Contacts of the helix formed by residues 48 - 59 (chain Z) 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 GLN 48 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397B U 2.8 36.3 + - - +
398B C 3.5 11.7 + - - -
3Z LYS* 3.2 22.6 - - + +
8Z LYS* 6.1 1.3 - - + -
30Z HIS* 3.3 34.8 - - + +
31Z ASP 4.5 0.7 - - - -
32Z LEU* 5.7 0.4 - - - -
47Z LYS* 1.3 84.8 - - - +
49Z ARG* 1.3 91.6 + - - +
50Z ASP* 3.1 26.3 - - - +
51Z VAL* 3.2 23.3 + - + +
52Z ALA* 2.9 19.8 + - - +
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Residues in contact with ARG 49 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B C 2.5 29.8 + - - +
399B U 4.6 7.9 - - - +
2090B A 2.6 68.9 + - - -
2091B C 2.5 61.6 + - - +
30Z HIS* 3.0 29.1 + - + +
31Z ASP 4.9 0.2 + - - -
32Z LEU* 5.8 2.6 - - + +
48Z GLN* 1.3 79.7 - - - +
50Z ASP* 1.3 59.2 + - - +
51Z VAL 2.5 14.5 + - - -
52Z ALA* 2.6 19.6 + - + +
53Z THR* 3.0 14.0 + - + +
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Residues in contact with ASP 50 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B G 4.7 11.1 + - - +
373B U 5.5 0.3 + - - -
397B U 5.1 2.0 - - - +
398B C 3.4 31.8 + - - +
399B U 4.0 35.2 + - - +
400B G 4.4 6.4 - - - +
6Z HIS* 4.5 13.5 + - + +
48Z GLN* 3.1 19.0 - - - +
49Z ARG* 1.3 79.6 - - - +
51Z VAL* 1.3 57.5 + - - +
53Z THR* 3.0 28.7 - - - +
54Z GLY* 5.0 0.3 - - - -
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Residues in contact with VAL 51 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Z LYS* 3.8 7.0 - - + -
4Z ASP* 3.9 1.1 - - - +
5Z ILE* 2.9 54.4 - - + +
6Z HIS* 3.2 24.2 - - + +
8Z LYS* 5.6 2.5 - - + -
47Z LYS* 3.2 28.5 - - + -
48Z GLN* 3.2 31.4 - - + +
49Z ARG 2.5 1.0 + - - -
50Z ASP* 1.3 80.9 - - - +
52Z ALA* 1.3 62.0 + - - -
53Z THR 3.0 7.7 - - - +
54Z GLY* 4.7 0.2 - - - -
55Z GLY 3.9 0.5 + - - -
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Residues in contact with ALA 52 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2091B C 5.7 3.4 - - - -
27H ARG* 3.7 22.7 - - - +
5Z ILE* 4.6 1.1 - - - +
34Z LEU* 6.1 1.8 - - + -
35Z ASP* 5.9 0.7 - - - +
47Z LYS* 3.7 27.1 - - + +
48Z GLN 2.9 11.5 + - - +
49Z ARG* 2.6 19.2 + - + +
51Z VAL* 1.3 67.7 - - - +
53Z THR* 1.3 66.1 + - - +
55Z GLY* 3.0 5.9 + - - -
56Z ARG* 2.9 24.7 + - - +
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Residues in contact with THR 53 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B G 2.9 25.5 + - + +
399B U 6.1 0.4 - - - +
27H ARG* 4.9 0.2 - - - +
49Z ARG* 3.3 16.4 - - + +
50Z ASP* 3.0 40.6 - - + +
51Z VAL 3.0 9.9 - - - +
52Z ALA* 1.3 82.4 - - - +
54Z GLY* 1.3 56.3 + - - +
56Z ARG* 2.7 41.0 + - - +
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Residues in contact with GLY 54 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B G 4.0 18.8 - - - +
50Z ASP 5.0 0.4 - - - -
53Z THR* 1.3 72.7 + - - +
55Z GLY* 1.3 63.1 + - - +
57Z VAL* 2.9 40.6 - - - +
58Z ASP* 3.3 0.3 + - - +
59Z ARG* 3.1 25.3 + - - +
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Residues in contact with GLY 55 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Z ILE* 4.0 14.9 - - - +
51Z VAL 3.9 3.8 + - - -
52Z ALA 3.0 9.5 + - - -
53Z THR 3.1 1.8 + - - -
54Z GLY* 1.3 74.1 - - - +
56Z ARG* 1.3 56.2 + - - +
57Z VAL 2.9 1.0 + - - -
59Z ARG* 2.6 49.7 + - - +
60Z PHE* 2.6 16.7 + - - +
63Z ARG* 5.0 0.4 - - - -
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Residues in contact with ARG 56 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B G 4.7 7.1 + - - -
1H MET* 4.1 10.1 - - - +
24H GLY* 5.2 11.1 - - - +
25H TYR* 2.6 71.6 + - + +
27H ARG* 3.7 45.2 - - + +
38H PRO* 5.9 3.5 - - - +
35Z ASP* 6.2 0.2 - - - +
52Z ALA 2.9 9.2 + - - +
53Z THR* 2.7 45.8 + - - +
55Z GLY* 1.3 73.5 - - - +
57Z VAL* 1.3 63.8 + - - +
58Z ASP 3.6 0.2 - - - -
60Z PHE* 4.4 12.1 - - + +
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Residues in contact with VAL 57 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B A 5.8 2.9 - - - +
372B G 2.9 54.1 - - + +
25H TYR* 4.4 4.4 + - - -
38H PRO* 5.9 0.3 - - - +
40H THR* 4.0 13.6 + - - +
53Z THR* 3.5 4.5 - - - +
54Z GLY* 2.9 29.4 + - - +
55Z GLY 2.9 0.6 - - - -
56Z ARG* 1.3 85.3 - - - +
58Z ASP* 1.3 72.0 + - + +
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Residues in contact with ASP 58 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H THR* 3.2 38.7 + - - +
41H LYS* 4.2 12.8 + - - +
42H LYS* 6.1 0.5 - - - +
54Z GLY 3.3 2.0 + - - +
56Z ARG 3.6 0.2 - - - -
57Z VAL* 1.3 87.0 - - + +
59Z ARG* 1.3 69.5 + - + +
62Z LYS* 3.7 18.1 - - - +
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Residues in contact with ARG 59 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B G 3.1 45.1 + - - -
5Z ILE* 5.1 1.6 - - - -
54Z GLY* 3.1 26.3 + - - +
55Z GLY* 2.6 18.7 + - - +
58Z ASP* 1.3 79.9 + - + +
60Z PHE* 1.3 67.7 + - - +
61Z ASN* 2.4 20.3 + - - +
62Z LYS* 3.2 23.3 + - - +
63Z ARG* 3.1 74.0 - - + +
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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