Contacts of the helix formed by residues 47 - 70 (chain C) in PDB entry 2GD4
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 ARG 47 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ASN* 2.5 19.9 + - - +
46C ARG* 1.3 85.4 - - + +
48C VAL* 1.3 52.0 + - - +
50C GLU* 2.6 31.9 + - - +
51C LEU* 2.7 20.4 + - - +
112C SER* 3.1 13.1 + - - -
114C LYS* 3.1 37.1 - - - +
115C THR* 3.0 44.4 + - + +
122C PHE* 3.1 40.1 - - + -
1G ZDO 3.5 27.5 + - - -
2G IDS 3.6 14.8 + - - -
3G SUS 4.5 2.9 + - - -
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Residues in contact with VAL 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C THR* 4.7 0.4 - - + -
45C ASN* 2.9 25.8 + - + +
47C ARG* 1.3 70.6 - - - +
49C TRP* 1.3 52.6 + - - +
50C GLU 2.7 11.3 + - - -
51C LEU* 3.0 6.3 + - - +
52C SER* 2.7 28.2 + - - -
122C PHE* 4.6 11.2 - - + -
125C LYS* 4.2 14.6 - - + +
126C LEU* 3.3 41.0 - - + +
129C ARG* 4.8 1.3 - - - -
417C LEU* 3.8 11.7 - - + -
5G SGN 3.2 32.3 - - - +
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Residues in contact with TRP 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLN* 3.3 44.2 - - + -
39C LYS 4.4 12.4 + - - -
40C ILE* 4.6 14.6 - - + -
41C PRO* 3.4 37.3 - - + +
44C THR* 4.0 4.7 - - + -
45C ASN 3.1 7.2 + - - +
46C ARG* 3.7 20.4 - - + +
48C VAL* 1.3 78.3 - - - +
50C GLU* 1.3 68.5 + - + +
52C SER* 3.7 2.5 - - - -
53C LYS* 3.3 52.8 + - + +
417C LEU* 3.3 37.7 + - + +
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Residues in contact with GLU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ARG* 3.2 25.4 + - - +
47C ARG* 2.6 22.7 + - - +
49C TRP* 1.3 80.2 - - + +
51C LEU* 1.3 52.7 + - - +
52C SER 2.7 13.6 + - - -
53C LYS* 3.0 15.5 + - - +
54C ALA* 3.1 11.4 + - - +
57C ARG* 4.1 4.7 + - - +
110C THR 4.3 1.3 - - - +
111C ILE* 2.9 28.2 - - + -
112C SER* 2.8 31.7 + - - -
115C THR* 3.3 22.7 + - - +
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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
----------------------------------------------------------
47C ARG 2.7 15.6 + - - +
48C VAL* 3.8 6.5 - - - +
50C GLU* 1.3 73.6 - - - +
52C SER* 1.3 60.4 + - - +
54C ALA* 3.5 16.3 - - - +
55C ASN* 3.6 4.5 + - - +
108C PHE* 4.7 4.0 - - + -
111C ILE* 4.1 20.1 - - + +
115C THR* 5.2 5.6 - - + -
119C ILE* 3.5 36.3 - - + +
122C PHE* 3.5 15.3 - - + -
123C PHE* 3.0 71.6 - - + +
126C LEU* 5.1 4.3 - - + -
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Residues in contact with SER 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C VAL 2.7 17.6 + - - -
49C TRP* 3.7 10.8 - - - -
50C GLU 2.7 0.8 + - - -
51C LEU* 1.3 75.6 - - - +
53C LYS* 1.3 59.8 + - - +
54C ALA 2.9 4.0 - - - -
55C ASN* 2.9 30.1 + - - +
56C SER* 3.2 6.2 + - - -
126C LEU* 4.5 13.0 - - - +
417C LEU* 3.9 13.5 + - - +
418C ASN 4.8 0.5 + - - -
419C THR* 3.0 37.5 + - - +
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Residues in contact with LYS 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLN* 3.9 14.6 + - - -
49C TRP* 3.3 61.9 + - + +
50C GLU* 3.0 5.0 + - - +
52C SER* 1.3 80.9 + - - +
54C ALA* 1.3 61.0 + - - +
56C SER* 3.2 14.3 - - - +
57C ARG* 3.0 53.2 + - - +
417C LEU 5.4 5.4 - - - +
418C ASN* 6.2 2.0 - - + +
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Residues in contact with ALA 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLU 3.1 7.7 + - - +
51C LEU* 3.5 16.8 - - - +
53C LYS* 1.3 74.0 - - - +
55C ASN* 1.3 68.7 + - - +
57C ARG* 2.8 37.1 + - - +
58C PHE* 3.0 12.6 + - - +
106C PHE 4.6 7.2 - - - +
107C LYS* 4.0 19.8 - - - +
108C PHE* 4.7 7.4 - - + -
111C ILE* 4.7 9.2 - - + -
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Residues in contact with ASN 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU 3.6 7.9 + - - +
52C SER* 2.9 12.7 + - - +
54C ALA* 1.3 78.5 - - - +
56C SER* 1.3 54.4 + - - +
58C PHE* 2.9 12.1 + - - +
59C ALA* 2.6 36.5 + - - +
80C PRO* 3.3 20.4 - - - +
81C LEU* 3.4 35.6 - - + +
84C SER* 3.0 35.6 - - - +
106C PHE 5.4 0.7 - - - -
108C PHE* 5.6 1.0 - - - -
123C PHE* 5.1 4.9 - - + -
419C THR* 4.8 4.0 - - + +
420C ILE* 3.8 10.5 + - - +
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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 SER* 3.2 6.8 + - - -
53C LYS* 3.2 18.6 - - - +
55C ASN* 1.3 81.1 - - - +
57C ARG* 1.3 65.4 + - - +
59C ALA* 3.1 13.6 + - - +
60C THR* 3.5 12.1 + - - +
301C PRO* 5.3 4.9 - - - -
304C LEU* 5.1 3.8 - - - +
418C ASN* 4.3 10.9 + - - -
419C THR* 5.2 0.7 - - - -
420C ILE* 3.5 36.4 + - - +
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Residues in contact with ARG 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLU* 4.1 6.5 + - - +
53C LYS* 3.0 46.6 + - - +
54C ALA* 2.8 46.3 + - - +
56C SER* 1.3 77.5 - - - +
58C PHE* 1.3 59.9 + - - +
60C THR* 3.3 14.9 + - - -
61C THR* 3.6 9.5 + - - -
107C LYS* 4.0 21.5 + - + +
110C THR* 3.8 34.6 + - - +
111C ILE* 5.8 0.8 - - - +
301C PRO* 4.3 19.2 - - + +
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Residues in contact with PHE 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ALA 3.0 8.4 + - - +
55C ASN* 2.9 24.5 + - - +
57C ARG* 1.3 76.0 - - - +
59C ALA* 1.3 67.3 + - - +
60C THR 3.3 0.7 + - - -
61C THR* 3.4 5.3 + - - -
62C PHE* 3.1 58.7 + + + +
80C PRO* 4.1 19.7 - - + -
83C ILE* 4.1 6.1 - - + -
84C SER* 4.0 6.5 - - - +
105C VAL 2.9 27.4 - - - -
106C PHE* 3.3 49.1 - + - +
107C LYS* 4.1 7.1 - - - +
335C LEU* 4.5 1.3 - - + -
338C MET* 3.8 12.6 - - + -
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Residues in contact with ALA 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ASN* 2.6 18.9 + - - +
56C SER* 3.1 10.7 + - - +
58C PHE* 1.3 76.0 - - - +
60C THR* 1.3 56.5 + - - +
62C PHE* 3.9 2.9 - - - +
63C TYR* 3.0 30.8 + - - +
80C PRO* 3.7 33.9 - - + -
420C ILE* 4.4 12.1 - - + -
423C MET* 3.5 13.0 - - - +
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Residues in contact with THR 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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56C SER 3.5 6.8 + - - +
57C ARG 3.3 6.2 + - - -
58C PHE 3.3 0.2 - - - -
59C ALA* 1.3 73.8 - - + +
61C THR* 1.3 79.0 + - - +
63C TYR* 3.2 3.3 + - - +
64C GLN* 3.1 25.4 + - - +
299C LEU* 4.2 28.2 - - + +
300C THR 3.9 26.2 - - - +
301C PRO* 3.3 29.3 - - + +
304C LEU* 4.6 12.3 - - + -
423C MET* 4.4 8.7 - - + -
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Residues in contact with THR 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ARG 3.6 12.8 + - - -
58C PHE 3.4 6.4 + - - -
60C THR* 1.3 82.3 + - - +
62C PHE* 1.3 66.1 + - - +
64C GLN* 3.0 29.8 - - - +
65C HIS* 3.0 33.7 - - + +
107C LYS* 4.0 16.9 + - - +
338C MET* 4.1 13.2 - - + -
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Residues in contact with PHE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C PHE* 3.1 45.3 + + + +
59C ALA* 3.9 4.5 - - - +
61C THR* 1.3 77.0 - - - +
63C TYR* 1.3 71.3 + - - +
65C HIS* 3.1 3.6 + - - +
66C LEU* 2.9 51.7 + - + -
78C LEU* 4.9 6.3 - - + -
80C PRO* 6.3 1.3 - - + -
83C ILE* 3.7 25.6 - - + -
329C PHE* 4.9 0.2 - + - -
331C LEU* 3.6 27.8 - - + -
334C GLN* 4.8 11.9 - - + -
335C LEU* 3.7 26.7 - - + -
338C MET* 3.9 15.7 - - - -
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Residues in contact with TYR 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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59C ALA 3.0 10.1 + - - +
60C THR* 3.6 4.0 - - - +
62C PHE* 1.3 80.5 - - - +
64C GLN* 1.3 56.9 + - + +
66C LEU* 3.2 6.2 + - + +
67C ALA* 2.7 40.9 + - + +
76C ILE* 3.9 29.7 - - + +
78C LEU* 4.7 7.0 - - + -
296C GLU* 2.4 48.7 + - + -
299C LEU* 4.2 15.7 - - + -
409C LEU* 3.4 10.9 - - + +
423C MET* 3.3 46.7 - - + -
424C GLY* 4.5 8.5 - - - -
425C ARG* 3.3 22.7 + - - +
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Residues in contact with GLN 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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60C THR 3.1 15.4 + - - +
61C THR* 3.0 20.7 - - - +
62C PHE 3.1 0.2 + - - -
63C TYR* 1.3 79.9 - - - +
65C HIS* 1.3 68.5 + - + +
67C ALA* 2.9 22.9 + - - +
68C ASP* 3.2 11.8 + - - +
296C GLU* 3.3 18.7 + - - +
297C LYS* 3.1 27.1 + - - +
299C LEU* 3.4 26.5 + - + +
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Residues in contact with HIS 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C THR* 3.0 38.2 - - - +
62C PHE 3.1 4.3 + - - +
64C GLN* 1.3 75.8 + - + +
66C LEU* 1.3 60.0 + - - +
67C ALA 2.8 10.5 + - - -
68C ASP* 2.8 22.7 + - - +
69C SER* 3.2 9.0 + - - -
334C GLN* 4.3 17.3 - - + +
337C ASP* 4.9 13.9 - - + +
338C MET* 3.0 50.1 - - + +
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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 PHE* 2.9 28.7 + - + +
63C TYR* 3.6 4.9 - - - +
65C HIS* 1.3 75.6 - - - +
67C ALA* 1.3 59.3 + - - +
69C SER* 2.7 32.7 + - - +
70C LYS* 3.7 20.3 + - + +
76C ILE* 4.4 13.4 - - + +
78C LEU* 3.3 34.5 - - + -
329C PHE* 3.3 40.4 - - + -
334C GLN* 4.1 19.9 + - + +
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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 TYR* 2.7 18.3 + - + +
64C GLN* 2.9 18.2 - - - +
65C HIS 2.8 1.4 + - - -
66C LEU* 1.3 76.7 - - - +
68C ASP* 1.3 63.7 + - - +
70C LYS* 3.3 20.3 + - - +
72C ASP* 5.1 3.9 - - - +
76C ILE* 5.5 4.3 - - - -
296C GLU* 3.9 25.6 - - + +
425C ARG* 4.5 13.9 + - - +
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Residues in contact with ASP 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C GLN 3.2 11.1 + - - +
65C HIS* 2.8 11.8 + - - +
67C ALA* 1.3 77.3 - - - +
69C SER* 1.3 65.5 + - - +
70C LYS 3.2 8.5 + - - +
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Residues in contact with SER 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C HIS 3.2 4.8 + - - -
66C LEU* 2.7 29.2 + - - +
68C ASP* 1.3 77.6 - - - +
70C LYS* 1.3 66.2 + - - +
334C GLN* 3.2 32.4 + - - -
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Residues in contact with LYS 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 3.7 23.1 - - - +
67C ALA 3.3 13.8 + - - +
68C ASP* 3.1 12.9 - - - +
69C SER* 1.3 91.5 + - - +
71C ASN* 1.3 63.7 + - - +
72C ASP* 3.9 2.1 + - - +
74C ASP* 4.1 11.4 - - + +
75C ASN 4.0 3.9 + - - +
76C ILE* 3.3 36.2 - - + +
327C ASP* 2.6 45.3 + - - -
329C PHE* 4.3 15.4 - - - -
425C ARG* 5.7 0.4 - - - +
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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