Contacts of the helix formed by residues 49 - 73 (chain C) in PDB entry 5Y3R
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 ALA 49 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C PRO* 1.3 73.8 - - + +
50C VAL* 1.3 77.0 + - + +
52C ALA* 3.0 16.0 + - - +
53C LEU* 3.0 22.5 + - - +
54C GLN 3.8 1.4 + - - -
847C SER* 5.1 10.5 - - - +
850C GLU* 6.1 1.1 - - - +
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Residues in contact with VAL 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C SER* 4.6 4.9 - - - -
48C PRO 2.6 10.0 + - - +
49C ALA* 1.3 82.7 - - + +
51C LEU* 1.3 66.2 + - + +
54C GLN* 2.3 53.2 + - - +
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Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 6.2 2.9 - - + -
45C SER* 3.9 12.8 - - - +
46C SER* 3.3 22.7 - - - +
47C SER* 2.9 47.8 + - - +
50C VAL* 1.3 84.0 - - + +
52C ALA* 1.3 53.4 + - - +
54C GLN* 3.2 26.9 - - - +
55C THR* 2.7 45.1 + - + +
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Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C SER* 6.4 0.4 - - - -
47C SER 2.5 19.8 + - - +
48C PRO* 3.8 12.8 - - + -
49C ALA 3.0 7.3 + - - +
51C LEU* 1.3 71.9 - - - +
53C LEU* 1.3 65.3 + - + +
55C THR* 2.0 27.4 + - - -
56C SER* 3.0 9.4 + - - -
96C MET* 4.2 8.1 - - + +
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Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA* 3.0 16.4 + - - +
52C ALA* 1.3 80.6 - - + +
54C GLN* 1.3 61.3 + - - +
56C SER* 2.6 40.3 + - - +
57C LEU* 2.9 16.0 + - - +
96C MET* 4.6 7.0 - - + -
99C LYS* 4.8 19.5 - - + -
3100C LYS* 5.5 7.3 + - - +
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Residues in contact with GLN 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C CYS* 4.7 20.0 - - - +
12C LEU* 4.9 8.2 - - + +
13C LEU* 5.2 0.8 - - + +
49C ALA 3.8 0.2 + - - -
50C VAL* 2.3 61.2 + - - +
51C LEU* 3.2 16.3 - - - +
53C LEU* 1.3 77.2 - - - +
55C THR* 1.3 63.7 + - + +
57C LEU* 3.3 9.4 + - - +
58C VAL* 2.9 29.4 + - + +
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Residues in contact with THR 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 4.9 9.6 - - + -
42C CYS* 4.5 26.0 - - - +
43C VAL* 6.3 0.2 - - - -
45C SER 5.4 2.0 - - - +
46C SER* 5.7 2.5 - - - +
51C LEU* 2.7 25.6 + - + +
52C ALA* 2.0 34.3 + - - -
54C GLN* 1.3 72.2 - - + +
56C SER* 1.3 54.9 + - - -
58C VAL* 2.1 41.1 + - + -
59C PHE* 2.7 28.2 + - + -
95C LYS* 5.5 7.9 + - - +
96C MET* 4.9 2.1 - - - +
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Residues in contact with SER 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ALA 3.1 1.9 + - - -
53C LEU* 2.6 47.2 + - - +
55C THR* 1.3 73.2 + - - +
57C LEU* 1.3 51.3 + - - -
59C PHE* 4.2 6.5 - - - +
60C SER* 2.1 39.6 + - - -
63C PHE* 5.1 0.3 - - - -
96C MET* 3.1 25.5 - - - +
99C LYS* 5.4 3.9 - - - +
3100C LYS* 6.1 2.2 - - - -
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Residues in contact with LEU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 4.6 5.3 - - + +
53C LEU 2.9 10.6 + - - +
54C GLN* 3.7 8.7 - - - +
55C THR 2.6 4.6 + - - -
56C SER* 1.3 76.5 - - - +
58C VAL* 1.3 58.3 + - + +
60C SER* 3.2 7.9 - - - +
61C ARG* 2.9 64.9 + - - +
3097C ASP* 5.9 2.2 - - + +
3100C LYS* 3.5 37.9 - - + +
3101C TYR* 3.6 35.4 - - + -
3104C GLN* 4.9 1.3 - - - +
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Residues in contact with VAL 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C CYS 4.5 0.9 - - - +
12C LEU* 3.6 39.7 - - + -
13C LEU* 3.4 41.1 - - + +
16C GLN* 4.7 6.1 - - - +
42C CYS* 5.8 2.2 - - - -
54C GLN* 2.9 33.5 + - + +
55C THR* 2.1 25.1 + - + +
57C LEU* 1.3 69.2 - - - +
59C PHE* 1.3 72.6 + - + +
62C ASP* 2.9 24.4 + - + +
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Residues in contact with PHE 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C CYS* 3.2 35.9 - - - -
55C THR* 2.7 27.2 + - + +
56C SER* 4.2 5.6 - - - +
58C VAL* 1.3 79.6 - - + +
60C SER* 1.3 63.8 + - - +
62C ASP* 4.7 4.5 - - + -
63C PHE* 2.8 53.2 + + + -
92C PHE* 3.3 40.8 - + + -
95C LYS* 3.5 40.6 - - + -
96C MET* 5.2 11.4 - - + -
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Residues in contact with SER 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C SER 2.1 30.3 + - - -
57C LEU* 3.2 17.8 - - - +
58C VAL 3.1 0.2 - - - -
59C PHE* 1.3 75.4 - - - +
61C ARG* 1.3 63.6 + - - +
63C PHE* 2.9 33.7 - - - +
64C GLY* 3.1 4.9 + - - -
103C TYR* 2.9 38.2 + - - -
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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
----------------------------------------------------------
13C LEU* 5.0 10.5 - - + -
16C GLN* 4.1 2.0 - - - -
17C GLU* 3.5 11.7 - - - +
57C LEU* 2.9 51.9 + - - +
58C VAL 4.3 0.9 - - - +
60C SER* 1.3 75.0 - - - +
62C ASP* 1.3 61.1 + - - +
63C PHE 3.3 0.2 - - - -
64C GLY* 3.8 4.6 - - - +
65C LEU* 2.9 29.8 + - - +
103C TYR* 4.9 1.8 - - - +
3097C ASP* 4.6 16.2 + - - +
3098C ARG* 4.9 1.8 - - - +
3101C TYR* 4.2 20.2 - - - +
3102C TYR* 3.9 24.2 + - - -
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Residues in contact with ASP 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLN* 2.9 37.7 - - - +
20C SER* 6.1 0.2 - - - -
58C VAL* 2.9 15.4 + - + +
59C PHE* 3.9 6.1 - - + +
61C ARG* 1.3 75.4 - - - +
63C PHE* 1.3 61.7 + - + +
65C LEU* 3.1 17.8 - - - +
66C LEU* 2.8 34.3 + - - +
85C ILE* 5.5 5.5 - - - +
89C LEU* 5.5 5.0 - - - +
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Residues in contact with PHE 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C PHE* 2.8 61.4 + + + -
60C SER* 2.9 10.5 - - - +
62C ASP* 1.3 73.2 - - + +
64C GLY* 1.3 68.3 + - - +
65C LEU 2.9 1.2 + - - -
66C LEU* 3.0 13.2 + - - -
67C VAL* 3.1 22.6 + - + +
89C LEU* 5.2 16.4 - - + -
92C PHE* 5.8 8.7 - + + -
96C MET* 6.5 0.9 - - + -
103C TYR* 3.1 51.1 - + + -
106C GLU* 4.7 1.3 - - - +
107C ILE* 4.3 25.4 - - + -
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Residues in contact with GLY 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C SER 3.1 8.9 + - - -
61C ARG* 3.7 5.1 + - - -
62C ASP 3.4 0.2 - - - -
63C PHE* 1.3 79.1 - - - +
65C LEU* 1.3 63.9 + - - +
67C VAL* 4.4 0.6 - - - +
68C PHE* 2.9 36.7 + - - -
103C TYR* 4.6 1.1 - - - -
106C GLU* 3.7 19.1 + - - -
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Residues in contact with LEU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLN* 3.1 22.9 - - + +
17C GLU* 3.2 43.5 - - + +
20C SER* 4.7 5.6 - - - +
24C ARG* 5.0 8.5 - - - +
61C ARG 2.9 22.1 + - - +
62C ASP* 3.1 28.0 - - - +
63C PHE 2.9 0.4 + - - -
64C GLY* 1.3 74.8 - - - +
66C LEU* 1.3 57.7 + - - +
68C PHE* 2.6 35.6 + - + +
69C VAL* 2.9 22.5 + - + +
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ASP* 2.8 24.1 + - - +
63C PHE* 4.4 1.1 - - - +
65C LEU* 1.3 73.8 - - + +
67C VAL* 1.3 71.3 + - - +
69C VAL* 3.4 17.9 - - + -
70C ARG* 2.9 46.3 + - + +
71C LYS 3.5 1.7 + - - -
73C LEU* 5.3 0.4 - - + -
82C ARG* 5.5 2.2 - - + -
85C ILE* 3.3 52.9 - - + -
86C LEU* 5.9 1.3 - - + -
89C LEU* 4.6 10.1 - - + -
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Residues in contact with VAL 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C PHE* 3.1 24.4 + - + +
64C GLY 4.4 0.7 - - - +
66C LEU* 1.3 80.1 - - - +
68C PHE* 1.3 65.4 + - + +
71C LYS* 2.3 50.7 + - + +
106C GLU* 4.7 14.8 - - + +
107C ILE* 5.3 5.2 - - + -
110C THR* 3.3 48.9 - - + +
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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
----------------------------------------------------------
24C ARG* 5.0 8.3 - - - +
64C GLY* 2.9 30.3 - - - -
65C LEU* 2.6 15.1 + - + +
67C VAL* 1.3 82.5 - - + +
69C VAL* 1.3 69.1 + - + +
71C LYS* 3.3 6.8 - - + +
72C SER* 2.9 22.9 + - - -
106C GLU* 5.0 6.7 - - - -
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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
----------------------------------------------------------
20C SER* 5.0 21.1 - - - +
24C ARG* 3.6 37.2 - - + +
65C LEU* 2.9 34.8 + - + +
66C LEU* 3.0 20.4 + - + -
68C PHE* 1.3 70.0 - - - +
70C ARG* 1.3 60.1 + - - +
72C SER* 2.1 31.2 + - - -
73C LEU* 2.9 30.2 + - + +
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Residues in contact with ARG 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 2.9 32.0 + - + +
69C VAL* 1.3 75.9 - - - +
71C LYS* 1.3 65.4 + - - +
73C LEU* 2.9 60.6 + - + +
74C ASN 3.0 8.9 + - - +
75C SER* 3.0 23.0 + - - +
78C PHE* 2.7 31.6 + - - +
79C ARG* 2.8 37.0 - - - +
81C CYS* 5.3 0.9 - - - -
82C ARG* 2.7 50.5 + - + +
85C ILE* 5.1 2.0 - - + -
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Residues in contact with LYS 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ASP* 3.4 8.1 - - - +
66C LEU 3.5 1.0 + - - -
67C VAL* 2.3 48.1 + - + +
68C PHE* 3.3 7.4 - - + +
70C ARG* 1.3 78.5 - - - +
72C SER* 1.3 64.4 - - - +
113C SER* 5.3 18.7 + - - -
114C VAL* 6.5 0.7 - - - -
117C LYS* 3.3 25.0 + - + +
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Residues in contact with SER 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ASP* 3.7 17.0 - - - +
24C ARG* 5.8 1.7 + - - -
68C PHE 2.9 11.6 + - - -
69C VAL* 2.1 30.1 + - - -
71C LYS* 1.3 76.9 - - - +
73C LEU* 1.3 74.1 + - - +
74C ASN* 3.3 7.4 + - - +
117C LYS* 3.8 1.2 + - - -
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Residues in contact with LEU 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ARG* 5.0 19.7 - - + +
66C LEU* 5.3 0.7 - - + -
69C VAL* 2.9 32.6 + - + +
70C ARG* 2.9 49.5 + - + +
72C SER* 1.3 81.9 + - - +
74C ASN* 1.3 56.4 + - - +
76C ILE* 5.8 0.2 - - - -
78C PHE* 3.5 41.7 - - + -
81C CYS* 5.5 3.1 - - + -
85C ILE* 6.5 0.2 - - + -
117C LYS* 2.5 26.9 + - - -
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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