Contacts of the helix formed by residues 64 - 76 (chain C) in PDB entry 3BXK
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 ASP 64 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C PHE* 3.5 5.4 - - - -
25C GLY 3.7 16.6 - - - +
26C THR* 4.3 8.1 - - + +
58C ASP* 4.5 8.3 - - - +
60C ASN* 5.2 5.7 + - - +
63C ILE* 1.3 74.0 - - - +
65C PHE* 1.3 65.9 + - - +
66C PRO* 3.3 20.1 - - + +
67C GLU* 2.8 33.4 + - - +
68C PHE* 3.0 20.4 + - - +
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Residues in contact with PHE 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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9C ILE* 3.6 33.7 - - + -
12C PHE* 3.8 7.9 - - + -
13C LYS* 3.4 55.9 - - + +
16C PHE* 3.5 35.4 - + + -
25C GLY 4.4 0.6 + - - -
64C ASP* 1.3 75.3 - - - +
66C PRO* 1.4 74.2 - - + +
68C PHE* 3.1 6.2 + + - +
69C LEU* 2.8 44.8 + - + +
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Residues in contact with PRO 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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64C ASP* 3.3 18.4 - - + +
65C PHE* 1.4 98.3 - - + +
67C GLU* 1.3 57.5 + - + +
69C LEU* 3.4 11.2 + - + +
70C THR* 3.0 31.2 + - - -
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Residues in contact with GLU 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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55C VAL* 3.4 29.3 - - - +
56C ASP* 3.2 2.1 - - - +
57C ALA* 3.1 32.4 + - + +
58C ASP* 3.3 14.2 + - - +
63C ILE* 3.6 7.6 - - + -
64C ASP* 2.8 37.3 + - - +
66C PRO* 1.3 75.5 - - + +
68C PHE* 1.3 67.1 + - - +
70C THR* 3.3 9.3 + - - -
71C MET 3.2 17.2 + - - -
150C CA 2.4 31.1 - - - -
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Residues in contact with PHE 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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12C PHE* 3.4 27.8 - - + -
15C ALA* 4.3 1.6 - - + -
16C PHE* 3.6 35.0 - + + -
19C PHE* 4.0 22.4 - + - -
27C ILE* 3.9 14.4 - - + -
55C VAL* 4.2 4.9 - - + -
63C ILE* 3.8 11.9 - - + +
64C ASP 3.0 12.0 + - - +
65C PHE* 3.3 12.1 - + - +
67C GLU* 1.3 76.3 - - - +
69C LEU* 1.3 57.1 + - - +
71C MET* 3.2 5.3 + - - +
72C MET* 3.0 61.0 + - + +
1961D ILE* 6.2 2.2 - - + -
1965D MET* 3.9 26.1 - - + +
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Residues in contact with LEU 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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4C LEU* 5.1 9.2 - - + -
9C ILE* 3.6 47.3 - - + -
12C PHE* 3.9 21.8 - - + -
65C PHE* 2.8 36.6 + - + +
66C PRO* 3.6 9.9 - - + +
68C PHE* 1.3 73.2 - - - +
70C THR* 1.3 65.7 + - - +
72C MET* 3.7 5.2 - - - +
73C ALA* 3.0 24.7 + - + +
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Residues in contact with THR 70 (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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66C PRO 3.0 17.0 + - - -
67C GLU* 3.3 12.1 + - - -
69C LEU* 1.3 75.9 - - - +
71C MET* 1.3 62.2 + - - +
73C ALA* 3.9 3.4 - - - +
74C ARG* 3.2 46.6 + - + +
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Residues in contact with MET 71 (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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54C GLU* 4.8 8.1 - - - +
55C VAL* 4.0 24.0 - - + -
67C GLU 3.2 10.6 + - - +
68C PHE 3.5 7.2 - - - +
70C THR* 1.3 77.3 - - - +
72C MET* 1.3 66.9 + - - +
73C ALA 3.3 0.2 + - - -
74C ARG* 3.0 42.4 + - - +
75C LYS* 3.0 70.8 + - + +
1961D ILE* 4.4 14.8 - - - -
1962D TYR* 5.2 2.2 - - + -
1965D MET* 3.6 25.1 - - + -
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Residues in contact with MET 72 (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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12C PHE* 3.9 43.7 - - + -
15C ALA* 4.6 4.0 - - + -
68C PHE* 3.0 42.2 + - + +
69C LEU* 3.7 5.6 - - - +
71C MET* 1.3 75.3 - - - +
73C ALA* 1.3 63.3 + - - +
75C LYS* 4.0 1.6 - - - +
76C MET* 3.1 29.5 + - - +
1962D TYR* 4.0 17.5 - - + -
1965D MET* 3.4 53.2 - - + +
1966D MET* 5.6 0.4 - - - -
1969D GLU* 4.4 10.5 - - + -
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Residues in contact with ALA 73 (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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4C LEU* 3.7 32.1 - - + -
12C PHE* 5.4 2.9 - - + -
69C LEU* 3.0 16.8 + - + +
70C THR* 3.9 4.0 - - - +
72C MET* 1.3 81.3 - - - +
74C ARG* 1.3 63.2 + - - +
76C MET* 3.5 23.3 + - - +
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Residues in contact with ARG 74 (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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54C GLU 4.1 14.5 + - - -
55C VAL* 5.3 1.2 - - - +
70C THR* 3.2 38.1 + - + +
71C MET* 3.0 42.9 - - - +
73C ALA* 1.3 81.3 - - - +
75C LYS* 1.3 62.2 + - + +
78C ASP* 3.3 25.5 + - + +
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Residues in contact with LYS 75 (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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54C GLU* 4.4 11.7 + - - -
71C MET* 3.0 48.5 + - + +
74C ARG* 1.3 79.0 - - + +
76C MET* 1.3 62.0 + - - +
78C ASP* 3.1 21.7 - - - +
80C ASP 6.1 0.4 - - - -
81C SER* 2.7 38.3 + - - +
84C GLU* 3.3 31.5 + - - -
1960D LYS* 5.7 1.0 - - - +
1962D TYR* 3.7 36.2 - - + +
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Residues in contact with MET 76 (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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82A GLU* 5.7 3.8 - - - +
4C LEU* 6.4 2.0 - - + -
8C GLN* 3.3 25.6 - - - +
12C PHE* 3.8 29.8 - - - -
72C MET* 3.1 19.6 + - - +
73C ALA* 3.6 16.4 - - - +
74C ARG 3.4 0.4 - - - -
75C LYS* 1.3 75.8 - - - +
78C ASP 2.6 33.4 + - - +
1962D TYR* 3.8 16.4 - - - +
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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