Contacts of the strand formed by residues 18 - 25 (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 GLY 18 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16S GLU 3.5 1.9 + - - -
17S PRO* 1.3 75.5 - - - +
19S LEU* 1.3 62.1 + - - -
20S GLN* 5.6 2.0 - - - -
49S LEU 3.6 0.9 - - - +
50S LYS* 3.5 14.2 - - - +
51S THR* 2.8 43.7 + - - +
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Residues in contact with LEU 19 (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* 1.3 74.7 - - - -
20S GLN* 1.3 65.7 + - - +
21S ILE* 4.2 5.2 - - + -
37S TYR* 3.3 33.5 + - + -
48S ILE* 3.7 27.6 - - + -
49S LEU 3.5 6.5 - - - +
50S LYS* 4.1 15.3 - - + +
111S TYR* 3.8 37.5 - - + +
112S PHE* 4.0 27.1 - - + -
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Residues in contact with GLN 20 (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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12S LYS* 3.1 34.1 + - - +
13S ALA* 3.8 3.2 - - - +
14S GLY* 3.0 25.0 + - - -
15S LYS 5.3 0.6 - - - +
16S GLU 5.2 3.9 - - - +
18S GLY 5.6 2.1 - - - +
19S LEU* 1.3 78.2 - - - +
21S ILE* 1.3 64.0 + - - +
22S TRP* 3.7 24.4 - - + -
37S TYR* 3.5 5.8 - - - +
48S ILE* 3.4 4.2 - - - +
49S LEU* 2.9 47.0 + - + +
51S THR* 4.3 3.6 + - - -
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Residues in contact with ILE 21 (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* 4.2 4.7 - - + -
20S GLN* 1.3 80.4 - - - +
22S TRP* 1.3 69.2 + - - +
31S PRO* 3.7 4.2 - - - +
32S VAL* 2.9 42.1 + - + +
37S TYR* 3.1 49.5 + - + -
38S GLY 4.5 0.4 - - - +
40S PHE* 4.3 9.9 - - + -
46S TYR* 4.0 16.6 - - + -
47S VAL 3.6 6.1 - - - +
48S ILE* 4.1 17.0 - - + -
112S PHE* 3.7 33.7 - - + -
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Residues in contact with TRP 22 (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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9S GLU* 2.8 50.7 + - + +
13S ALA* 4.0 21.3 - - + -
20S GLN* 3.7 34.8 - - + -
21S ILE* 1.3 77.4 + - - +
23S ARG* 1.3 61.2 - - - +
29S LEU* 3.6 35.9 - - + -
30S VAL 3.2 9.2 - - - +
31S PRO* 3.6 25.0 - - + +
32S VAL* 3.9 4.7 - - - -
46S TYR* 3.4 7.1 - - - +
47S VAL* 2.9 57.1 + - + +
49S LEU* 3.9 26.7 - - + -
86S LEU* 4.1 12.8 - - + -
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Residues in contact with ARG 23 (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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22S TRP* 1.3 76.5 - - - +
24S VAL* 1.3 76.7 + - - +
25S GLU* 2.9 41.6 + - - +
29S LEU* 3.8 2.1 - - - -
30S VAL* 2.7 35.9 + - - +
32S VAL* 3.8 7.7 - - + +
41S PHE* 3.3 26.1 - - - -
44S ASP* 2.8 36.9 + - + +
45S ALA 3.6 10.5 - - - +
46S TYR* 3.6 31.2 - - + -
122S GLY* 4.2 0.6 - - - -
123S VAL* 3.8 19.0 - - - +
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Residues in contact with VAL 24 (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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22S TRP 4.3 0.4 + - - -
23S ARG* 1.3 78.1 - - - +
25S GLU* 1.3 65.4 + - - +
26S LYS 4.7 0.4 - - - +
27S PHE 4.5 10.8 - - - +
28S ASP 3.4 9.4 - - - +
29S LEU* 5.0 0.7 - - + +
44S ASP* 5.1 0.5 - - - -
45S ALA* 3.2 20.7 + - + +
47S VAL* 4.7 5.8 - - + -
74S ASP* 4.7 1.1 - - - +
75S GLU* 3.8 32.4 - - + +
78S ALA* 3.9 19.7 - - + -
79S ALA* 3.7 33.2 - - + +
82S PHE* 4.2 12.6 - - + -
123S VAL* 3.7 10.2 - - - +
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Residues in contact with GLU 25 (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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23S ARG* 2.9 54.6 + - - +
24S VAL* 1.3 80.8 - - - +
26S LYS* 1.3 72.9 + - - +
27S PHE 3.4 0.4 - - - -
28S ASP* 2.9 25.4 + - - +
30S VAL* 3.6 37.0 - - + +
31S PRO 5.0 1.4 - - - +
32S VAL* 5.9 0.2 - - - +
123S VAL* 4.2 16.5 - - + +
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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