Contacts of the helix formed by residues 67 - 78 (chain C) in PDB entry 4BSX
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 67 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU* 5.2 4.0 - - - +
64C LEU* 2.9 15.9 - - + +
66C MSE 1.3 77.2 + - - +
68C ALA* 1.3 65.5 + - - +
69C VAL* 3.2 14.9 + - - +
70C ALA* 2.8 33.8 + - + +
71C ARG* 3.0 24.9 - - - +
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Residues in contact with ALA 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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66C MSE 3.7 3.6 + - - -
67C ASP* 1.3 75.0 + - - +
69C VAL* 1.3 59.6 + - + +
71C ARG* 3.3 29.6 + - - +
72C LEU* 3.1 26.3 + - - +
87C GLU* 4.5 6.1 - - - +
90C PRO* 3.8 25.9 - - + +
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Residues in contact with VAL 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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8C LEU* 4.9 7.2 - - + -
42C LEU* 4.0 15.5 - - + -
67C ASP* 3.2 13.8 + - - +
68C ALA* 1.3 75.8 - - + +
70C ALA* 1.3 60.8 + - - +
72C LEU* 3.3 3.8 + - + +
73C VAL* 2.9 34.8 + - + +
90C PRO* 4.2 8.7 - - + -
91C ASP 3.8 22.2 - - - +
92C VAL* 4.2 20.6 - - + -
95C ALA* 3.8 31.4 - - + -
96C VAL* 6.3 0.4 - - + -
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Residues in contact with ALA 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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42C LEU* 4.0 21.0 - - + +
61C LEU* 3.8 10.3 - - + +
64C LEU* 3.4 44.4 - - + +
67C ASP* 2.8 17.3 + - + +
69C VAL* 1.3 77.3 - - - +
71C ARG* 1.3 57.0 + - - +
73C VAL* 3.5 2.6 + - - +
74C ALA* 2.9 27.9 + - - +
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Residues in contact with ARG 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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65C LYS* 2.7 54.1 + - + +
66C MSE 3.1 24.4 + - - +
67C ASP 3.0 8.3 - - - +
68C ALA* 3.4 27.8 - - - +
70C ALA* 1.3 74.7 - - - +
72C LEU* 1.3 64.7 + - - +
74C ALA* 3.2 7.6 + - - +
75C ARG* 3.0 52.7 + - - +
87C GLU* 2.9 39.8 + - - +
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Residues in contact with LEU 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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8C LEU* 4.4 15.3 - - + -
68C ALA 3.1 13.0 + - - +
69C VAL 3.3 7.6 + - - +
71C ARG* 1.3 76.5 - - - +
73C VAL* 1.3 56.5 + - - +
75C ARG* 3.8 8.8 - - - +
76C GLN* 2.8 65.6 + - - +
77C TRP* 4.2 4.4 - - + -
89C PRO* 4.4 12.8 - - + -
90C PRO* 3.7 22.9 - - + +
92C VAL* 4.0 26.9 - - + -
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Residues in contact with VAL 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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8C LEU* 4.1 32.3 - - + -
12C PHE* 4.5 0.9 - - + -
42C LEU* 4.0 17.0 - - + -
45C ALA* 5.8 0.2 - - + -
46C MSE 4.4 14.8 - - + -
49C LEU* 4.2 15.3 - - + -
61C LEU* 4.0 20.9 - - + -
69C VAL* 2.9 22.5 + - + +
70C ALA 3.7 3.8 - - - +
72C LEU* 1.3 72.5 - - - +
74C ALA* 1.3 66.5 + - - +
77C TRP* 3.0 31.8 + - + -
78C ALA 3.1 6.6 + - - -
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Residues in contact with ALA 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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61C LEU* 3.8 20.2 - - + +
70C ALA 2.9 15.7 + - - +
71C ARG* 3.2 11.4 + - - +
73C VAL* 1.3 76.0 - - - +
75C ARG* 1.3 59.7 + - + +
78C ALA* 3.1 14.6 - - - +
79C GLY 2.9 24.4 + - - -
80C VAL* 3.0 25.4 + - + +
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Residues in contact with ARG 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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21B ASP* 3.9 41.7 - - + +
22B LYS* 4.7 0.5 + - - -
25B TYR* 4.2 0.7 - - - +
71C ARG* 3.0 42.8 + - - +
72C LEU* 3.9 7.8 - - - +
74C ALA* 1.3 80.5 - - + +
76C GLN* 1.3 64.7 + - + +
79C GLY* 3.4 18.7 + - - -
80C VAL* 3.1 24.5 + - + +
82C SER* 3.4 37.4 + - - +
83C THR* 5.3 0.4 - - - +
84C GLU* 5.2 8.5 - - - +
87C GLU* 2.9 41.2 + - - +
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Residues in contact with GLN 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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20B GLN* 6.2 0.2 - - - +
21B ASP* 2.9 37.1 + - - +
24B LEU* 3.4 33.9 - - + +
25B TYR* 3.1 14.6 + - - -
28B HIS* 2.8 24.7 + - - +
72C LEU* 2.8 48.1 + - + +
75C ARG* 1.3 79.5 - - + +
77C TRP* 1.3 75.2 + - + +
89C PRO* 5.7 4.4 - - - +
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Residues in contact with TRP 77 (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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25B TYR* 3.7 13.9 - - - -
28B HIS* 3.3 52.9 + + + +
29B LYS* 6.0 0.3 - - - +
8C LEU* 3.7 33.2 - - + -
9C PRO* 4.2 25.5 - - + +
12C PHE* 3.3 49.3 - + + +
49C LEU* 3.8 16.9 - - + +
54C GLU* 4.9 1.4 - - - +
72C LEU* 4.5 9.0 - - + -
73C VAL* 3.0 21.3 + - + +
76C GLN* 1.3 102.7 - - + +
78C ALA* 1.3 58.1 + - - +
79C GLY 3.6 0.9 - - - -
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Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 3.5 7.2 - - - -
49C LEU* 3.9 17.7 - - + -
54C GLU* 4.8 0.7 - - - -
58C ARG* 2.9 44.4 + - + -
61C LEU* 3.8 18.2 - - + -
73C VAL 3.1 4.0 + - - +
74C ALA* 3.1 24.0 - - - +
77C TRP* 1.3 77.0 - - - +
79C GLY* 1.3 59.3 + - - +
80C VAL* 3.4 1.2 + - + -
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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