Contacts of the helix formed by residues 54 - 79 (chain A) in PDB entry 1H7I
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 SER 54 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A SER* 1.3 79.2 - - - +
55A GLN* 1.3 65.9 + - - +
56A VAL 3.2 2.0 - - - -
57A THR* 3.2 6.4 + - - -
58A GLN* 2.8 47.7 + - - +
119A ARG* 3.6 20.2 - - - +
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Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLN* 5.0 0.7 + - - -
50A GLU* 3.1 45.1 + - + +
53A SER* 3.2 18.0 + - - +
54A SER* 1.3 78.6 + - - +
56A VAL* 1.3 61.9 + - - +
58A GLN* 3.3 11.0 + - - +
59A GLU* 3.0 55.6 + - + +
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.4 18.8 + - + +
39A TRP* 4.8 4.0 - - + -
40A VAL* 3.7 30.3 - - + -
47A VAL* 4.3 4.7 - - + +
50A GLU* 3.4 39.7 + - + +
51A LEU* 3.8 27.6 - - + +
53A SER 4.9 0.4 + - - +
54A SER 3.2 0.8 - - - -
55A GLN* 1.3 75.7 - - - +
57A THR* 1.3 60.2 + - + +
59A GLU* 3.3 0.3 + - - -
60A LEU* 2.9 39.4 + - + +
115A LEU* 4.0 3.8 - - + -
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Residues in contact with THR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 5.7 0.9 - - + -
53A SER 5.5 0.2 + - - -
54A SER* 3.2 11.3 + - - -
56A VAL* 1.3 78.7 - - + +
58A GLN* 1.3 57.5 + - - +
60A LEU* 3.9 7.9 - - - +
61A ARG* 3.0 38.3 + - - +
112A CYS* 3.6 34.6 - - - +
115A LEU* 3.8 20.9 - - + -
116A VAL* 4.3 7.5 - - + +
119A ARG* 3.1 30.0 + - - +
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Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A SER* 2.8 40.2 + - - +
55A GLN* 3.7 10.5 - - - +
57A THR* 1.3 78.8 + - - +
59A GLU* 1.3 58.6 + - + +
61A ARG* 3.1 7.4 + - - +
62A ALA* 2.9 29.2 + - - +
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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
----------------------------------------------------------
36A TYR* 2.8 47.9 + - + +
50A GLU* 3.8 2.8 - - - +
55A GLN* 3.0 46.0 + - + +
58A GLN* 1.3 73.8 - - + +
60A LEU* 1.3 66.5 + - - +
62A ALA* 3.3 6.7 + - - +
63A LEU* 3.0 30.6 + - + +
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.5 35.4 - - + +
36A TYR* 3.6 25.3 - - + -
37A LEU* 4.2 18.8 - - + -
40A VAL* 4.8 0.7 - - + -
56A VAL* 2.9 27.2 + - + +
57A THR* 3.9 1.1 - - - +
59A GLU* 1.3 76.2 - - - +
61A ARG* 1.3 64.5 + - - +
63A LEU* 3.2 3.9 + - - +
64A MET* 2.9 24.3 + - - +
111A VAL* 4.4 11.2 - - + -
112A CYS* 3.8 19.3 - - - -
115A LEU* 3.5 32.3 - - + -
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Residues in contact with ARG 61 (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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57A THR* 3.0 25.8 + - - +
58A GLN* 3.1 8.0 + - - +
60A LEU* 1.3 78.3 - - - +
62A ALA* 1.3 58.3 + - - +
64A MET* 3.2 19.7 - - + +
65A ASP* 2.9 43.2 + - - +
109A GLU* 2.7 41.8 + - - -
112A CYS* 3.5 27.3 - - - +
113A GLY 5.3 0.2 - - - +
116A VAL* 5.8 4.0 - - - +
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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
----------------------------------------------------------
58A GLN 2.9 15.6 + - - +
59A GLU* 3.7 7.6 - - - +
61A ARG* 1.3 77.9 - - - +
63A LEU* 1.3 63.4 + - + +
65A ASP* 3.2 9.3 + - - +
66A GLU* 3.1 22.7 + - - +
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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
----------------------------------------------------------
29A ALA* 4.8 2.3 - - - +
32A ARG* 3.7 30.5 - - + +
33A PHE* 3.8 17.9 - - + +
36A TYR* 3.6 41.1 - - + -
59A GLU* 3.0 23.9 + - + +
60A LEU* 3.8 4.7 - - - +
62A ALA* 1.3 74.3 - - + +
64A MET* 1.3 67.0 + - - +
66A GLU* 3.3 17.4 + - - +
67A THR* 2.9 28.0 + - - -
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Residues in contact with MET 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.7 3.4 - - + -
60A LEU 2.9 12.3 + - - +
61A ARG* 3.2 17.5 - - - +
63A LEU* 1.3 77.0 - - - +
65A ASP* 1.3 70.6 + - - +
67A THR* 3.1 5.3 + - - -
68A MET* 3.0 32.1 + - + +
105A GLY* 4.2 4.7 - - - +
108A MET* 3.1 73.1 - - + +
109A GLU* 3.4 28.5 - - + +
112A CYS* 3.4 22.9 - - - -
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Residues in contact with ASP 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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61A ARG* 2.9 32.1 + - - +
62A ALA* 3.2 7.9 + - - +
64A MET* 1.3 82.5 - - - +
66A GLU* 1.3 58.6 + - - +
68A MET* 3.2 7.9 + - - +
69A LYS* 2.9 33.9 + - + +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA* 4.4 6.9 - - + +
32A ARG* 3.3 33.6 + - - -
62A ALA 3.1 11.9 + - - +
63A LEU* 3.6 20.0 - - - +
65A ASP* 1.3 76.5 - - - +
67A THR* 1.3 62.1 + - - +
69A LYS* 3.3 22.0 + - - +
70A GLU* 3.1 39.2 + - + +
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Residues in contact with THR 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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26A TRP* 3.9 16.3 - - + +
29A ALA* 3.3 27.2 + - - +
30A LEU* 3.4 37.5 + - + +
33A PHE* 4.5 3.3 - - - +
63A LEU 2.9 16.4 + - - -
64A MET* 3.1 8.1 + - - -
66A GLU* 1.3 75.9 - - - +
68A MET* 1.3 58.6 + - - +
70A GLU* 3.4 2.0 + - - +
71A LEU* 2.9 30.1 + - + +
104A LEU* 4.5 5.8 - - + -
108A MET* 4.2 14.4 - - + -
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Residues in contact with MET 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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64A MET* 3.0 23.2 + - + +
65A ASP* 3.7 7.6 - - - +
67A THR* 1.3 78.0 - - - +
69A LYS* 1.3 64.8 + - - +
71A LEU* 3.2 15.7 + - - +
72A LYS* 2.9 45.3 + - - +
101A GLN* 3.5 46.0 - - + +
102A ALA* 4.9 2.0 - - - +
104A LEU* 4.6 2.0 - - - -
105A GLY* 4.1 18.2 - - - -
108A MET* 3.9 23.3 - - + -
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Residues in contact with LYS 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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65A ASP 2.9 18.0 + - - +
66A GLU* 3.5 22.3 - - - +
68A MET* 1.3 77.8 - - - +
70A GLU* 1.3 71.3 + - + +
72A LYS* 3.2 11.6 + - - +
73A ALA* 3.0 23.6 + - - +
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Residues in contact with GLU 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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25A ARG* 2.8 52.5 + - + +
26A TRP* 3.8 23.8 - - - +
29A ALA* 4.6 7.9 - - + -
66A GLU* 3.1 36.0 + - + +
67A THR* 4.0 1.3 - - - +
69A LYS* 1.3 84.5 - - + +
71A LEU* 1.3 63.9 + - - +
73A ALA* 3.2 8.9 + - - +
74A TYR* 2.8 24.8 + - - +
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TRP* 3.4 38.7 - - + +
67A THR 2.9 17.1 + - - +
68A MET* 3.5 11.2 - - - +
70A GLU* 1.3 78.5 - - - +
72A LYS* 1.3 62.4 + - - +
74A TYR* 3.2 3.1 + - + +
75A LYS* 3.0 24.5 + - + +
101A GLN* 3.4 36.9 + - + +
104A LEU* 4.1 13.9 - - + -
155A LEU* 3.7 23.8 - - + -
159A LEU* 3.8 23.1 - - + -
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Residues in contact with LYS 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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68A MET* 2.9 38.6 + - - +
69A LYS* 3.2 8.4 + - - +
71A LEU* 1.3 76.8 - - - +
73A ALA* 1.3 62.2 + - - +
75A LYS* 3.6 14.3 + - - +
76A SER* 3.3 22.0 + - - -
101A GLN* 3.5 31.3 + - - +
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Residues in contact with ALA 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 LYS 3.0 16.4 + - - +
70A GLU* 3.9 9.9 - - - +
72A LYS* 1.3 75.7 - - - +
74A TYR* 1.3 63.7 + - - +
76A SER* 3.5 6.8 + - - -
77A GLU* 3.1 35.1 + - - +
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Residues in contact with TYR 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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24A GLN* 3.5 42.9 + - + +
25A ARG* 6.5 0.9 - - + -
26A TRP* 3.6 28.3 - + + +
70A GLU 2.8 20.1 + - - +
71A LEU 3.2 4.2 + - - +
73A ALA* 1.3 73.1 - - - +
75A LYS* 1.3 63.5 + - - +
77A GLU* 3.2 12.6 + - + +
78A LEU* 3.0 60.7 + - + +
159A LEU* 4.2 21.4 + - + +
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Residues in contact with LYS 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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71A LEU 3.0 12.1 + - - +
72A LYS* 3.9 18.3 + - - +
74A TYR* 1.3 80.2 - - - +
76A SER* 1.3 58.8 + - - +
78A LEU* 3.1 13.7 + - - +
79A GLU* 2.9 49.6 + - - +
94A SER* 5.4 4.0 - - - +
97A LEU* 3.9 32.8 - - + -
98A GLN* 3.5 36.0 + - + +
101A GLN* 3.2 28.0 + - - +
159A LEU* 4.9 3.4 - - + -
162A TYR* 4.7 2.0 - - + +
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Residues in contact with SER 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 LYS 3.3 15.1 + - - -
73A ALA* 3.8 7.4 + - - -
75A LYS* 1.3 80.3 - - - +
77A GLU* 1.3 62.4 + - - +
79A GLU* 3.5 25.2 - - - +
80A GLU* 4.0 10.9 + - - +
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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
----------------------------------------------------------
73A ALA* 3.1 23.4 + - - +
74A TYR* 3.7 14.5 - - + +
75A LYS 3.2 0.4 - - - -
76A SER* 1.3 73.9 - - - +
78A LEU* 1.3 66.9 + - + +
79A GLU 3.0 2.5 - - - -
80A GLU* 2.9 27.0 + - + +
81A GLN* 4.3 3.8 + - - +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TYR* 3.0 59.1 + - + +
75A LYS* 3.1 8.7 + - - +
77A GLU* 1.3 72.2 - - + +
79A GLU* 1.3 60.1 + - - +
80A GLU 2.9 11.2 + - - -
81A GLN* 2.9 18.2 + - + +
82A LEU* 3.7 11.9 - - + +
159A LEU* 3.7 24.2 - - + +
162A TYR* 4.1 39.3 - - + +
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LYS* 2.9 37.3 + - - +
76A SER* 3.5 19.3 - - - +
77A GLU 3.0 0.2 - - - -
78A LEU* 1.3 79.5 - - - +
80A GLU* 1.3 60.5 + - - +
81A GLN 3.2 2.4 + - - -
82A LEU* 3.7 28.8 + - + +
90A ARG* 6.2 2.2 - - - -
94A SER* 4.5 5.4 + - - -
162A TYR* 3.4 26.6 + - + +
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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