Contacts of the helix formed by residues 39 - 48 (chain J) in PDB entry 2WWA
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 ASN 39 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1922G U 4.3 22.1 - - - +
37J SER* 3.8 6.9 + - - +
38J ARG* 1.4 75.3 - - - +
40J ALA* 1.4 61.1 + - - +
41J ILE 3.3 2.6 + - - -
42J ARG* 3.6 43.1 + - - +
43J LYS* 3.8 7.1 + - - +
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Residues in contact with ALA 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35J ALA* 3.7 37.0 - - + +
37J SER* 3.8 14.7 + - - +
38J ARG 3.5 0.2 - - - -
39J ASN* 1.4 77.8 - - - +
41J ILE* 1.4 58.1 + - - +
42J ARG 3.5 0.4 - - - -
43J LYS* 4.1 9.4 - - - +
44J LEU* 3.5 24.4 + - - +
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Residues in contact with ILE 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J GLN* 3.6 27.6 - - - +
10J LEU* 3.3 37.9 - - + +
11J ALA* 4.2 3.1 - - - +
14J VAL* 3.6 22.9 - - + +
35J ALA* 3.9 7.0 - - + -
37J SER 3.6 22.0 - - - +
38J ARG* 3.6 20.2 - - + +
40J ALA* 1.4 80.2 - - - +
42J ARG* 1.4 60.5 + - - +
43J LYS 3.4 0.7 - - - -
44J LEU* 3.9 13.8 - - + +
45J VAL* 3.2 30.3 + - - +
50J ILE* 4.7 10.3 - - + -
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Residues in contact with ARG 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1922G U 3.4 20.5 + - - +
1923G U 5.0 8.9 + - - -
14J VAL* 4.8 15.1 - - + +
38J ARG 3.7 16.2 + - - +
39J ASN* 3.6 35.7 + - - +
40J ALA 3.5 0.6 - - - -
41J ILE* 1.4 78.1 - - - +
43J LYS* 1.4 62.8 + - - +
45J VAL* 3.6 5.5 + - - +
46J LYS* 3.2 19.1 + - - +
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Residues in contact with LYS 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1920G C 3.6 16.4 + - - +
1921G U 3.4 45.8 + - - +
1922G U 3.6 10.9 + - - +
39J ASN 3.8 8.0 + - - +
40J ALA* 4.1 12.1 - - - +
42J ARG* 1.4 78.7 - - - +
44J LEU* 1.4 67.0 + - + +
46J LYS* 3.4 3.8 + - - +
47J ASN* 2.9 39.2 + - - +
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Residues in contact with LEU 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J GLU* 5.7 0.4 - - - +
31J GLU* 3.9 23.8 - - + +
32J ILE* 3.8 24.0 - - + +
35J ALA* 4.1 11.2 - - + -
40J ALA 3.5 19.1 - - - +
41J ILE* 3.8 8.6 + - + +
42J ARG 3.4 0.2 - - - -
43J LYS* 1.4 79.2 - - + +
45J VAL* 1.4 63.9 + - - +
47J ASN* 3.6 3.8 + - - +
48J GLY 3.2 3.3 + - - -
49J THR* 3.0 53.2 + - + +
50J ILE* 3.4 30.7 + - + -
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Residues in contact with VAL 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J ALA* 6.3 0.4 - - + -
14J VAL* 4.9 5.8 - - + -
15J VAL* 4.4 24.5 - - + -
41J ILE* 3.2 19.8 + - + +
42J ARG* 3.9 6.5 - - - +
44J LEU* 1.4 77.0 - - - +
46J LYS* 1.4 62.4 + - - +
48J GLY* 3.3 11.1 + - - -
50J ILE* 3.5 40.6 - - + +
51J VAL* 5.5 1.5 - - - +
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Residues in contact with LYS 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1919G C 3.2 37.0 + - - +
1921G U 3.3 35.9 + - - +
1922G U 3.2 30.7 - - - +
1923G U 3.3 24.5 + - + +
42J ARG 3.2 17.6 + - - +
43J LYS 3.4 4.2 + - - +
45J VAL* 1.4 73.6 - - - +
47J ASN* 1.4 64.4 + - - +
48J GLY* 3.6 0.3 + - - -
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Residues in contact with ASN 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1920G C 3.4 30.9 + - - -
1921G U 3.4 10.3 + - - +
43J LYS* 2.9 43.7 + - - +
44J LEU* 3.8 5.4 - - - +
46J LYS* 1.4 76.0 - - - +
48J GLY* 1.4 58.2 + - - +
49J THR* 3.7 18.9 + - - +
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Residues in contact with GLY 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J TRP* 4.0 8.0 - - - -
25J ASP* 5.9 0.2 - - - -
44J LEU 3.2 3.2 + - - -
45J VAL 3.3 13.1 + - - -
46J LYS 4.5 0.2 - - - -
47J ASN* 1.4 76.3 - - - +
49J THR* 1.4 63.1 + - - +
50J ILE 3.3 5.8 - - - -
51J VAL* 3.6 19.8 - - - +
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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