Contacts of the strand formed by residues 34 - 42 (chain F) in PDB entry 5O6I
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 SER 34 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27F LEU 3.3 7.4 - - - -
28F LYS* 3.5 23.1 - - - -
29F TYR* 4.3 4.0 - - - +
32F ASN 4.7 0.7 - - - -
33F ARG* 1.3 78.0 - - - +
35F GLU* 1.3 63.0 + - - +
36F TYR* 3.8 4.9 - - - -
3I C 3.8 4.4 - - - -
4I G 2.6 55.2 + - - -
5I C 3.1 22.7 + - - -
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Residues in contact with GLU 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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25F TYR 3.8 0.3 - - - +
26F LYS* 3.6 2.6 - - - +
27F LEU* 2.7 40.4 + - + +
29F TYR* 2.6 38.8 + - + +
34F SER* 1.3 77.2 - - - +
36F TYR* 1.3 68.4 + - - +
37F ARG* 2.9 35.9 + - + +
70F GLN* 5.2 0.3 + - - -
81F ARG* 4.6 2.1 + - - -
83F SER* 2.9 33.1 + - - +
4I G 5.2 0.4 - - - -
5I C 3.8 11.9 - - + +
6I C 3.1 27.9 + - - -
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Residues in contact with TYR 36 (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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25F TYR 3.4 4.5 - - - -
26F LYS* 3.8 33.5 + - + -
28F LYS* 3.8 11.0 + - - -
34F SER* 3.8 11.0 - - - -
35F GLU* 1.3 79.7 - - - +
37F ARG* 1.3 61.6 + - - +
83F SER* 3.3 5.8 + - - -
84F SER 2.8 30.0 + - - -
85F LYS* 3.5 49.9 + - + +
88F TYR* 3.6 31.2 - + + -
89F TYR* 4.0 15.9 + + - -
4I G 2.8 38.4 + - - -
5I C 3.9 8.1 + - - -
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Residues in contact with ARG 37 (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 GLY 3.9 0.5 - - - +
24F LEU* 3.5 6.4 - - - -
25F TYR* 2.8 41.5 + - + +
27F LEU* 4.2 12.1 - - + +
29F TYR* 4.1 1.5 + - - -
35F GLU* 2.9 37.0 + - - +
36F TYR* 1.3 77.4 - - - +
38F VAL* 1.3 65.4 + - - +
39F VAL* 4.1 15.7 - - + -
79F GLU* 4.5 0.4 + - - -
81F ARG* 3.2 43.7 - - + +
82F VAL 3.5 4.0 - - - +
83F SER* 4.8 0.7 - - - +
88F TYR* 3.9 3.2 - - - -
17G T 3.5 17.5 + - - -
18G C 3.4 15.8 - - - +
7I G 2.7 30.3 + - - -
8I G 2.9 22.4 + - - -
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Residues in contact with VAL 38 (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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18F ILE* 3.6 31.0 - - + -
23F GLY 3.9 2.5 - - - -
24F LEU* 3.8 11.0 - - + -
37F ARG* 1.3 75.9 - - - +
39F VAL* 1.3 62.6 + - - +
56F MET* 4.1 12.3 - - + -
80F LEU* 3.7 2.5 - - - +
81F ARG* 3.3 4.0 - - - -
82F VAL* 2.9 38.0 + - + +
84F SER 4.8 0.7 - - - +
87F LEU* 3.8 23.1 - - + +
88F TYR* 3.8 31.4 - - + +
91F PHE* 3.9 11.0 - - + -
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Residues in contact with VAL 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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18F ILE* 3.8 6.5 - - - +
22F GLY* 3.1 7.6 - - - -
23F GLY 3.1 31.6 + - - +
25F TYR* 3.9 25.4 - - + -
37F ARG* 4.1 13.7 - - + -
38F VAL* 1.3 80.6 - - - +
40F ILE* 1.3 71.9 + - - +
41F THR* 3.8 25.6 - - + -
79F GLU* 3.6 25.1 - - + +
80F LEU* 3.2 7.9 - - - +
81F ARG* 4.2 6.3 - - + -
16G T 4.4 9.2 - - + -
17G T 5.8 0.4 - - + -
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Residues in contact with ILE 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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14F LEU* 4.2 20.6 - - + -
17F LEU* 3.9 33.4 - - + +
18F ILE* 3.6 25.1 - - + -
21F ASP* 4.6 3.4 - - + -
22F GLY* 4.0 3.8 - - - -
39F VAL* 1.3 79.4 - - - +
41F THR* 1.3 69.6 + - - +
48F ILE* 3.9 3.1 - - + +
52F PHE* 4.0 27.4 - - + -
56F MET* 4.3 11.4 - - + -
79F GLU 3.6 0.2 - - - -
80F LEU* 2.6 57.8 + - + +
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Residues in contact with THR 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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21F ASP* 2.5 36.1 + - - +
22F GLY* 4.9 0.4 - - - -
39F VAL* 3.8 18.8 - - + -
40F ILE* 1.3 79.3 - - - +
42F GLN* 1.3 75.3 + - - +
48F ILE* 4.4 0.4 - - - -
77F ARG* 3.7 22.9 - - - +
78F TYR 3.2 12.3 - - - +
79F GLU* 4.3 3.4 - - + -
14G A 3.4 23.0 - - - +
15G G 4.0 19.9 - - + +
16G T 4.6 1.6 - - + -
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Residues in contact with GLN 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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17F LEU* 5.9 0.5 - - - +
21F ASP* 2.8 25.1 + - - +
41F THR* 1.3 78.4 - - - +
43F LYS* 1.3 64.7 + - - +
44F SER* 4.0 11.2 - - - +
47F LEU* 4.1 24.7 - - + +
48F ILE* 3.5 23.5 - - + +
52F PHE* 3.9 18.7 - - + -
77F ARG* 4.0 3.3 - - - +
78F TYR* 2.9 35.0 + - - +
115F VAL* 4.7 8.1 + - - +
120F LYS* 6.1 3.6 - - - +
201F MN 3.9 3.6 + - - -
14G A 3.2 28.8 + - - +
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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