Contacts of the strand formed by residues 39 - 45 (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 VAL 39 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37F LYS 4.9 3.8 - - - +
38F TRP* 1.3 72.3 - - - +
40F PRO* 1.3 68.8 - - - +
73F PRO* 3.8 29.2 - - + -
74F MET 3.8 13.7 - - - +
75F PHE* 3.8 31.4 - - + -
76F GLY 5.6 1.6 - - - +
103F GLY* 3.2 3.2 - - - -
104F PHE* 2.8 51.9 + - + +
106F SER* 5.5 10.1 - - - +
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Residues in contact with PRO 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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33F LEU* 4.1 16.8 - - + -
34F LEU* 3.9 16.2 - - + -
38F TRP 3.4 9.4 - - - +
39F VAL* 1.3 85.5 - - - +
41F CYS* 1.3 61.9 + - - +
73F PRO* 3.5 1.0 - - - +
74F MET* 2.8 57.4 + - + +
77F CYS* 4.1 4.9 - - + +
83F VAL* 3.9 34.3 - - + -
101F ILE* 5.2 0.9 - - + -
102F ILE 3.4 7.6 - - - +
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Residues in contact with CYS 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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40F PRO* 1.3 77.0 - - - +
42F LEU* 1.3 82.1 + - - +
43F GLU* 4.9 2.5 - - - -
69F MET* 4.0 26.0 - - - -
70F TRP 4.9 0.4 - - - -
72F LEU 4.5 3.4 - - - -
73F PRO* 4.0 24.7 - - + -
74F MET* 5.3 1.8 - - - -
101F ILE* 3.6 3.7 - - - +
102F ILE* 2.9 44.2 + - + +
104F PHE* 3.8 23.6 - - + -
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Residues in contact with LEU 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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41F CYS* 1.3 90.0 - - - +
43F GLU* 1.3 66.3 + - - +
69F MET 3.8 0.2 - - - -
70F TRP* 2.9 47.3 + - + +
72F LEU 5.7 0.4 + - - -
74F MET* 4.9 6.5 - - - -
83F VAL* 4.1 28.0 - - + +
86F GLU* 3.7 17.3 - - + +
87F LEU* 3.6 36.3 - - + +
90F CYS* 4.2 7.9 - - + -
99F ILE* 4.5 10.1 - - + -
100F ARG 3.4 9.4 - - - +
101F ILE* 4.4 12.6 - - + -
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Residues in contact with GLU 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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41F CYS* 4.9 3.2 - - - -
42F LEU* 1.3 79.5 - - - +
44F PHE* 1.3 63.2 + - - +
66F TYR* 6.1 0.2 - - - -
67F TRP* 3.9 21.4 + - + +
68F THR 3.1 11.9 - - - +
69F MET* 4.7 7.1 - - + +
70F TRP 4.4 0.4 - - - +
99F ILE* 3.4 5.8 - - - +
100F ARG* 2.9 70.1 + - + -
102F ILE* 3.6 27.2 - - + +
111F GLN* 5.2 1.4 + - - -
187H ARG* 2.8 32.8 + - - -
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Residues in contact with PHE 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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43F GLU* 1.3 75.7 - - - +
45F GLU* 1.3 64.4 + - - +
46F THR* 4.8 2.5 - - + -
67F TRP* 4.0 3.4 - - - -
68F THR* 2.8 68.4 + - + +
69F MET 3.7 16.8 - - - -
70F TRP* 3.9 25.4 - + + -
90F CYS* 4.1 11.4 - - - -
94F TYR* 3.6 48.5 - + - -
97F ALA* 4.2 6.5 - - + -
98F PHE 3.2 13.0 - - - +
99F ILE* 4.1 13.5 - - + -
3I VAL* 4.0 11.0 - - + -
6I ILE* 4.4 11.7 - - + -
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Residues in contact with GLU 45 (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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44F PHE* 1.3 78.1 - - - +
46F THR* 1.3 64.0 + - - +
47F ASP* 3.2 13.5 + - - +
48F HIS* 2.9 53.4 + - - +
49F GLY* 4.2 1.6 - - - +
67F TRP* 3.4 38.0 - - + +
68F THR* 4.3 6.1 - - - +
97F ALA* 3.9 0.4 - - - -
98F PHE* 2.8 36.7 + - + -
227H LYS* 2.9 30.9 + - - -
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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