Contacts of the helix formed by residues 53 - 63 (chain J) in PDB entry 2X86
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 LYS 53 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30J VAL* 3.7 7.6 - - - -
31J ASP 2.7 14.4 + - - +
32J ASN* 3.7 25.0 - - + +
51J MET 3.8 0.2 + - - -
52J ASP* 1.3 76.5 - - - +
54J GLU* 1.3 64.0 + - + +
57J LEU* 3.0 18.0 + - - +
88J TYR* 3.0 15.8 + - - -
92J ASN* 2.8 26.3 + - - +
96J TYR* 2.7 33.9 + - + +
400J NAP 2.8 61.0 + - + +
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Residues in contact with GLU 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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87I LYS* 5.5 4.5 - - - +
52J ASP* 2.9 15.6 + - - +
53J LYS* 1.3 83.7 - - + +
55J ASP* 1.3 64.9 + - - +
57J LEU* 3.4 18.8 + - - +
58J ILE* 3.1 41.9 + - + +
96J TYR* 5.5 0.9 - - - -
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Residues in contact with ASP 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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87I LYS* 5.6 0.7 + - - -
91I ASP* 4.3 14.6 - - - +
95I GLN* 5.8 2.4 - - - +
51J MET* 4.0 15.2 - - + +
52J ASP* 3.1 26.8 + - - +
54J GLU* 1.3 75.9 - - - +
56J PHE* 1.3 67.9 + - - +
58J ILE* 3.2 14.8 + - - +
59J GLN* 3.0 34.7 + - - +
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Residues in contact with PHE 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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3J ILE* 4.1 28.7 - - + -
5J THR* 4.2 11.4 - - + -
28J LEU* 4.4 2.7 - - + -
30J VAL* 3.6 34.5 - - + -
51J MET* 4.0 16.3 - - + +
52J ASP 3.0 15.5 + - - +
53J LYS 3.6 4.3 - - - +
55J ASP* 1.3 77.2 - - - +
57J LEU* 1.3 57.6 + - - +
59J GLN* 3.1 4.9 + - - +
60J ILE* 2.8 47.7 + - + +
66J PHE* 3.6 31.2 - + - -
72J ILE* 4.7 4.9 - - + -
96J TYR* 3.5 17.3 - + - -
100J LEU* 3.7 24.5 - - + -
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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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53J LYS 3.0 17.6 + - - +
54J GLU* 3.7 20.2 - - - +
56J PHE* 1.3 76.7 - - - +
58J ILE* 1.3 63.1 + - + +
60J ILE* 3.2 9.4 + - + +
61J MET* 2.9 48.3 + - + +
96J TYR* 3.6 42.4 + - + -
99J GLU* 4.0 32.3 - - + -
100J LEU* 5.2 1.6 - - + -
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Residues in contact with ILE 58 (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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54J GLU* 3.1 37.4 + - + +
55J ASP* 3.2 15.5 + - - +
57J LEU* 1.3 78.8 - - + +
59J GLN* 1.3 63.8 - - + +
61J MET* 3.3 13.5 + - + +
62J ALA* 3.0 29.2 + - + +
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Residues in contact with GLN 59 (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 MET* 4.1 21.2 - - - +
55J ASP* 3.0 21.0 + - - +
56J PHE 3.6 6.5 - - - +
58J ILE* 1.3 79.3 - - + +
60J ILE* 1.3 65.7 + - - +
62J ALA* 3.2 2.2 + - - -
63J GLY 3.0 4.5 + - - -
64J GLU* 3.0 52.4 + - + +
66J PHE* 3.4 28.8 - - + -
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Residues in contact with ILE 60 (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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56J PHE* 2.8 44.9 + - + +
57J LEU* 3.4 11.2 - - + +
59J GLN* 1.3 75.2 - - - +
61J MET* 1.3 64.6 + - + +
63J GLY* 3.0 18.9 + - - -
66J PHE* 3.7 20.0 - - + -
72J ILE* 5.4 0.9 - - + -
99J GLU* 3.9 17.3 - - + +
100J LEU* 3.9 15.9 - - + -
103J TYR* 3.5 54.2 - - + +
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Residues in contact with MET 61 (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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57J LEU* 2.9 46.1 + - + +
58J ILE* 3.8 12.1 - - + +
60J ILE* 1.3 77.2 - - - +
62J ALA* 1.3 60.4 + - - +
63J GLY 3.2 1.2 + - - -
99J GLU* 3.4 45.3 - - + +
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Residues in contact with ALA 62 (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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58J ILE* 3.0 19.0 + - + +
59J GLN* 3.7 5.8 - - - +
60J ILE 3.2 0.6 - - - -
61J MET* 1.3 76.6 - - - +
63J GLY* 1.3 63.2 + - - +
64J GLU* 4.0 18.2 - - - +
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Residues in contact with GLY 63 (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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59J GLN 3.0 0.2 + - - -
60J ILE 3.0 16.3 + - - -
61J MET 3.2 1.4 + - - -
62J ALA* 1.3 80.4 - - - +
64J GLU* 1.3 65.8 + - - +
65J GLU* 3.6 6.8 + - - +
103J TYR* 4.3 0.2 - - - -
107J ARG* 3.5 25.7 + - - -
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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
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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