Contacts of the helix formed by residues 53 - 63 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30O VAL* 3.7 7.6 - - - -
31O ASP 2.7 11.3 + - - +
32O ASN* 3.7 21.4 - - + +
51O MET 3.8 0.2 + - - -
52O ASP* 1.3 77.2 - - - +
54O GLU* 1.3 63.2 + - + +
56O PHE 3.5 0.2 + - - -
57O LEU* 3.0 18.2 + - - +
88O TYR* 3.0 16.4 + - - -
92O ASN* 2.8 25.0 + - - +
96O TYR* 2.7 26.8 + - + +
400O NAP 2.6 74.7 + - + +
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Residues in contact with GLU 54 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87N LYS* 5.5 5.4 - - - +
52O ASP* 2.9 15.3 + - - +
53O LYS* 1.3 82.8 - - + +
55O ASP* 1.3 65.0 + - - +
57O LEU* 3.4 18.1 + - - +
58O ILE* 3.1 41.7 + - + +
96O TYR* 5.5 1.1 - - - -
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Residues in contact with ASP 55 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87N LYS* 5.5 1.0 + - - -
91N ASP* 4.3 14.4 - - - +
95N GLN* 5.9 1.9 - - - +
51O MET* 4.0 15.6 - - + +
52O ASP* 3.1 27.1 + - - +
54O GLU* 1.3 75.8 - - - +
56O PHE* 1.3 67.9 + - - +
58O ILE* 3.2 13.6 + - - +
59O GLN* 3.0 33.8 + - - +
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Residues in contact with PHE 56 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3O ILE* 4.1 28.5 - - + -
5O THR* 4.2 11.0 - - + -
28O LEU* 4.4 2.9 - - + -
30O VAL* 3.6 34.8 - - + -
51O MET* 4.0 15.4 - - + +
52O ASP 3.0 16.0 + - - +
53O LYS 3.6 4.5 - - - +
55O ASP* 1.3 77.6 - - - +
57O LEU* 1.3 57.3 + - - +
59O GLN* 3.1 4.5 + - - +
60O ILE* 2.8 48.3 + - + +
66O PHE* 3.6 31.2 - + - -
72O ILE* 4.7 4.5 - - + -
96O TYR* 3.5 15.5 - + - -
100O LEU* 3.7 25.8 - - + -
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Residues in contact with LEU 57 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53O LYS 3.0 17.7 + - - +
54O GLU* 3.7 20.6 - - - +
56O PHE* 1.3 77.1 - - - +
58O ILE* 1.3 64.1 + - + +
60O ILE* 3.2 8.7 + - + +
61O MET* 2.9 47.8 + - + +
91O ASP 6.1 0.2 - - - +
96O TYR* 3.6 42.3 + - + -
99O GLU* 4.0 31.9 - - + -
100O LEU* 5.2 1.1 - - + -
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Residues in contact with ILE 58 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54O GLU* 3.1 38.1 + - + +
55O ASP* 3.2 15.5 + - - +
57O LEU* 1.3 79.2 - - + +
59O GLN* 1.3 63.0 + - + +
61O MET* 3.3 13.5 + - + +
62O ALA* 3.0 29.9 + - + +
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Residues in contact with GLN 59 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51O MET* 4.1 22.0 - - - +
55O ASP* 3.0 21.0 + - - +
56O PHE* 3.6 7.2 - - - +
58O ILE* 1.3 79.7 - - + +
60O ILE* 1.3 66.4 + - - +
62O ALA* 3.2 2.3 + - - -
63O GLY 3.0 4.5 + - - -
64O GLU* 3.0 54.7 + - + +
66O PHE* 3.4 28.8 - - + -
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Residues in contact with ILE 60 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56O PHE* 2.8 44.6 + - + +
57O LEU* 3.4 10.8 - - + +
59O GLN* 1.3 74.4 - - - +
61O MET* 1.3 67.0 + - + +
63O GLY* 3.0 19.6 + - - -
66O PHE* 3.7 20.9 - - + -
99O GLU* 3.9 17.0 - - + +
100O LEU* 3.9 15.7 - - + -
103O TYR* 3.5 54.8 - - + -
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Residues in contact with MET 61 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57O LEU* 2.9 45.0 + - + +
58O ILE* 3.8 12.1 - - + +
60O ILE* 1.3 76.5 - - + +
62O ALA* 1.3 58.2 + - - +
63O GLY 3.2 1.2 + - - -
99O GLU* 3.4 44.9 - - + +
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Residues in contact with ALA 62 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58O ILE* 3.0 20.3 + - + +
59O GLN* 3.7 5.6 - - - +
60O ILE 3.2 0.4 - - - -
61O MET* 1.3 77.7 - - - +
63O GLY* 1.3 61.1 + - - +
64O GLU* 4.0 18.3 - - - +
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Residues in contact with GLY 63 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59O GLN 3.0 0.2 + - - -
60O ILE 3.0 16.3 + - - -
61O MET 3.2 1.4 + - - -
62O ALA* 1.3 81.0 - - - +
64O GLU* 1.3 65.8 + - - +
65O GLU* 3.6 7.1 + - - +
103O TYR* 4.3 0.4 - - - -
107O ARG* 3.5 25.6 + - - -
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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