Contacts of the helix formed by residues 58 - 79 (chain A) in PDB entry 3S51
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 GLU 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A THR* 4.0 13.2 + - - +
18A GLN* 3.0 36.0 + - - +
22A GLN* 5.3 5.5 + - - -
55A PRO* 3.0 12.4 + - + +
56A CYS 4.0 2.8 - - - -
57A SER* 1.3 91.8 + - - +
59A GLU* 1.3 60.4 + - - +
60A ASP* 4.6 5.9 - - - +
61A GLY* 3.3 9.4 + - - +
62A ALA* 2.9 24.6 + - - +
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A CYS 6.1 0.4 - - - +
58A GLU* 1.3 68.5 - - - +
60A ASP* 1.3 59.3 + - - +
61A GLY 2.9 5.2 - - - -
62A ALA* 2.8 5.3 + - + +
63A LEU* 2.5 64.8 + - + +
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Residues in contact with ASP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLN 4.8 0.5 - - - +
21A LEU* 5.3 2.6 - - - +
22A GLN* 3.0 40.8 + - - +
25A LYS* 5.8 4.3 - - - -
58A GLU* 3.5 6.8 - - - +
59A GLU* 1.3 77.1 - - - +
61A GLY* 1.3 57.3 + - - +
63A LEU* 5.0 3.8 - - - -
64A ARG* 2.8 39.9 + - - +
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Residues in contact with GLY 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 6.1 1.6 - - - -
21A LEU* 5.3 1.6 - - - -
53A GLY 5.0 0.9 - - - -
54A SER* 3.0 45.7 - - - +
55A PRO* 3.4 6.5 - - - -
58A GLU* 3.3 12.1 + - - +
59A GLU 2.9 0.8 - - - -
60A ASP* 1.3 78.2 - - - +
62A ALA* 1.3 58.5 + - - +
64A ARG 3.3 1.0 + - - -
65A ARG* 3.0 19.1 + - - +
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PRO 3.0 10.2 + - - +
56A CYS* 4.1 14.4 - - - +
58A GLU 2.9 14.4 + - - +
59A GLU* 2.8 13.5 + - + +
61A GLY* 1.3 72.1 - - - +
63A LEU* 1.3 63.6 + - + +
64A ARG 3.0 1.3 + - - -
65A ARG* 3.2 23.7 + - - +
66A TYR 3.5 2.4 + - - -
100A PHE* 5.9 0.4 - - + -
101A PRO* 4.6 11.2 - - + -
104A LEU* 3.3 28.3 - - + +
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLU* 2.5 53.7 + - + +
60A ASP* 5.0 3.6 - - - -
62A ALA* 1.3 78.6 - - + +
64A ARG* 1.3 57.9 + - - +
66A TYR* 3.9 14.6 - - - +
67A LYS* 4.3 4.9 + - - +
101A PRO* 6.2 0.7 - - + -
104A LEU* 4.2 23.1 - - + -
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Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.1 75.2 + - - +
22A GLN* 4.5 1.0 - - - +
24A LEU* 3.9 10.7 - - - +
25A LYS* 3.8 26.8 - - - +
28A ASP* 3.8 21.9 + - - +
50A VAL* 5.2 2.8 - - - +
54A SER* 4.5 3.4 - - - -
60A ASP* 2.8 32.8 + - - +
61A GLY 3.3 4.5 + - - +
62A ALA 3.0 0.2 - - - -
63A LEU* 1.3 77.2 - - - +
65A ARG* 1.3 65.2 + - - +
66A TYR 3.0 2.0 - - - -
67A LYS* 2.9 19.3 + - + +
68A ILE* 3.3 20.4 + - + +
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.4 32.1 + - + +
52A LYS* 6.1 1.0 - - - +
54A SER* 3.0 37.0 + - - +
55A PRO* 4.9 3.7 - - - +
56A CYS* 3.8 9.1 - - - -
61A GLY 3.0 10.6 + - - +
62A ALA* 3.2 10.5 + - - +
64A ARG* 1.3 75.9 - - - +
66A TYR* 1.3 56.6 + - - +
68A ILE* 3.1 11.7 + - - +
69A TYR* 2.8 35.6 + - + -
96A GLU* 3.4 24.3 + - - +
99A HIS* 3.0 42.8 + - - -
100A PHE* 3.0 48.7 - - + -
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Residues in contact with TYR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ALA 3.5 4.4 + - - +
63A LEU* 3.9 12.8 - - - +
64A ARG 3.0 0.4 - - - -
65A ARG* 1.3 79.5 - - - +
67A LYS* 1.3 63.4 + - + +
69A TYR* 4.1 5.6 - - - +
70A SER* 3.4 24.5 + - - -
100A PHE* 4.2 5.8 - - - -
104A LEU* 3.4 33.4 - - + -
107A ASP* 3.4 32.7 + - + +
108A LEU* 3.8 27.5 - - + +
111A ASP* 2.8 31.5 + - - -
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ASP* 5.7 6.7 - - + +
29A LEU* 4.9 17.0 - - - +
63A LEU 4.3 4.2 + - - +
64A ARG* 2.9 14.7 + - + +
66A TYR* 1.3 82.3 - - + +
68A ILE* 1.3 66.0 + - + +
70A SER* 3.2 9.8 + - - -
71A CYS* 3.1 25.0 + - + +
74A GLN* 4.9 16.4 + - - +
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Residues in contact with ILE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ASP* 5.2 13.7 - - + +
32A LEU* 4.8 10.3 - - + -
47A LEU* 3.8 28.9 - - + -
50A VAL* 3.7 28.7 - - + -
51A LEU* 4.4 14.4 - - + -
54A SER* 4.3 8.7 - - - +
64A ARG* 3.4 20.2 - - + +
65A ARG* 3.4 21.1 - - - +
67A LYS* 1.3 77.8 - - + +
69A TYR* 1.3 61.6 + - + +
71A CYS* 2.8 23.3 + - - +
72A CYS* 2.9 20.8 + - - -
93A LEU* 5.9 0.4 - - + -
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Residues in contact with TYR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.9 22.4 - - + -
65A ARG* 2.8 28.4 + - + +
66A TYR* 4.1 3.1 - - - +
68A ILE* 1.3 74.0 - - + +
70A SER* 1.3 58.5 + - - +
72A CYS* 3.7 1.6 + - - +
73A ILE* 3.0 34.6 + - - +
93A LEU* 3.1 55.7 + - + +
96A GLU* 3.2 32.3 - - + +
97A VAL* 3.2 24.9 + - + -
100A PHE* 3.6 27.6 - + - -
108A LEU* 4.0 26.7 - - + -
129A LEU* 4.4 7.6 - - + -
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A TYR* 3.4 23.8 + - - -
67A LYS* 3.2 14.4 + - - -
68A ILE 3.1 0.8 - - - -
69A TYR* 1.3 78.0 - - - +
71A CYS* 1.3 59.0 + - - +
73A ILE* 3.9 9.0 - - - +
74A GLN* 3.1 45.5 + - - +
108A LEU* 5.1 4.0 - - - +
111A ASP* 4.8 8.7 + - - -
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Residues in contact with CYS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ASP* 4.0 11.0 - - + -
29A LEU* 3.7 48.2 - - - -
32A LEU* 4.7 12.1 - - + -
33A LEU* 4.7 7.0 - - - -
67A LYS* 3.1 17.3 + - + +
68A ILE* 2.8 11.0 + - - +
70A SER* 1.3 76.8 - - - +
72A CYS* 1.3 65.1 + - - +
74A GLN* 3.2 10.8 + - - +
75A LEU* 3.0 28.9 + - - +
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Residues in contact with CYS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 5.2 6.5 - - - +
47A LEU* 4.0 29.6 - - - -
68A ILE* 2.9 26.0 + - - +
69A TYR 3.9 0.9 - - - +
71A CYS* 1.3 76.1 - - - +
73A ILE* 1.3 63.2 + - - +
75A LEU* 3.3 6.8 + - - +
76A VAL* 3.0 29.5 + - - +
89A ILE* 3.5 14.0 - - + +
93A LEU* 3.4 38.1 - - + -
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Residues in contact with ILE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A TYR* 3.0 26.8 + - + +
70A SER* 3.9 8.3 - - - +
72A CYS* 1.3 78.1 - - - +
74A GLN* 1.3 63.2 + - + +
75A LEU 3.4 0.3 + - - -
76A VAL* 3.5 6.7 + - - +
77A GLU* 2.9 44.7 + - - +
93A LEU* 4.3 3.1 - - + -
108A LEU* 4.7 11.9 - - + -
112A PHE* 3.6 32.8 - - + -
126A SER* 4.1 15.2 + - - +
129A LEU* 3.8 23.1 - - + -
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Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 4.4 10.5 - - + +
67A LYS* 4.9 11.7 + - - +
70A SER* 3.1 39.4 + - - +
71A CYS* 3.2 20.6 + - - +
73A ILE* 1.3 76.7 - - + +
75A LEU* 1.3 57.1 + - + +
77A GLU* 3.1 16.3 - - - +
78A SER* 2.7 35.4 + - - +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 4.0 18.2 - - + +
33A LEU* 3.5 55.6 - - + +
36A GLN* 5.7 3.8 - - + +
71A CYS* 3.0 20.6 + - - +
72A CYS* 3.8 5.4 - - - +
74A GLN* 1.3 76.6 - - + +
76A VAL* 1.3 67.0 + - - +
78A SER* 3.9 7.4 - - - +
79A GLY* 2.9 23.8 + - - -
81A LEU* 3.3 31.0 - - + +
89A ILE* 5.4 4.9 - - + -
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A CYS 3.0 21.0 + - - +
73A ILE* 3.8 6.5 - - - +
74A GLN 3.5 0.2 - - - -
75A LEU* 1.3 77.5 - - - +
77A GLU* 1.3 56.0 + - - +
79A GLY 4.1 5.9 - - - +
81A LEU* 4.0 8.6 - - - +
86A ALA* 3.9 24.8 - - + +
89A ILE* 3.7 27.1 - - + -
90A ILE* 3.7 30.7 - - + -
93A LEU* 6.0 0.2 - - + -
123A ASN* 2.7 33.8 + - - +
125A LYS* 4.1 7.9 - - + -
126A SER* 4.2 11.4 - - - +
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ILE* 2.9 22.9 + - - +
74A GLN* 3.1 31.5 + - - +
76A VAL* 1.3 81.2 - - - +
78A SER* 1.3 75.4 + - - +
79A GLY 4.0 3.5 - - - +
119A ASP* 5.2 1.9 - - - +
120A ARG 5.8 0.4 - - - +
121A LEU* 2.8 55.5 - - + +
122A VAL* 4.6 3.5 - - - +
123A ASN* 3.7 16.2 + - + +
126A SER* 2.8 25.7 + - - +
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Residues in contact with SER 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLN* 2.7 22.8 + - - +
75A LEU* 3.9 6.2 + - - +
77A GLU* 1.3 81.2 - - - +
79A GLY* 1.3 74.6 + - - +
120A ARG 5.9 1.8 - - - -
121A LEU 4.9 0.4 - - - -
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Residues in contact with GLY 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 2.9 19.5 + - - +
76A VAL 4.1 7.6 - - - +
77A GLU 4.0 5.5 - - - +
78A SER* 1.3 86.9 + - - +
80A ASP* 1.3 58.8 + - - +
81A LEU* 3.1 22.1 + - - +
123A ASN* 5.3 0.9 + - - -
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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
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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