Contacts of the helix formed by residues 60 - 83 (chain C) in PDB entry 3D5K
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 ASN 60 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A LYS* 6.4 0.2 - - - +
56C ALA 3.1 20.7 + - - +
57C LEU 6.0 0.2 - - - -
58C GLU 3.8 1.4 - - - +
59C ASN* 1.3 76.0 - - - +
61C ARG* 1.3 63.0 + - - +
62C ASP* 2.8 19.4 + - - +
63C LEU* 2.8 33.8 + - + +
64C ARG* 3.3 19.8 + - - +
157C LEU* 3.4 26.1 - - + +
236C LEU 4.5 3.6 + - - -
237C LEU* 3.2 34.1 + - - +
238C LEU 3.4 5.8 + - - -
239C GLY* 4.4 3.8 - - - -
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Residues in contact with ARG 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PRO* 3.4 21.8 - - - +
356A ALA* 3.5 24.3 - - - +
359A GLU* 2.6 42.7 + - - +
360A LYS* 3.7 21.5 - - + +
363A GLN* 3.6 34.9 + - - +
59C ASN* 2.7 35.3 + - - +
60C ASN* 1.3 73.8 + - - +
62C ASP* 1.3 66.2 + - - +
63C LEU 3.4 0.2 - - - -
64C ARG* 3.3 33.6 + - - +
65C VAL* 3.1 28.4 + - - +
236C LEU 5.9 0.2 + - - -
239C GLY 3.6 6.5 + - - -
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Residues in contact with ASP 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LYS* 2.8 44.6 + - - +
60C ASN* 2.8 14.8 + - - +
61C ARG* 1.3 79.4 - - - +
63C LEU* 1.3 56.0 + - - +
65C VAL* 3.3 11.4 + - - +
66C ALA* 3.1 24.3 + - - +
153C ALA* 5.7 0.8 - - - +
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Residues in contact with LEU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ALA 4.7 0.2 - - - +
57C LEU* 3.9 37.5 - - + +
60C ASN* 2.8 19.8 + - + +
62C ASP* 1.3 71.2 - - - +
64C ARG* 1.3 60.1 + - - +
65C VAL 3.3 0.2 - - - -
66C ALA* 3.4 7.3 + - + +
67C ALA* 3.0 27.2 + - - +
150C GLN* 4.0 16.4 - - + +
153C ALA* 3.9 11.0 - - + +
154C GLN* 3.5 40.6 - - + +
157C LEU* 3.7 26.7 - - + -
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Residues in contact with ARG 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ALA* 4.5 10.5 - - + -
359A GLU* 4.2 7.2 + - - -
58C GLU* 2.7 30.3 + - - +
59C ASN* 3.6 16.7 - - - +
60C ASN 3.3 11.6 + - - +
61C ARG* 3.4 48.0 - - - +
62C ASP 3.2 0.4 - - - -
63C LEU* 1.3 78.9 - - - +
65C VAL* 1.3 60.8 + - - +
67C ALA* 3.5 7.2 + - + +
68C LEU* 3.2 37.7 + - + +
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Residues in contact with VAL 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ILE* 4.0 28.0 - - + +
356A ALA* 3.9 18.4 - - + -
357A GLN* 4.3 19.5 - - + +
61C ARG 3.1 17.1 + - - +
62C ASP* 3.5 11.7 - - - +
63C LEU 3.3 0.2 - - - -
64C ARG* 1.3 73.9 - - - +
66C ALA* 1.3 60.8 + - - +
68C LEU* 3.1 9.3 + - - +
69C ASN* 2.8 43.2 + - - +
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Residues in contact with ALA 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ASP 3.1 13.4 + - - +
63C LEU* 3.5 11.0 - - + +
65C VAL* 1.3 78.0 - - - +
67C ALA* 1.3 60.6 + - - +
69C ASN* 3.5 17.8 + - - +
70C VAL* 3.5 18.0 + - - +
146C THR* 4.9 1.2 - - - +
149C ALA 5.0 1.3 - - - +
150C GLN* 4.0 16.0 - - + +
153C ALA* 4.0 26.2 - - + -
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Residues in contact with ALA 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU* 3.0 16.6 + - + +
64C ARG* 3.6 8.5 - - + +
65C VAL 3.2 0.2 - - - -
66C ALA* 1.3 75.6 - - - +
68C LEU* 1.3 64.2 + - + +
70C VAL* 3.4 15.2 + - - +
71C GLU* 3.5 14.3 + - - +
150C GLN* 4.0 25.4 - - - +
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Residues in contact with LEU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ILE* 3.2 23.6 - - + +
352A ASP* 3.6 52.3 - - + +
353A ILE* 3.6 20.4 - - + +
356A ALA* 4.9 2.5 - - + -
64C ARG* 3.2 30.0 + - + +
65C VAL* 3.1 3.4 + - - +
67C ALA* 1.3 77.7 - - + +
69C ASN* 1.3 60.9 + - - +
70C VAL 3.4 0.2 - - - -
71C GLU* 3.3 22.6 + - - +
72C ALA 2.9 22.2 + - - -
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Residues in contact with ASN 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A GLN* 5.4 1.2 - - - +
353A ILE* 3.4 24.0 - - - +
65C VAL* 2.8 27.9 + - - +
66C ALA* 3.6 14.3 - - - +
67C ALA 3.3 0.2 - - - -
68C LEU* 1.3 74.3 - - - +
70C VAL* 1.3 60.3 + - - +
72C ALA* 3.0 6.3 + - - +
73C PHE* 2.9 44.0 + - + -
146C THR* 3.7 15.5 - - + -
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Residues in contact with VAL 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ALA 3.5 11.2 - - - +
67C ALA 3.4 7.6 + - - +
69C ASN* 1.3 75.2 - - - +
71C GLU* 1.3 58.2 + - + +
73C PHE* 3.2 1.2 + - - -
74C ARG* 2.9 28.1 + - - +
143C TYR* 3.6 28.1 - - + +
146C THR* 3.5 36.3 - - + +
147C GLU* 3.8 19.3 - - + +
150C GLN* 3.5 25.1 - - + +
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Residues in contact with GLU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ILE* 3.6 27.8 - - + +
67C ALA 3.5 10.9 + - - +
68C LEU* 3.3 27.7 + - - +
69C ASN 3.2 0.6 - - - -
70C VAL* 1.3 79.2 - - + +
72C ALA* 1.3 57.8 + - - +
74C ARG* 3.4 11.0 + - - +
75C ALA* 3.0 28.9 + - - +
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Residues in contact with ALA 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A TYR* 3.6 20.1 - - + -
349A ILE* 3.7 20.1 - - + +
350A GLN* 4.0 20.2 - - - +
353A ILE* 4.8 1.6 - - + -
68C LEU 2.9 14.9 + - - +
69C ASN* 3.0 12.8 + - - +
71C GLU* 1.3 75.7 - - - +
73C PHE* 1.3 64.2 + - + +
75C ALA* 3.6 3.7 + - - +
76C GLN* 3.2 21.1 + - - +
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Residues in contact with PHE 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 ASN* 2.9 36.3 + - + +
70C VAL 3.8 3.6 - - - +
72C ALA* 1.3 77.9 - - + +
74C ARG* 1.3 65.2 + - - +
75C ALA 3.3 0.4 - - - -
76C GLN* 3.4 10.8 + - + +
77C TYR* 3.1 21.7 + - - +
139C ALA 4.4 2.9 - - - +
142C GLN* 4.1 29.4 - - + -
143C TYR* 3.9 16.3 - - - +
146C THR* 3.3 33.9 - - + +
281C GLN* 6.0 3.6 - - - -
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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
----------------------------------------------------------
70C VAL 2.9 13.4 + - - +
71C GLU* 3.4 13.0 + - - +
73C PHE* 1.3 77.5 - - - +
75C ALA* 1.3 56.7 + - - +
77C TYR* 3.1 12.7 + - + +
78C ARG* 2.9 53.6 + - + +
143C TYR* 3.6 36.0 + - + -
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Residues in contact with ALA 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ALA* 3.5 22.7 - - - +
346A TYR* 4.2 17.0 - - + +
349A ILE* 4.5 3.8 - - + -
71C GLU 3.0 16.8 + - - +
72C ALA* 3.6 9.0 - - - +
73C PHE 3.3 0.2 - - - -
74C ARG* 1.3 77.8 - - - +
76C GLN* 1.3 55.3 + - - +
78C ARG* 3.2 21.1 + - - +
79C ILE* 3.1 33.0 + - - +
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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
----------------------------------------------------------
346A TYR* 4.2 21.7 - - + -
72C ALA 3.2 10.5 + - - +
73C PHE* 3.7 15.3 - - + +
74C ARG 3.2 0.8 - - - -
75C ALA* 1.3 77.0 - - - +
77C TYR* 1.3 62.0 + - - +
79C ILE* 3.6 30.7 + - - +
80C GLN* 3.3 33.2 + - + +
139C ALA* 4.7 5.8 - - + -
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Residues in contact with TYR 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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73C PHE 3.1 12.4 + - - +
74C ARG* 3.1 19.6 + - + +
76C GLN* 1.3 74.6 - - - +
78C ARG* 1.3 64.4 + - + +
79C ILE 3.3 0.4 - - - -
80C GLN* 3.4 1.3 + - - +
81C ARG* 2.9 65.8 + - + +
136C ARG* 3.7 33.5 + - + -
139C ALA* 3.9 20.8 - - - +
140C LEU* 3.7 51.0 - - + +
143C TYR* 4.8 5.2 - + + -
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Residues in contact with ARG 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ALA 4.5 3.5 - - - +
338A GLY* 4.4 7.0 + - - +
339A SER* 4.8 0.9 + - - -
341A ARG* 4.4 15.7 - - - +
342A ALA* 3.6 36.3 - - + +
345A ASP* 2.5 41.6 + - - +
349A ILE* 5.9 0.8 - - - +
74C ARG* 2.9 40.6 + - + +
75C ALA* 3.2 19.7 + - - +
77C TYR* 1.3 79.8 - - + +
79C ILE* 1.3 64.9 + - - +
81C ARG* 3.4 36.7 + - - +
82C ALA* 3.3 22.7 + - - +
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Residues in contact with ILE 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A SER* 4.0 17.3 + - - +
342A ALA* 3.6 15.0 - - + +
343A SER* 3.5 32.8 - - - +
346A TYR* 5.1 4.3 - - + -
75C ALA 3.1 16.6 + - - +
76C GLN* 3.7 37.2 - - - +
77C TYR 3.3 0.2 - - - -
78C ARG* 1.3 76.3 - - - +
80C GLN* 1.3 64.0 + - + +
82C ALA* 3.1 13.6 + - - +
83C ASP* 3.3 21.8 + - - +
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Residues in contact with GLN 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C GLN* 3.3 26.3 + - + +
77C TYR 3.9 4.0 - - - +
79C ILE* 1.3 76.5 - - + +
81C ARG* 1.3 60.7 + - - +
82C ALA 3.6 0.2 + - - -
83C ASP* 3.1 35.9 + - - +
84C LEU* 4.4 5.7 - - - +
132C LEU* 4.6 5.4 - - - +
135C LEU* 3.9 40.9 + - - +
136C ARG* 4.1 19.8 + - - +
138C GLN* 5.4 1.6 + - - -
139C ALA* 3.9 20.3 - - + +
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Residues in contact with ARG 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ALA 5.5 5.9 + - - -
77C TYR* 2.9 47.5 + - + +
78C ARG* 3.4 41.3 + - - +
80C GLN* 1.3 76.5 - - - +
82C ALA* 1.3 59.7 + - - +
83C ASP 3.6 0.5 + - - -
84C LEU* 3.6 20.2 + - + +
85C PHE* 3.8 16.6 - - + -
136C ARG* 4.0 24.6 - - + +
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Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ALA* 3.2 40.8 + - + +
339A SER* 3.6 28.9 - - - +
78C ARG 3.3 11.8 + - - +
79C ILE 3.1 4.3 + - - +
81C ARG* 1.3 74.6 - - - +
83C ASP* 1.3 61.1 + - - +
84C LEU 3.1 6.5 + - - -
85C PHE* 3.4 19.8 + - - +
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Residues in contact with ASP 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A SER* 4.8 4.3 + - - -
79C ILE* 3.3 21.1 + - - +
80C GLN* 3.1 33.0 - - - +
81C ARG 3.3 0.8 - - - -
82C ALA* 1.3 77.5 - - - +
84C LEU* 1.3 59.7 + - - +
85C PHE 3.4 5.9 + - - +
87C ARG* 5.5 4.9 + - - -
124C TRP* 4.7 6.4 - - - -
125C GLU* 4.9 0.7 + - - +
132C LEU* 4.1 29.9 - - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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