.1 22.3 + - - +
80F PRO* 1.3 80.0 - - - +
82F GLN* 1.3 55.9 + - - +
84F LEU* 3.8 9.6 - - - +
85F ASN* 2.9 39.6 + - - +
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Residues in contact with GLN 82 (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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74F MET* 3.8 16.6 - - + +
77F CYS* 3.6 22.4 - - - +
78F THR* 3.3 8.3 + - - -
79F ASP* 2.9 47.3 + - + +
81F ALA* 1.3 78.8 - - - +
83F VAL* 1.3 56.1 + - - +
85F ASN* 3.3 7.8 - - - +
86F GLU* 3.0 32.1 + - - +
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Residues in contact with VAL 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F VAL* 3.8 28.7 - - + -
34F LEU* 4.8 1.8 - - + -
40F PRO* 3.9 30.1 - - + -
42F LEU* 4.1 19.9 - - + +
74F MET* 4.2 9.9 - - - -
77F CYS* 4.0 14.6 - - - -
79F ASP 4.3 1.3 - - - +
80F PRO* 3.1 7.7 + - + +
82F GLN* 1.3 74.1 - - - +
84F LEU* 1.3 59.5 + - - +
86F GLU* 3.1 4.7 + - - +
87F LEU* 2.9 27.3 + - - +
101F ILE* 4.3 24.7 - - + -
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Residues in contact with LEU 84 (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* 5.6 5.4 - - + +
26F LEU* 3.8 30.3 - - + -
27F ALA* 4.2 25.1 - - + -
30F VAL* 4.1 20.0 - - + -
80F PRO* 3.0 23.3 + - + +
81F ALA* 4.0 7.9 - - - +
83F VAL* 1.3 76.3 - - - +
85F ASN* 1.3 61.6 + - - +
87F LEU* 3.3 13.1 + - + +
88F GLU* 3.1 28.4 + - + +
101F ILE* 5.2 1.8 - - + -
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Residues in contact with ASN 85 (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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81F ALA* 2.9 25.2 + - - +
82F GLN* 3.3 9.4 - - - +
84F LEU* 1.3 75.1 - - - +
86F GLU* 1.3 66.8 + - + +
88F GLU* 3.2 9.0 + - - +
89F GLU* 3.0 24.2 + - - +
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Residues in contact with GLU 86 (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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42F LEU* 3.7 16.8 - - + +
70F TRP* 2.8 34.0 + - + +
71F LYS* 2.9 30.0 + - - +
74F MET* 3.8 21.2 - - + +
82F GLN 3.0 14.8 + - - +
83F VAL* 3.6 7.9 - - - +
85F ASN* 1.3 81.1 - - + +
87F LEU* 1.3 53.3 + - - +
89F GLU* 3.2 10.5 + - - +
90F CYS* 2.7 36.9 + - - +
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Residues in contact with LEU 87 (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* 3.9 28.3 - - + -
42F LEU* 3.6 12.7 - - + +
83F VAL 2.9 13.4 + - - +
84F LEU* 3.4 15.3 - - + +
85F ASN 3.2 0.2 - - - -
86F GLU* 1.3 75.9 - - - +
88F GLU* 1.3 64.5 + - - +
90F CYS* 3.2 1.6 + - - +
91F LYS* 2.9 47.5 + - + +
99F ILE* 3.9 29.6 - - + -
101F ILE* 4.4 11.2 - - + -
117F ALA* 4.0 25.4 - - + +
118F TYR* 4.5 2.5 - - + -
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Residues in contact with GLU 88 (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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84F LEU 3.1 18.4 + - - +
85F ASN* 3.2 9.6 + - - +
87F LEU* 1.3 81.5 - - - +
89F GLU* 1.3 57.9 + - - +
91F LYS* 2.8 37.3 + - - +
92F LYS* 2.9 30.2 + - - +
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Residues in contact with GLU 89 (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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70F TRP* 3.5 11.7 - - + -
71F LYS* 3.0 34.0 + - - -
85F ASN* 3.0 14.9 + - - +
86F GLU* 3.5 14.1 - - - +
88F GLU* 1.3 78.3 - - - +
90F CYS* 1.3 59.2 + - - +
92F LYS* 2.8 62.7 + - - +
93F GLU* 3.1 3.5 + - - +
1I MET 5.3 0.9 - - - +
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Residues in contact with CYS 90 (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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42F LEU* 4.2 7.2 - - + -
44F PHE* 4.1 20.2 - - - -
70F TRP* 3.6 43.3 - - + -
86F GLU 2.7 19.9 + - - +
87F LEU 3.7 4.0 - - - +
89F GLU* 1.3 73.3 - - - +
91F LYS* 1.3 52.8 + - - +
93F GLU* 3.2 2.6 + - - +
94F TYR* 2.7 36.6 + - - +
99F ILE* 3.7 29.2 - - + -
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Residues in contact with LYS 91 (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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87F LEU* 2.9 33.2 + - + +
88F GLU* 2.8 39.2 + - - +
89F GLU 3.3 0.2 - - - -
90F CYS* 1.3 76.6 - - - +
92F LYS* 1.3 62.6 + - - +
94F TYR 4.4 2.7 - - - -
95F PRO* 3.1 28.3 - - - +
99F ILE* 3.7 12.3 - - + +
117F ALA 5.6 0.7 - - - +
118F TYR* 3.6 47.8 - - + -
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Residues in contact with LYS 92 (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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88F GLU 2.9 15.1 + - - +
89F GLU* 2.8 59.5 + - - +
91F LYS* 1.3 77.1 - - - +
93F GLU* 1.3 94.3 + - - +
95F PRO* 3.7 8.9 - - - +
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Residues in contact with GLU 93 (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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70F TRP* 3.5 21.8 - - + -
89F GLU* 3.1 11.3 + - - +
90F CYS 3.8 2.7 - - - +
92F LYS* 1.3 104.9 + - - +
94F TYR* 1.3 84.8 + - + +
95F PRO* 3.5 5.9 - - - +
96F ASN* 5.1 0.3 - - - +
3I VAL* 4.3 16.8 + - - +
5I PRO* 6.0 1.4 - - - +
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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