Contacts of the helix formed by residues 14 - 22 (chain S) in PDB entry 2J28
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 14 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517B C 5.5 1.8 - - - +
13S SER* 1.3 77.1 + - - +
15S GLN* 1.3 64.6 + - - +
16S LYS 2.9 6.0 + - - -
17S VAL* 2.9 5.1 + - - +
18S ARG* 2.9 23.8 + - - +
76S VAL* 4.3 11.2 - - + +
77S ASP 4.7 1.8 - - - -
78S GLU* 4.0 29.4 - - + +
99S ARG* 5.2 3.5 - - - +
100S THR 4.4 1.0 + - - +
101S SER* 3.6 19.3 - - - -
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Residues in contact with GLN 15 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120 ARG* 2.9 44.1 + - - +
518B G 6.1 0.4 - - - +
1265B A 5.9 0.2 - - - +
1266B G 3.2 52.6 + - + +
13S SER* 4.2 4.0 - - - +
14S ALA* 1.3 78.1 - - - +
16S LYS* 1.3 58.0 + - - +
17S VAL 3.4 0.2 - - - -
18S ARG* 4.0 8.3 - - - -
19S LEU* 3.0 38.1 + - + +
99S ARG* 5.1 6.1 + - - -
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Residues in contact with LYS 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1266B G 2.8 42.7 + - + +
2010B G 5.8 2.0 - - - -
2011B U 2.8 37.2 - - - +
2012B G 2.9 38.8 + - - +
12S SER* 3.3 16.6 - - - +
13S SER* 3.1 24.5 + - - +
14S ALA 2.9 1.0 + - - -
15S GLN* 1.3 80.0 - - - +
17S VAL* 1.3 62.5 + - - +
19S LEU* 3.9 15.4 + - - +
20S VAL 4.2 0.2 + - - -
43S ALA* 3.7 18.0 - - + +
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Residues in contact with VAL 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S ALA* 5.6 2.0 - - + -
12S SER* 3.7 22.2 - - - +
13S SER 3.6 20.2 - - - +
14S ALA 2.9 4.4 + - - +
16S LYS* 1.3 75.9 - - - +
18S ARG* 1.3 67.3 + - - +
19S LEU 3.2 0.4 - - - -
20S VAL* 2.8 40.3 + - + +
21S ALA* 3.4 4.7 + - + +
43S ALA* 4.2 9.0 - - - +
45S VAL* 5.0 2.9 - - + -
47S VAL* 4.1 9.9 - - + -
76S VAL* 4.1 13.7 - - + -
101S SER* 4.3 4.0 - - - +
103S ILE* 3.5 30.7 - - + -
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Residues in contact with ARG 18 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190 ASP* 5.3 9.1 - - - +
518B G 4.9 5.4 + - - +
519B U 3.3 27.1 + - - +
14S ALA 2.9 14.8 + - - +
15S GLN* 4.0 11.2 - - - +
16S LYS 3.4 0.2 - - - -
17S VAL* 1.3 76.2 - - - +
19S LEU* 1.3 68.3 + - - +
21S ALA* 3.0 13.5 + - + +
22S ASP* 2.6 69.3 + - - +
76S VAL* 3.7 24.3 - - + +
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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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160 ARG* 5.3 16.4 - - - +
190 ASP* 5.0 24.2 - - + +
200 ALA 6.1 0.2 - - - +
210 LEU* 3.6 25.7 - - + +
15S GLN* 3.0 24.9 - - + +
16S LYS* 3.9 10.3 - - - +
17S VAL 3.2 0.4 - - - -
18S ARG* 1.3 90.7 - - + +
20S VAL* 1.3 59.8 + - - +
21S ALA 3.3 0.6 + - - -
22S ASP* 3.3 12.0 + - - +
41S LYS* 4.9 16.6 + - - +
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Residues in contact with VAL 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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210 LEU* 5.9 1.1 - - - -
16S LYS 4.2 1.0 + - - -
17S VAL* 2.8 22.3 + - + +
19S LEU* 1.3 78.5 - - - +
21S ALA* 1.3 60.3 + - - +
24S ILE* 2.9 22.5 - - - +
36S LEU* 3.9 14.0 - - + +
39S THR* 4.6 9.4 - - + +
41S LYS* 4.0 15.9 - - + +
43S ALA* 3.3 43.1 - - + +
44S ALA* 3.8 17.9 - - + +
47S VAL* 3.8 18.2 - - + -
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Residues in contact with ALA 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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17S VAL* 4.1 9.6 - - + +
18S ARG* 3.0 9.5 + - - +
20S VAL* 1.3 84.1 - - + +
22S ASP* 1.3 66.1 + - - +
24S ILE* 3.0 17.1 + - - -
47S VAL* 4.9 10.8 - - + -
74S ILE* 3.0 40.8 - - + +
75S PHE* 6.0 2.0 - - - +
76S VAL* 5.8 5.8 - - + -
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Residues in contact with ASP 22 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190 ASP* 4.6 6.1 - - - +
210 LEU* 5.0 3.6 - - + -
519B U 4.7 1.6 + - - +
18S ARG* 2.6 71.8 + - - +
19S LEU* 3.3 15.0 - - - +
20S VAL 3.8 0.8 - - - -
21S ALA* 1.3 72.9 - - - +
23S LEU* 1.3 58.6 + - + +
24S ILE 2.7 15.2 + - - -
25S ARG* 3.1 28.2 + - - +
74S ILE* 5.2 0.7 - - - -
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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
------------------------------------------------------------
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