Contacts of the helix formed by residues 54 - 68 (chain C) in PDB entry 6B0Z
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 54 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ARG* 2.4 48.1 + - - +
52C THR* 3.1 1.9 - - - -
53C ASN* 1.3 70.3 - - - +
55C GLN* 1.3 61.9 + - - +
56C VAL 3.4 1.3 - - - +
57C THR* 3.3 36.8 + - - +
58C LYS* 3.9 13.2 + - - +
92C TRP* 3.6 35.1 - - + +
93C LYS* 4.6 9.1 + - - +
95C PRO* 5.0 1.2 - - - +
98C THR* 4.7 7.3 + - - +
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Residues in contact with GLN 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C THR* 3.0 19.8 + - - +
53C ASN* 3.1 3.2 - - + +
54C ASP* 1.3 75.0 - - - +
56C VAL* 1.3 60.5 + - - +
57C THR 3.0 2.2 + - - -
58C LYS* 3.2 18.7 + - - +
59C ASP* 2.8 64.5 + - - +
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Residues in contact with VAL 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C TYR* 4.1 12.8 - - + -
43C ASP 3.4 33.2 - - - +
44C LEU* 3.5 12.1 - - + +
48C ASN* 3.4 23.8 - - - +
49C ARG* 4.1 15.0 - - + -
52C THR* 3.3 22.3 + - + +
55C GLN* 1.3 78.6 - - - +
57C THR* 1.3 60.0 + - - +
59C ASP* 3.6 9.4 + - - +
60C ALA* 2.9 28.4 + - - +
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Residues in contact with THR 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 4.0 12.0 - - + +
49C ARG* 3.9 16.5 - - - +
54C ASP* 3.3 37.7 + - - +
55C GLN 3.0 0.8 - - - -
56C VAL* 1.3 80.6 - - - +
58C LYS* 1.3 64.3 + - - +
60C ALA* 3.2 13.5 + - - +
61C ALA* 3.2 11.6 + - - +
95C PRO* 4.0 25.7 - - + +
98C THR* 3.8 26.0 - - + -
99C ILE* 4.5 7.1 - - + +
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Residues in contact with LYS 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ASP* 4.4 11.7 - - - +
55C GLN* 3.2 23.7 + - - +
57C THR* 1.3 80.3 - - + +
59C ASP* 1.3 63.1 + - - +
61C ALA* 3.2 15.3 + - - +
62C GLU* 3.4 18.9 + - + +
98C THR* 3.8 24.5 - - + -
102C ILE* 4.5 12.6 - - + +
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Residues in contact with ASP 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C TYR* 3.9 19.5 + - + +
55C GLN* 2.8 51.4 + - - +
56C VAL* 3.6 9.2 - - - +
58C LYS* 1.3 76.3 - - - +
60C ALA* 1.3 62.5 + - - +
61C ALA 3.2 0.9 + - - -
62C GLU* 3.3 15.3 + - - +
63C ALA* 3.3 12.6 + - - +
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Residues in contact with ALA 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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11C VAL* 4.0 1.6 - - + +
13C MET* 3.9 22.9 - - + -
42C TYR* 3.7 34.2 - - + -
44C LEU* 4.1 5.2 - - + -
56C VAL 2.9 18.7 + - - +
57C THR 3.2 6.0 + - - +
59C ASP* 1.3 75.2 - - - +
61C ALA* 1.3 62.5 + - - +
63C ALA* 3.6 3.5 + - - +
64C ILE* 3.2 27.2 + - - +
99C ILE* 5.7 0.4 - - + -
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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
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57C THR 3.2 10.1 + - - +
58C LYS* 3.2 9.6 + - - +
59C ASP 3.1 1.0 - - - -
60C ALA* 1.3 75.2 - - - +
62C GLU* 1.3 64.8 + - - +
64C ILE* 3.1 16.0 + - - +
65C LYS 3.1 16.6 + - - -
99C ILE* 4.3 20.4 - - + +
102C ILE* 3.7 33.9 - - + -
103C LEU* 3.4 9.4 - - + +
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Residues in contact with GLU 62 (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 LYS* 3.6 13.9 - - + +
59C ASP* 3.3 7.7 + - - +
61C ALA* 1.3 72.6 - - - +
63C ALA* 1.3 60.2 + - - +
65C LYS* 3.1 22.1 + - - +
66C LYS* 2.8 29.0 + - - +
102C ILE* 4.1 25.4 - - - +
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Residues in contact with ALA 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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11C VAL* 3.5 14.2 - - + +
40C HIS* 5.1 1.3 - - + +
42C TYR* 3.5 39.5 - - + +
59C ASP 3.3 3.6 + - - +
60C ALA 3.8 6.1 - - - +
61C ALA 3.3 0.6 - - - -
62C GLU* 1.3 79.6 - - - +
64C ILE* 1.3 56.3 + - - +
66C LYS* 3.1 9.2 + - + -
67C HIS* 2.8 40.5 + - + +
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Residues in contact with ILE 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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11C VAL* 4.1 20.6 - - + -
13C MET* 3.6 31.0 - - + -
60C ALA 3.2 17.9 + - - +
61C ALA* 3.1 15.6 + - - +
63C ALA* 1.3 77.8 - - - +
65C LYS* 1.3 56.2 + - - +
68C ASN* 2.5 37.1 + - - +
69C VAL 4.6 1.6 - - - -
70C GLY* 4.3 7.4 - - - +
99C ILE* 4.2 7.4 - - + -
103C LEU* 3.7 26.9 - - + -
302C THR* 3.7 14.2 - - + +
303C VAL 4.0 15.7 - - - +
304C GLU* 4.4 7.0 - - + -
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Residues in contact with LYS 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 3.1 7.7 + - - +
62C GLU* 3.5 24.0 - - - +
64C ILE* 1.3 75.8 - - - +
66C LYS* 1.3 60.5 + - - +
68C ASN* 3.3 12.6 - - - +
102C ILE* 3.2 29.1 + - + +
103C LEU* 3.7 31.9 + - + +
297C CYS* 6.2 0.4 - - - -
299C ASP* 5.9 1.3 - - - +
302C THR* 4.4 12.2 + - + +
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Residues in contact with LYS 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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40C HIS* 5.9 0.8 - - - -
62C GLU 2.8 15.8 + - - +
63C ALA* 3.4 9.0 - - + +
65C LYS* 1.3 80.0 - - - +
67C HIS* 1.3 91.0 + - + +
68C ASN* 3.8 7.0 + - - +
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Residues in contact with HIS 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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9C SER* 3.9 26.6 + - - +
11C VAL* 3.8 22.7 - - + -
38C ASP* 4.8 0.9 - - - -
40C HIS* 3.1 42.0 + + - -
63C ALA* 2.8 30.5 + - + +
66C LYS* 1.3 107.7 + - + +
68C ASN* 1.3 67.5 + - - +
69C VAL 3.2 4.8 + - - +
343C ARG* 3.0 28.8 + - - -
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Residues in contact with ASN 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 ILE 2.5 22.0 + - - -
65C LYS 3.3 17.8 - - - +
66C LYS 3.8 5.7 + - - +
67C HIS* 1.3 73.8 + - - +
69C VAL* 1.3 61.2 + - - +
301C LYS* 3.4 32.8 - - - +
302C THR* 3.3 18.4 + - - -
303C VAL 2.9 26.5 + - - -
342C HIS* 3.9 0.2 - - - -
343C ARG* 4.9 2.4 - - - +
346C LEU* 4.1 16.9 - - + +
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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