Contacts of the helix formed by residues 64 - 78 (chain C) in PDB entry 4BZ5
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 64 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C THR* 4.3 0.4 - - - -
62C PHE 3.9 1.0 + - - -
63C HIS* 1.3 75.9 - - - +
65C THR* 1.3 65.4 + - - +
66C GLU* 3.3 20.1 - - - +
67C TYR* 3.1 19.4 + - - +
68C VAL* 3.1 23.0 + - - +
145C ARG* 3.1 31.6 + - - +
146C SER* 2.5 27.4 + - - -
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Residues in contact with THR 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C TYR* 2.9 36.9 + - + +
60C THR* 3.9 15.5 - - + +
63C HIS 3.8 0.2 + - - -
64C SER* 1.3 72.9 - - - +
66C GLU* 1.3 68.6 + - - +
68C VAL 3.4 0.6 + - - +
69C ASP* 2.9 36.6 + - - -
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C SER* 3.3 24.1 + - - +
65C THR* 1.3 90.7 + - - +
67C TYR* 1.3 59.5 + - - +
69C ASP* 3.5 9.5 + - - +
70C ALA* 3.0 27.7 + - - +
95C PHE* 3.8 24.6 - - + -
145C ARG* 4.7 6.3 + - - -
146C SER* 4.3 3.9 + - - +
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Residues in contact with TYR 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C HIS* 3.7 28.5 - + + -
64C SER* 3.1 22.3 + - - +
66C GLU* 1.3 75.7 - - - +
68C VAL* 1.3 67.9 + - - +
70C ALA* 3.1 3.4 + - - +
71C LEU* 2.9 27.7 + - + +
95C PHE* 3.7 36.3 - + + -
97C LEU* 4.1 14.9 - - + +
144C LYS 4.5 2.0 - - - -
145C ARG 3.8 3.6 - - - +
146C SER* 3.7 16.2 - - - -
147C GLU* 3.9 2.5 - - - -
148C ALA* 3.3 40.1 + - - +
153C TYR* 2.6 34.0 + - - +
154C LEU* 4.1 7.9 - - + -
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Residues in contact with VAL 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C MET* 5.6 1.3 - - - -
56C TYR* 3.8 27.4 - - + -
59C VAL* 3.7 31.6 - - + -
60C THR* 4.1 8.7 - - + -
63C HIS* 3.8 14.6 - - + -
64C SER 3.1 17.6 + - - +
65C THR 3.9 3.4 - - - +
67C TYR* 1.3 76.4 - - - +
69C ASP* 1.3 62.2 + - - +
71C LEU* 3.2 7.5 + - - +
72C LYS* 3.0 25.0 + - + +
108C PHE* 4.1 23.6 - - + -
154C LEU* 4.7 4.5 - - + -
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Residues in contact with ASP 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C TYR* 2.8 31.0 + - - -
65C THR* 2.9 26.1 + - - +
66C GLU* 3.6 9.0 - - - +
68C VAL* 1.3 75.4 - - - +
70C ALA* 1.3 57.5 + - - +
72C LYS* 3.4 12.1 + - - +
73C LYS* 3.0 27.8 + - - +
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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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66C GLU 3.0 17.0 + - - +
67C TYR 3.1 5.3 + - - +
69C ASP* 1.3 74.2 - - - +
71C LEU* 1.3 61.6 + - - +
73C LYS* 3.1 5.9 + - - -
74C LEU* 2.8 29.8 + - - +
91C LEU* 4.8 8.1 - - + -
92C MET* 3.5 13.7 - - + +
95C PHE* 3.6 30.3 - - + -
97C LEU* 4.2 9.6 - - + -
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C TYR* 2.9 20.8 + - + +
68C VAL* 3.2 6.0 + - - +
70C ALA* 1.3 75.8 - - - +
72C LYS* 1.3 62.7 + - - +
74C LEU* 3.3 7.2 + - + +
75C GLN* 3.2 20.6 + - - +
97C LEU* 3.8 21.0 - - + +
107C VAL* 4.1 15.1 - - + +
108C PHE* 3.7 24.4 - - + +
111C SER* 4.3 4.0 - - - -
153C TYR* 3.8 39.0 - - + +
154C LEU* 3.7 37.5 - - + -
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Residues in contact with LYS 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C MET* 4.5 10.0 - - + +
56C TYR* 5.1 7.4 - - + -
68C VAL* 3.0 28.6 + - + +
69C ASP* 3.6 14.4 - - - +
71C LEU* 1.3 77.0 - - - +
73C LYS* 1.3 62.0 + - - +
75C GLN* 3.3 5.4 + - - +
76C MET* 3.1 20.6 + - - +
108C PHE* 3.6 45.0 - - + -
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Residues in contact with LYS 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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69C ASP 3.0 17.3 + - - +
70C ALA* 3.6 5.8 - - - +
72C LYS* 1.3 73.0 - - - +
74C LEU* 1.3 60.9 + - - +
76C MET* 3.1 28.9 + - + +
77C LEU* 2.8 38.7 + - + +
88C ASP* 3.1 30.4 + - - -
91C LEU* 4.4 17.3 - - + +
92C MET* 4.0 15.3 - - + -
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Residues in contact with LEU 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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70C ALA 2.8 17.1 + - - +
71C LEU* 3.5 12.1 - - + +
73C LYS* 1.3 72.7 - - - +
75C GLN* 1.3 62.5 + - - +
77C LEU* 3.4 2.5 + - - +
78C HIS* 3.1 54.6 + - + +
84C LEU* 5.2 4.3 - - + -
92C MET* 3.6 30.6 - - + +
97C LEU* 3.8 38.1 - - + +
102C PRO 4.4 2.9 - - - +
103C GLY* 3.5 28.0 - - - +
107C VAL* 4.0 12.1 - - + -
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Residues in contact with GLN 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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71C LEU 3.2 3.8 + - - -
72C LYS 3.5 8.5 - - - +
74C LEU* 1.3 76.0 - - - +
76C MET* 1.3 67.9 + - - +
78C HIS* 3.2 3.5 + - - +
79C CYS* 3.1 27.2 + - - -
104C PHE 4.2 3.4 - - - -
105C PRO 3.2 20.9 - - - +
106C SER* 3.1 8.8 - - - -
107C VAL* 3.8 16.3 - - + +
108C PHE* 2.7 39.2 + - + +
109C ASP* 2.9 36.4 + - - -
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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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72C LYS 3.1 13.3 + - - +
73C LYS* 3.5 37.9 - - + +
75C GLN* 1.3 77.3 - - - +
77C LEU* 1.3 78.3 + - + +
79C CYS* 3.0 25.7 + - - +
80C GLU* 3.5 20.2 + - - +
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C LYS* 2.8 27.1 + - + +
74C LEU* 3.7 5.6 - - + +
75C GLN 3.2 0.2 - - - -
76C MET* 1.3 96.1 - - + +
78C HIS* 1.3 59.9 + - + +
79C CYS 3.1 0.2 - - - -
80C GLU* 3.0 45.2 + - - +
82C LYS 4.4 4.3 - - - +
84C LEU* 3.7 42.5 - - + +
88C ASP* 3.9 24.7 - - - +
92C MET* 3.8 24.0 - - + -
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Residues in contact with HIS 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C LEU* 3.1 45.9 + - + +
75C GLN 3.2 2.2 + - - +
77C LEU* 1.3 81.4 - - + +
79C CYS* 1.3 58.2 + - - +
80C GLU 3.4 5.0 + - - +
84C LEU* 4.7 12.6 - - + +
102C PRO* 6.1 0.2 - - + -
103C GLY* 3.5 34.1 + - - -
104C PHE* 3.7 26.2 + - - +
105C PRO* 3.6 18.8 - - + +
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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
------------------------------------------------------------
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