Contacts of the helix formed by residues 59 - 67 (chain X) in PDB entry 5JPQ
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 SER 59 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54X TRP* 5.9 2.0 - - - -
55X ASN 3.2 12.7 + - - -
56X ALA 3.0 16.1 - - - +
58X ARG* 1.3 79.3 - - - +
60X LYS* 1.3 65.9 + - - +
61X LEU* 4.5 2.0 - - - -
62X ALA* 3.3 15.6 + - - +
63X GLY 3.1 10.4 + - - -
89X THR* 5.5 2.9 - - - -
90X THR* 4.3 27.1 - - - +
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Residues in contact with LYS 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56X ALA 5.0 0.7 - - - -
58X ARG 3.9 3.4 + - - -
59X SER* 1.3 68.9 - - - +
61X LEU* 1.3 60.8 + - - +
63X GLY* 3.1 3.4 + - - +
64X ALA* 2.8 29.7 + - - +
90X THR* 5.1 4.2 - - - -
153X ASP* 6.1 3.8 - - + -
180X VAL* 5.5 11.9 - - + -
216X LEU* 5.8 7.7 - - + +
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Residues in contact with LEU 61 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X SER* 3.2 4.1 - - - -
60X LYS* 1.3 76.1 - - - +
62X ALA* 1.3 64.5 + - - +
64X ALA* 3.1 8.0 + - - +
65X ILE* 3.0 24.3 + - - +
90X THR* 5.4 9.7 - - - -
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Residues in contact with ALA 62 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27X LEU* 5.2 6.1 - - + -
54X TRP* 4.0 24.5 - - + +
56X ALA* 3.8 19.0 - - + +
59X SER* 3.3 20.9 + - - +
61X LEU* 1.3 77.9 - - - +
63X GLY* 1.3 62.4 + - - +
65X ILE* 3.5 8.0 + - - +
66X LEU* 3.1 23.2 + - - +
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Residues in contact with GLY 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56X ALA* 4.0 16.5 - - - +
59X SER 3.1 13.8 + - - -
60X LYS* 3.1 5.4 + - - -
61X LEU 3.1 0.2 - - - -
62X ALA* 1.3 76.3 - - - +
64X ALA* 1.3 56.4 + - - +
66X LEU* 3.0 7.8 + - - +
67X LYS* 2.9 28.8 + - - +
216X LEU* 5.8 7.2 - - - -
219X TYR* 4.6 12.1 - - - -
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Residues in contact with ALA 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X LYS 2.8 18.0 + - - +
61X LEU* 3.6 8.3 - - - +
63X GLY* 1.3 72.0 - - - +
65X ILE* 1.3 60.8 + - - +
67X LYS* 3.3 13.9 + - - +
68X GLY 3.4 1.2 + - - -
69X LEU* 3.1 29.4 + - + +
214X ILE* 5.1 12.1 - - + +
216X LEU* 5.8 4.6 - - + +
225X ILE* 4.8 18.6 - - + -
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Residues in contact with ILE 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61X LEU 3.0 11.9 + - - +
62X ALA* 3.5 12.3 - - - +
63X GLY 3.2 0.2 - - - -
64X ALA* 1.3 76.3 - - - +
66X LEU* 1.3 55.7 + - - +
67X LYS 3.0 0.9 - - - -
68X GLY* 2.8 22.3 + - - -
69X LEU* 3.7 11.6 + - + +
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Residues in contact with LEU 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56X ALA* 5.1 8.3 - - + -
62X ALA 3.1 11.8 + - - +
63X GLY* 3.0 11.9 + - - +
65X ILE* 1.3 75.1 - - - +
67X LYS* 1.3 57.0 + - - +
68X GLY 3.3 2.0 + - - -
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Residues in contact with LYS 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63X GLY 2.9 14.0 + - - +
64X ALA* 3.6 9.4 - - - +
65X ILE 3.0 1.0 - - - -
66X LEU* 1.3 78.7 - - - +
68X GLY* 1.3 60.6 + - - +
214X ILE* 4.9 12.6 - - + +
215X ASN 4.3 18.2 - - - +
216X LEU* 5.5 2.7 - - - -
217X ASP 6.0 1.3 - - - +
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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