Contacts of the helix formed by residues 58 - 69 (chain C) in PDB entry 4J2X
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 58 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C ARG 3.9 9.4 - - - +
57C LEU* 1.4 78.2 - - - +
59C ARG* 1.4 63.9 + - - +
60C GLU* 4.1 5.9 + - - +
61C ALA* 3.1 29.1 + - - +
62C MET* 3.1 12.3 + - - +
370C MET* 3.9 16.0 - - + +
411C TRP* 4.2 2.5 - - - -
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Residues in contact with ARG 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C THR* 1.4 69.6 - - - +
60C GLU* 1.4 50.6 + - - +
62C MET* 3.0 6.9 + - - +
63C ARG* 2.8 59.4 + - - +
411C TRP* 4.3 11.1 - - + -
414C ASP* 2.8 57.8 + - - +
415C VAL* 4.0 16.6 - - - +
416C GLU* 5.2 2.5 - - + +
436C ALA 4.7 7.1 + - - -
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Residues in contact with GLU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C THR* 3.3 5.4 - - - +
59C ARG* 1.4 76.5 - - - +
61C ALA* 1.4 51.6 + - - +
63C ARG* 3.2 30.0 + - + +
64C ASN* 2.8 61.7 + - - +
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Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LEU* 3.8 21.4 - - + +
58C THR* 3.1 26.9 + - - +
60C GLU* 1.4 75.4 + - - +
62C MET* 1.4 56.0 + - - +
64C ASN* 3.5 7.4 + - - +
65C TYR* 2.9 26.7 + - - +
367C TYR* 5.8 0.3 - - - -
369C GLY 4.1 7.7 - - - +
370C MET* 3.9 12.6 - - - -
461C ILE* 5.1 0.2 - - - +
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Residues in contact with MET 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LEU* 3.8 13.6 - - + +
58C THR 3.1 6.6 + - - +
59C ARG 3.0 9.4 + - - +
61C ALA* 1.4 74.3 - - - +
63C ARG* 1.4 58.0 + - - +
65C TYR* 2.9 37.5 + - - +
66C LEU* 3.0 34.6 + - + +
411C TRP* 3.7 39.5 - - + -
413C GLY 3.6 18.2 - - - +
414C ASP* 3.9 6.3 - - - -
453C THR* 4.1 16.4 - - + +
455C VAL* 3.7 30.5 - - + -
461C ILE* 4.4 3.8 - - + -
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Residues in contact with ARG 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ARG* 2.8 37.2 + - - +
60C GLU* 3.3 46.1 - - + +
62C MET* 1.4 70.3 - - - +
64C ASN* 1.4 62.3 + - - +
66C LEU* 3.6 10.6 + - - +
67C LYS* 3.1 27.6 + - - +
414C ASP* 2.8 44.5 + - + +
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Residues in contact with ASN 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C GLU* 2.8 51.5 + - - +
61C ALA* 3.6 7.4 - - - +
63C ARG* 1.4 72.2 - - - +
65C TYR* 1.4 64.3 + - - +
67C LYS* 3.6 34.9 - - + +
68C GLU* 4.1 6.6 + - - +
69C ARG 5.4 0.5 - - - +
367C TYR* 5.3 2.0 + - - -
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Residues in contact with TYR 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C ALA 2.9 15.0 + - - +
62C MET* 2.9 19.4 + - - +
64C ASN* 1.4 75.2 - - - +
66C LEU* 1.3 67.0 + - + +
67C LYS 3.1 2.3 + - - -
69C ARG* 2.7 92.1 + - - +
71C ASP* 2.6 33.0 + - - -
367C TYR* 3.5 43.5 - + + -
453C THR* 4.5 5.2 - - + -
461C ILE* 3.6 42.6 - - + +
463C SER* 3.5 5.4 - - - -
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C MET* 3.0 38.2 + - + +
63C ARG* 3.9 9.0 - - - +
65C TYR* 1.3 80.0 - - + +
67C LYS* 1.4 62.1 + - - +
68C GLU 3.6 0.2 - - - -
69C ARG* 3.6 44.0 + - - +
413C GLY* 3.9 28.3 - - - -
414C ASP* 4.2 3.6 - - + +
451C PRO* 3.7 20.6 - - + -
453C THR* 4.7 5.2 - - - +
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Residues in contact with LYS 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ARG 3.1 18.2 + - - +
64C ASN* 3.6 30.1 - - + +
65C TYR 3.1 0.2 + - - -
66C LEU* 1.4 76.3 - - - +
68C GLU* 1.4 89.2 + - - +
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Residues in contact with GLU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ASN 4.1 5.4 + - - +
65C TYR 3.5 1.6 + - - -
67C LYS* 1.4 112.7 + - - +
69C ARG* 1.4 70.2 + - - +
70C GLY* 3.4 3.3 + - - -
108C LYS* 4.9 6.0 + - - +
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Residues in contact with ARG 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ASN 5.4 0.3 - - - +
65C TYR* 2.7 78.4 + - - +
66C LEU* 3.6 36.9 + - - +
68C GLU* 1.4 71.4 - - - +
70C GLY* 1.3 63.9 + - - +
71C ASP* 3.6 11.7 - - - +
108C LYS* 3.3 13.0 + - - -
367C TYR* 3.5 14.7 + - - -
451C PRO* 4.1 15.4 - - - +
453C THR* 4.9 4.0 + - - +
463C SER* 3.6 19.2 + - - +
464C THR 5.5 2.4 + - - +
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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