Contacts of the strand formed by residues 45 - 53 (chain S) in PDB entry 1C0F
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 ALA 45 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23S ARG* 3.6 3.8 - - - +
24S VAL* 3.2 25.6 + - + +
44S ASP* 1.3 75.2 - - - +
46S TYR* 1.3 68.0 + - - +
66S TRP 3.2 10.8 - - - +
67S LEU* 3.8 15.9 - - + -
71S CYS* 3.9 4.4 - - - +
75S GLU* 3.5 40.7 + - + +
79S ALA* 4.1 4.3 - - + -
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Residues in contact with TYR 46 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21S ILE* 4.0 9.0 - - + -
22S TRP 3.4 17.0 - - - +
23S ARG* 3.6 25.9 - - + +
24S VAL 4.6 0.7 - - - +
32S VAL* 3.8 14.4 - - + -
39S ASP 4.0 6.3 + - - -
40S PHE* 3.5 35.2 - + + -
41S PHE* 3.2 54.1 + - - +
44S ASP* 3.9 8.5 - - + -
45S ALA* 1.3 77.7 - - - +
47S VAL* 1.3 66.3 + - - +
48S ILE* 4.0 15.3 - - + -
65S TYR* 3.2 7.1 - - - +
66S TRP* 2.8 43.3 + + + +
79S ALA* 4.1 1.7 - - - +
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Residues in contact with VAL 47 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21S ILE* 3.6 1.0 - - - -
22S TRP* 2.9 39.6 + - + +
24S VAL* 4.7 2.9 - - + -
29S LEU* 3.8 27.6 - - + -
46S TYR* 1.3 78.1 - - - +
48S ILE* 1.3 64.3 + - - +
63S LEU* 4.1 20.9 - - + -
64S HIS 3.4 4.9 - - - +
79S ALA* 3.9 29.8 - - + +
82S PHE* 4.4 3.4 - - + -
83S THR* 3.9 17.9 - - - +
86S LEU* 4.2 16.2 - - + -
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Residues in contact with ILE 48 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19S LEU* 3.7 27.8 - - + -
20S GLN 3.4 6.1 - - - +
21S ILE* 4.1 23.6 - - + -
40S PHE* 4.2 4.5 - - + -
46S TYR* 4.0 6.7 - - + -
47S VAL* 1.3 86.6 - - - +
49S LEU* 1.3 63.2 + - - +
62S ASP 3.7 1.2 - - - +
63S LEU* 3.4 6.0 - - - +
64S HIS* 2.7 49.4 + - + +
66S TRP* 3.9 17.7 - - + -
108S PHE* 3.6 39.3 - - + -
111S TYR* 4.5 9.6 - - + -
112S PHE* 5.0 0.9 - - + -
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Residues in contact with LEU 49 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13S ALA* 4.0 13.7 - - + -
14S GLY* 3.4 35.4 - - - +
18S GLY 3.6 1.7 - - - +
19S LEU* 3.5 3.3 - - - +
20S GLN* 2.9 48.1 + - - +
22S TRP* 3.9 13.4 - - + -
48S ILE* 1.3 75.1 - - - +
50S LYS* 1.3 58.9 + - - +
51S THR* 3.9 7.6 + - - +
61S TYR* 3.8 29.8 - - + -
62S ASP 3.5 13.9 - - - +
63S LEU* 3.8 24.5 - - + -
86S LEU* 5.8 1.1 - - + -
90S LEU* 4.2 11.9 - - + -
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Residues in contact with LYS 50 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18S GLY* 3.5 18.6 + - - +
19S LEU* 4.1 11.6 - - + +
48S ILE* 4.1 1.2 + - - +
49S LEU* 1.3 71.9 - - - +
51S THR* 1.3 61.3 + - - +
52S VAL* 3.9 27.3 + - + +
60S GLN* 3.5 5.2 + - - +
61S TYR* 3.6 1.2 - - - -
62S ASP* 3.0 36.3 + - + +
111S TYR* 3.4 57.6 - - + +
113S LYS* 6.3 1.0 - - - +
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Residues in contact with THR 51 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S GLY* 3.5 22.2 - - - +
16S GLU 3.3 31.8 + - - +
17S PRO* 3.2 5.7 - - + +
18S GLY* 2.8 38.5 + - - +
20S GLN* 4.3 3.3 + - - -
49S LEU* 3.9 7.1 + - - +
50S LYS* 1.3 74.2 + - - +
52S VAL* 1.3 63.0 + - - +
59S LEU* 3.6 31.4 - - + -
60S GLN 3.3 3.6 - - - -
61S TYR* 3.7 14.8 - - + -
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Residues in contact with VAL 52 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17S PRO* 4.8 0.7 - - - -
50S LYS* 3.9 29.8 - - + +
51S THR* 1.3 77.0 - - - +
53S GLN* 1.3 75.2 + - - +
54S LEU* 3.5 3.1 + - + -
59S LEU* 3.4 6.7 - - - -
60S GLN* 2.8 68.0 + - + +
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Residues in contact with GLN 53 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17S PRO* 3.6 31.4 - - + +
52S VAL* 1.3 82.4 - - - +
54S LEU* 1.3 86.7 + - - +
55S ARG* 4.3 0.6 + - - -
57S GLY* 3.5 25.1 + - - -
58S ASN 3.8 2.0 + - - -
59S LEU* 4.0 12.9 - - - +
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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