Contacts of the helix formed by residues 49 - 57 (chain J) in PDB entry 4LLL
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 THR 49 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47J GLY 4.0 5.6 - - - +
48J LEU* 1.3 71.6 - - - +
50J GLN* 1.3 61.3 + - - +
51J ASN* 3.7 9.7 + - - +
52J ASP* 2.4 51.9 + - - +
53J ILE* 3.0 17.2 + - - +
88J ARG* 4.4 13.2 - - + +
89J LYS 3.1 17.5 - - - +
90J ASN* 3.2 25.6 - - - +
91J ILE* 4.3 2.5 - - - -
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Residues in contact with GLN 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J THR* 1.3 74.5 - - - +
51J ASN* 1.3 60.4 + - - +
53J ILE* 3.2 3.5 + - - +
54J ALA* 2.6 36.5 + - - +
61J GLY 5.4 1.6 - - - +
64J VAL* 3.7 11.1 - - + +
65J SER* 4.0 25.2 + - - +
68J LEU* 3.2 33.2 - - + +
79J ARG* 3.5 28.1 - - - +
89J LYS* 4.0 20.9 + - + +
91J ILE* 4.3 7.5 - - + +
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Residues in contact with ASN 51 (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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49J THR* 3.3 6.8 + - - +
50J GLN* 1.3 84.3 + - - +
52J ASP* 1.3 61.4 + - - +
54J ALA* 3.6 9.9 - - + +
55J LYS* 2.9 31.4 + - - +
61J GLY* 5.4 9.7 - - - -
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Residues in contact with ASP 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J TYR* 4.5 5.0 + - - -
47J GLY 4.3 1.2 - - - +
48J LEU* 3.4 19.2 - - + -
49J THR* 2.4 51.8 + - - +
51J ASN* 1.3 80.5 - - - +
53J ILE* 1.3 54.5 - - - +
55J LYS* 3.8 3.2 + - - +
56J ALA* 3.2 24.6 + - - +
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Residues in contact with ILE 53 (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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36J THR* 4.5 11.9 - - + +
39J TYR* 3.6 25.4 - - + -
40J LEU* 4.2 14.1 - - + -
48J LEU* 4.1 12.1 - - + -
49J THR 3.0 12.2 + - - +
50J GLN* 3.8 6.5 - - - +
52J ASP* 1.3 77.2 - - - +
54J ALA* 1.3 61.7 + - - +
56J ALA* 3.5 4.2 - - - +
57J LEU* 2.9 54.9 + - + +
64J VAL* 4.8 6.3 - - + -
68J LEU* 4.7 11.0 - - + -
91J ILE* 3.8 39.0 - - + -
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Residues in contact with ALA 54 (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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50J GLN 2.6 21.7 + - - +
51J ASN* 3.2 14.1 + - + +
53J ILE* 1.3 75.1 - - - +
55J LYS* 1.3 59.8 + - - +
57J LEU* 3.4 1.1 + - - -
58J GLN* 3.1 4.3 + - - -
59J ARG 3.0 41.3 + - - +
60J THR 4.1 6.3 - - - +
61J GLY* 4.8 4.5 - - - +
64J VAL* 3.5 23.1 - - + +
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Residues in contact with LYS 55 (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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51J ASN 2.9 16.3 + - - +
52J ASP* 4.2 4.0 - - - +
54J ALA* 1.3 72.4 - - - +
56J ALA* 1.3 67.0 + - - +
57J LEU 3.2 0.5 + - - -
58J GLN* 3.2 17.2 + - - +
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Residues in contact with ALA 56 (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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7I TYR* 4.4 16.8 + - - -
39J TYR* 3.6 36.6 - - + +
52J ASP 3.2 18.4 + - - +
53J ILE 3.5 6.3 - - - +
54J ALA 3.3 0.2 - - - -
55J LYS* 1.3 80.4 - - - +
57J LEU* 1.3 62.6 + - + +
58J GLN* 3.7 0.3 + - - +
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Residues in contact with LEU 57 (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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7I TYR* 6.0 4.7 - - + -
11I MET* 3.8 20.8 - - + +
35J HIS* 4.9 11.4 - - + +
36J THR* 4.1 25.1 - - + +
39J TYR* 4.9 14.8 - - + -
53J ILE* 2.9 40.1 + - + +
54J ALA 4.2 0.9 - - - +
56J ALA* 1.3 81.1 - - + +
58J GLN* 1.3 70.4 + - - +
59J ARG* 3.1 23.2 + - + +
64J VAL* 5.3 6.3 - - + -
67J LEU* 5.1 6.1 - - + -
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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