Contacts of the helix formed by residues 51 - 72 (chain F) in PDB entry 3L73
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 PRO 51 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ARG 3.7 3.6 - - - +
50F LEU* 1.3 85.7 - - + +
52F GLU* 1.3 67.6 + - - +
53F ASP* 3.0 17.7 + - - +
54F LEU* 3.0 30.0 + - + -
55F TYR* 3.1 9.0 + - - +
93F TYR* 3.1 26.2 - - + +
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Residues in contact with GLU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F LEU 3.6 3.1 + - - -
51F PRO* 1.3 70.3 - - - +
53F ASP* 1.3 62.7 + - + +
55F TYR* 3.4 9.8 + - - +
56F ASN* 3.0 46.3 + - - +
9G ARG* 5.0 11.0 + - - +
11G ARG* 2.7 41.4 + - - -
12G HIS* 5.3 0.3 - - - -
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Residues in contact with ASP 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D TYR* 4.3 2.7 + - - +
51F PRO* 3.5 13.6 - - - +
52F GLU* 1.3 78.4 - - + +
54F LEU* 1.3 96.7 + - - +
56F ASN* 3.5 6.3 + - - +
57F GLU* 3.2 37.5 + - - +
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Residues in contact with LEU 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F LEU* 4.4 21.0 - - + +
51F PRO* 3.0 28.4 + - + +
53F ASP* 1.3 100.3 + - - +
55F TYR* 1.3 57.0 + - - +
57F GLU* 3.7 20.1 - - - +
58F ARG* 3.1 27.9 + - - +
61F ARG* 4.6 2.6 + - - -
87F LYS* 3.9 14.1 - - + +
89F TYR* 4.5 22.5 - - + +
93F TYR* 5.0 4.0 - - + +
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Residues in contact with TYR 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F LEU* 3.9 35.7 - - + -
48F LYS* 6.0 0.4 - - - -
50F LEU* 4.3 19.6 - - + +
51F PRO 3.1 10.3 + - - +
52F GLU* 3.4 15.5 - - - +
54F LEU* 1.3 77.0 - - - +
56F ASN* 1.3 73.0 + - - +
58F ARG* 3.4 11.5 + - - +
59F MET* 2.9 42.5 + - + +
8G ALA* 5.4 1.9 - - - +
9G ARG* 3.6 41.3 + - + +
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Residues in contact with ASN 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D TYR* 3.6 21.9 + - + +
52F GLU* 3.0 45.0 + - - +
53F ASP* 3.5 3.7 + - - +
55F TYR* 1.3 90.4 - - - +
57F GLU* 1.3 57.8 + - - +
59F MET* 3.5 7.7 + - - +
60F PHE* 3.0 27.5 + - - +
9G ARG* 4.8 2.8 - - - +
10G VAL* 5.3 0.2 - - - -
11G ARG* 3.7 42.7 + - - +
12G HIS* 4.6 8.6 + - - +
13G ILE* 5.3 0.7 - - - +
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Residues in contact with GLU 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D TYR* 3.7 27.5 + - + +
53F ASP* 3.2 34.0 + - - +
54F LEU* 3.7 12.0 - - - +
55F TYR 3.1 0.6 - - - -
56F ASN* 1.3 75.8 - - - +
58F ARG* 1.3 64.7 + - - +
60F PHE* 3.3 2.9 + - - +
61F ARG* 3.0 39.8 + - - +
87F LYS* 2.7 32.8 + - - +
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Residues in contact with ARG 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C SER* 5.2 1.6 - - - -
34F ASP 3.8 12.1 + - - -
35F ASP* 3.5 12.2 + - - +
37F LEU* 5.4 2.8 + - - +
39F GLU* 3.1 28.5 + - - +
43F VAL* 5.8 1.8 - - - +
47F LEU* 3.5 40.7 - - - +
50F LEU* 4.5 3.1 - - - -
54F LEU 3.1 14.4 + - - +
55F TYR* 3.7 11.7 - - - +
57F GLU* 1.3 79.8 - - - +
59F MET* 1.3 69.7 + - - +
61F ARG* 3.2 22.1 + - - +
62F ILE* 2.9 49.1 + - + +
89F TYR* 2.9 36.2 + - + +
90F LEU* 5.3 1.6 - - - +
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Residues in contact with MET 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C SER* 5.4 7.2 - - - +
215C ASP* 6.1 0.4 - - + -
216C SER* 3.5 29.8 - - - +
55F TYR* 2.9 32.7 + - + +
56F ASN* 3.5 11.2 - - - +
57F GLU 3.2 0.2 - - - -
58F ARG* 1.3 84.0 - - - +
60F PHE* 1.3 57.9 + - - +
62F ILE* 3.3 14.9 + - + +
63F LYS* 2.8 28.8 + - - +
8G ALA* 4.6 10.3 - - + -
9G ARG 3.8 13.5 - - - +
10G VAL* 3.8 33.4 - - + -
11G ARG 5.6 1.3 - - - +
13G ILE* 4.8 7.6 - - + -
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Residues in contact with PHE 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D MET* 3.2 30.7 - - + -
236D ALA* 3.7 14.6 - - - -
237D TYR* 3.5 55.6 - + + -
56F ASN 3.0 17.3 + - - +
57F GLU 3.3 3.8 + - - +
59F MET* 1.3 75.1 - - - +
61F ARG* 1.3 59.9 + - + +
63F LYS 3.2 0.7 + - - -
64F ARG* 2.7 65.3 + - + +
13G ILE* 3.6 28.4 - - + +
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Residues in contact with ARG 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F GLY 3.4 22.0 - - - +
31F LEU* 3.4 10.7 - - + +
32F MET* 3.5 21.9 - - - +
35F ASP* 2.6 27.1 + - - +
54F LEU 4.6 2.8 + - - -
57F GLU* 3.0 29.6 + - - +
58F ARG* 3.2 30.2 - - - +
60F PHE* 1.3 79.2 - - + +
62F ILE* 1.3 58.0 + - - +
64F ARG* 3.4 23.9 + - - +
65F ALA 3.0 22.2 + - - -
87F LYS* 3.8 18.9 - - - +
89F TYR* 3.2 33.5 - - - -
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Residues in contact with ILE 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C ILE* 3.6 27.6 - - + -
213C SER* 3.8 20.2 - - - +
216C SER* 4.0 9.6 - - - +
31F LEU* 4.0 13.0 - - + -
35F ASP* 4.0 18.2 - - + +
39F GLU* 5.4 0.4 - - - +
58F ARG* 2.9 60.6 + - + +
59F MET* 3.7 11.0 - - + +
61F ARG* 1.3 72.9 - - - +
63F LYS* 1.3 67.2 + - - +
64F ARG 3.0 1.1 - - - -
65F ALA* 3.0 4.5 + - - +
66F LEU* 2.9 23.3 + - + +
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Residues in contact with LYS 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C SER* 3.1 39.2 + - - +
217C ASP* 3.6 25.5 + - + +
233D ARG* 4.1 9.2 - - - +
235D MET* 3.8 16.6 - - + -
59F MET 2.8 19.5 + - - +
60F PHE* 3.8 3.6 - - - +
62F ILE* 1.3 76.3 - - - +
64F ARG* 1.3 62.6 + - - +
66F LEU* 3.4 7.2 + - - +
67F ASP* 3.1 21.3 + - - +
10G VAL* 5.8 4.0 - - + -
13G ILE* 3.9 38.1 - - + -
15G THR* 4.4 10.8 - - - +
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Residues in contact with ARG 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D MET* 3.4 23.5 - - + +
29F TYR 3.0 26.0 + - - -
30F GLY* 3.7 19.6 + - - -
60F PHE* 2.7 44.5 + - + +
61F ARG* 3.4 23.7 + - - +
62F ILE 3.0 0.2 - - - -
63F LYS* 1.3 73.6 - - - +
65F ALA* 1.3 62.3 + - - +
67F ASP* 3.1 5.8 + - + +
68F LEU* 3.0 29.8 + - + +
75F LEU* 4.2 29.8 - - - +
79F GLN* 5.5 4.6 - - - +
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Residues in contact with ALA 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C LEU* 3.6 23.2 - - + +
212C ILE* 4.6 1.1 - - + -
29F TYR* 4.0 21.6 - - + +
31F LEU* 3.5 34.5 - - + -
61F ARG 3.0 5.0 + - - +
62F ILE* 3.0 8.6 + - - +
64F ARG* 1.3 76.1 - - - +
66F LEU* 1.3 58.0 + - - +
68F LEU* 3.1 5.4 + - - +
69F SER* 2.8 24.8 + - - -
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Residues in contact with LEU 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C SER* 4.5 4.8 + - - +
27C ASN* 3.5 30.1 - - - +
208C ASN* 3.7 20.0 - - - +
210C LEU* 4.0 11.9 - - + -
212C ILE* 4.2 12.6 - - + -
213C SER 3.9 7.0 - - - +
214C SER* 3.6 29.4 - - - -
216C SER* 4.0 8.7 - - - +
217C ASP* 4.0 26.0 - - + +
62F ILE* 2.9 17.0 + - + +
63F LYS* 3.7 7.4 - - - +
64F ARG 3.2 0.2 - - - -
65F ALA* 1.3 77.5 - - - +
67F ASP* 1.3 62.8 + - - +
69F SER* 3.3 3.2 + - - -
70F LEU* 3.1 21.3 + - - +
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Residues in contact with ASP 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C ASP* 4.3 0.4 + - - -
230D LEU 4.2 1.2 - - - +
233D ARG* 2.6 43.6 + - - +
235D MET* 4.3 15.7 - - - +
63F LYS 3.1 11.6 + - - +
64F ARG* 3.1 9.4 + - + +
66F LEU* 1.3 74.0 - - - +
68F LEU* 1.3 68.4 + - - +
70F LEU* 3.5 5.6 - - - +
71F LYS* 2.6 69.1 + - - +
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Residues in contact with LEU 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F TYR* 3.8 39.3 - - + +
64F ARG* 3.0 21.7 + - + +
65F ALA* 3.4 7.2 - - - +
67F ASP* 1.3 81.0 - - - +
69F SER* 1.3 59.0 + - - +
71F LYS* 3.1 7.5 + - + -
72F HIS 2.8 24.4 + - - -
73F ARG* 3.2 26.4 + - + +
74F ILE* 4.0 24.0 - - - +
75F LEU* 3.9 30.3 - - + +
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Residues in contact with SER 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ASN* 3.4 27.3 + - - +
209C PRO* 4.0 10.0 - - - +
210C LEU* 3.9 22.0 - - - +
2007C PEE 6.1 0.5 - - - -
29F TYR* 4.2 10.2 + - - -
65F ALA 2.8 12.7 + - - -
66F LEU 3.5 8.3 - - - -
67F ASP 3.2 0.2 - - - -
68F LEU* 1.3 76.7 - - - +
70F LEU* 1.3 64.0 + - - +
72F HIS* 3.0 25.8 + - - +
73F ARG 5.2 0.2 - - - -
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Residues in contact with LEU 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C SER* 3.2 35.7 - - - +
27C ASN* 3.6 12.0 - - - +
227D TRP* 4.3 13.4 - - + -
230D LEU* 4.1 29.8 - - + +
231D LYS* 3.2 36.8 - - + -
233D ARG* 3.8 26.2 - - - +
66F LEU 3.1 7.9 + - - +
67F ASP* 3.5 14.1 - - - +
69F SER* 1.3 77.3 - - - +
71F LYS* 1.3 68.7 + - + +
72F HIS* 3.5 9.7 + - - -
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Residues in contact with LYS 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D LEU 3.1 13.5 + - - -
231D LYS* 2.7 43.1 - - + +
232D SER 4.4 1.3 - - - -
233D ARG 2.8 25.0 + - - -
2003D CDL 4.9 2.3 + - - -
13E TYR* 5.9 1.8 - - - -
67F ASP* 2.6 59.4 + - - +
68F LEU* 3.5 9.9 - - + +
69F SER 3.1 0.4 - - - -
70F LEU* 1.3 84.4 - - + +
72F HIS* 1.3 70.3 + - - +
73F ARG* 3.5 30.9 + - + +
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Residues in contact with HIS 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C SER* 4.9 7.1 - - - -
228C LYS* 6.0 2.0 + - - -
2007C PEE 5.1 6.8 + - - -
231D LYS* 4.9 2.9 - - - -
2003D CDL 3.5 43.8 - - - -
68F LEU 2.8 5.0 + - - -
69F SER* 3.0 15.8 + - - +
70F LEU* 3.7 17.9 + - - -
71F LYS* 1.3 79.3 - - - +
73F ARG* 1.3 78.0 + - - +
36G ASN* 4.3 1.6 - - - +
39G ARG* 3.6 16.3 + - - +
40G ARG* 3.4 22.9 + - - +
2004G CDL 3.7 38.4 + - - -
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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) + - + + + + + -
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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