Contacts of the helix formed by residues 53 - 78 (chain S) in PDB entry 1RZZ
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 GLY 53 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28S ASN* 4.1 16.6 - - - -
51S TYR* 3.6 23.7 + - - -
52S LEU* 1.3 74.2 - - - +
54S SER* 1.3 61.1 + - - -
55S LEU 3.5 2.0 - - - -
56S GLY 4.0 5.2 - - - +
57S VAL* 3.0 32.0 + - - +
132S ARG* 4.6 1.0 - - - +
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Residues in contact with SER 54 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53S GLY* 1.3 69.7 - - - -
55S LEU* 1.3 60.8 + - - +
57S VAL* 3.2 5.9 + - - +
58S LEU* 2.8 31.1 + - - +
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Residues in contact with LEU 55 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53S GLY 3.5 0.2 - - - -
54S SER* 1.3 78.4 - - - +
56S GLY* 1.3 57.5 + - - +
58S LEU* 3.3 14.7 + - + +
59S SER* 2.8 31.1 + - - -
128S SER* 3.3 44.4 - - - +
131S GLY* 3.7 9.9 - - - -
132S ARG* 3.5 22.7 - - + +
135S LEU* 3.8 21.8 - - + -
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Residues in contact with GLY 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52S LEU* 4.3 12.1 - - - +
53S GLY 3.6 7.3 + - - +
54S SER 3.2 0.6 - - - -
55S LEU* 1.3 77.3 - - - +
57S VAL* 1.3 55.1 + - - +
59S SER* 3.6 3.2 - - - -
60S LEU* 2.7 38.3 + - - +
129S TRP* 5.3 2.7 - - - -
132S ARG* 4.1 33.0 - - - +
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Residues in contact with VAL 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52S LEU* 4.4 17.0 - - + +
53S GLY 3.0 19.5 + - - +
54S SER* 3.2 7.2 + - - +
56S GLY* 1.3 72.1 - - - +
58S LEU* 1.3 58.7 + - - +
60S LEU* 3.3 8.0 + - + +
61S PHE* 2.8 36.9 + - + +
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Residues in contact with LEU 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54S SER 2.8 17.5 + - - +
55S LEU* 3.5 22.7 - - + +
57S VAL* 1.3 78.2 - - - +
59S SER* 1.3 63.9 + - - +
61S PHE* 3.2 12.6 + - + +
62S SER* 3.0 31.1 + - - +
124S VAL* 4.2 24.0 - - + -
128S SER* 4.3 7.6 - - - -
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Residues in contact with SER 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55S LEU 2.8 18.2 + - - -
56S GLY* 3.6 4.9 - - - -
58S LEU* 1.3 73.4 - - - +
60S LEU* 1.3 57.3 + - - +
62S SER 3.5 0.2 + - - -
63S GLY* 3.0 25.8 + - - -
125S ALA* 2.8 28.6 + - - +
128S SER* 2.9 23.0 + - - -
129S TRP* 3.4 30.7 - - - +
132S ARG* 5.4 0.2 - - - -
2005S BPH 3.9 5.7 - - - +
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Residues in contact with LEU 60 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52S LEU* 4.3 29.8 - - + -
56S GLY 2.7 19.7 + - - +
57S VAL* 3.7 7.6 - - + +
59S SER* 1.3 71.0 - - - +
61S PHE* 1.3 67.1 + - - +
63S GLY* 3.6 0.5 + - - -
64S LEU* 3.2 46.4 + - + +
129S TRP* 6.0 2.9 - - + -
2005S BPH 3.9 17.2 - - + +
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Residues in contact with PHE 61 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57S VAL* 2.8 25.3 + - + +
58S LEU* 3.2 12.5 + - + +
60S LEU* 1.3 74.5 - - - +
62S SER* 1.3 64.1 + - - +
64S LEU* 3.1 10.5 + - + +
65S MET* 2.9 64.0 + - + +
121S PHE* 4.9 9.4 - + - -
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Residues in contact with SER 62 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58S LEU* 3.0 19.8 + - - +
61S PHE* 1.3 80.3 - - - +
63S GLY* 1.3 55.2 + - - +
65S MET* 2.9 9.8 + - - +
66S TRP* 2.7 31.7 + - - +
121S PHE* 3.1 40.1 - - - +
124S VAL* 3.4 20.4 - - - +
125S ALA* 3.7 11.9 - - - -
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Residues in contact with GLY 63 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59S SER 3.0 12.7 + - - -
60S LEU 4.0 0.2 - - - -
62S SER* 1.3 74.9 - - - +
64S LEU* 1.3 60.7 + - - +
66S TRP* 3.3 13.0 + - - +
67S PHE* 3.1 22.9 + - - +
125S ALA* 3.5 13.1 - - - +
2005S BPH 3.4 30.1 - - - +
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Residues in contact with LEU 64 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60S LEU* 3.2 37.3 + - + +
61S PHE* 3.1 11.7 + - + +
63S GLY* 1.3 73.2 - - - +
65S MET* 1.3 58.0 + - + +
67S PHE* 3.2 4.5 + - + +
68S PHE* 2.7 68.6 + - + -
2005S BPH 3.8 30.5 - - + -
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Residues in contact with MET 65 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61S PHE* 2.9 54.3 + - + +
62S SER 2.9 7.4 + - - +
64S LEU* 1.3 76.1 - - - +
66S TRP* 1.3 56.3 + - - +
68S PHE* 3.8 20.0 - - + +
69S THR* 2.8 38.6 + - - +
121S PHE* 3.5 38.6 - - + -
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Residues in contact with TRP 66 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62S SER 2.7 15.5 + - - +
63S GLY* 3.4 21.1 - - - +
65S MET* 1.3 72.5 - - - +
67S PHE* 1.3 80.4 + + + +
69S THR* 3.3 3.5 + - - -
70S ILE* 3.2 44.7 + - + +
118S ALA* 3.2 36.8 - - + +
121S PHE* 3.8 10.3 - - + +
122S MET* 3.6 39.0 - - + +
177S TYR* 3.4 29.4 - + - -
2001S BCL 4.9 2.9 - - + -
2003S BCL 3.8 40.6 - - + -
2005S BPH 4.8 6.5 - - + -
2010S SPO 4.2 21.5 - - + -
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Residues in contact with PHE 67 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63S GLY 3.1 13.7 + - - +
64S LEU* 3.6 7.4 - - + +
66S TRP* 1.3 95.1 - + + +
68S PHE* 1.3 70.6 + + - +
70S ILE* 3.7 3.5 + - - -
71S GLY 3.1 19.9 + - - -
2005S BPH 3.8 39.7 - - + -
2010S SPO 3.4 73.1 - - + +
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Residues in contact with PHE 68 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64S LEU* 2.7 53.2 + - + +
65S MET* 3.8 22.7 - - + +
67S PHE* 1.3 84.6 - + - +
69S THR* 1.3 60.3 + - - +
71S GLY* 3.0 0.9 + - - +
72S ILE* 2.8 32.4 + - - +
2010S SPO 3.7 42.4 - - + +
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Residues in contact with THR 69 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65S MET* 2.8 29.0 + - - +
66S TRP 3.3 4.5 + - - -
68S PHE* 1.3 75.1 - - - +
70S ILE* 1.3 63.0 + - - +
72S ILE* 2.9 25.9 - - + +
73S TRP* 3.3 6.8 + - - +
94S LEU* 4.4 2.1 - - + +
114S LEU* 3.5 44.1 - - + +
117S ILE* 4.2 5.9 - - + +
118S ALA* 3.7 15.7 - - + +
121S PHE* 3.9 16.5 - - - -
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Residues in contact with ILE 70 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66S TRP* 3.2 47.8 + - + +
67S PHE* 3.8 6.3 - - - +
69S THR* 1.3 76.0 - - - +
71S GLY* 1.3 63.7 + - - +
73S TRP* 3.2 4.0 + - - +
74S PHE* 3.0 54.8 + - + -
94S LEU* 4.1 19.1 - - + -
118S ALA* 4.4 2.2 - - + -
177S TYR* 3.7 23.6 - - + -
2010S SPO 3.6 39.9 - - + -
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Residues in contact with GLY 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67S PHE 3.1 7.1 + - - -
68S PHE 3.0 6.3 + - - -
70S ILE* 1.3 75.2 - - - +
72S ILE* 1.3 65.6 + - - +
74S PHE* 3.1 5.4 + - - +
75S TRP* 2.9 32.7 + - - -
2010S SPO 3.3 35.7 - - - -
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Residues in contact with ILE 72 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68S PHE 2.8 15.5 + - - +
69S THR* 2.9 24.2 - - + +
71S GLY* 1.3 71.4 - - - +
73S TRP* 1.3 68.2 + - - +
75S TRP* 3.3 7.7 + - + +
76S TYR* 3.0 22.3 + - - +
80S TRP* 3.7 31.3 - - + -
114S LEU* 4.5 16.2 - - + -
2010S SPO 4.1 7.0 - - - -
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Residues in contact with TRP 73 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69S THR 3.8 7.4 - - - +
70S ILE 3.2 8.0 + - - +
71S GLY 3.1 0.2 - - - -
72S ILE* 1.3 83.6 - - - +
74S PHE* 1.3 54.8 + + - +
76S TYR* 3.0 43.5 + + + +
77S GLN* 2.8 63.8 + - + +
93S SER 2.9 29.7 + - - -
94S LEU* 3.8 28.6 - - + +
95S GLU 5.1 0.2 - - - +
110S LYS* 3.8 43.1 - - + -
114S LEU* 3.6 23.8 - - + -
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Residues in contact with PHE 74 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70S ILE* 3.0 38.1 + - + +
71S GLY* 3.4 8.7 - - - +
73S TRP* 1.3 81.9 - + - +
75S TRP* 1.3 63.0 + - - +
77S GLN* 3.3 5.0 + - - +
78S ALA* 3.0 22.7 + - - +
85S PHE* 3.8 13.9 - - + -
89S LEU* 3.8 20.2 - - + -
92S PHE* 3.5 46.0 - + + -
93S SER* 3.6 23.8 - - - -
94S LEU 4.0 0.4 - - - -
177S TYR 3.7 12.1 - - - -
178S GLY* 4.4 5.8 - - - -
179S ILE 5.7 0.2 - - - -
2010S SPO 4.0 35.4 - - + -
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Residues in contact with TRP 75 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71S GLY 2.9 27.6 + - - -
72S ILE* 3.6 7.0 - - + +
73S TRP 3.2 0.2 - - - -
74S PHE* 1.3 72.1 - - - +
76S TYR* 1.3 67.4 + - - +
78S ALA* 3.0 9.9 + - + -
80S TRP* 3.0 68.6 + + + -
82S PRO* 3.7 46.7 - - + -
85S PHE* 3.3 44.0 - + + -
2010S SPO 3.1 34.5 + - + -
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Residues in contact with TYR 76 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72S ILE 3.0 13.4 + - - +
73S TRP* 3.0 46.6 + + + +
75S TRP* 1.3 77.6 - - - +
77S GLN* 1.3 64.8 + - + +
78S ALA 3.0 1.6 + - - -
79S GLY* 3.1 12.8 + - - -
80S TRP* 4.1 28.8 + + + -
110S LYS* 3.3 33.0 + - + -
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Residues in contact with GLN 77 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278R GLY* 3.3 22.7 + - - -
279R ILE* 3.8 23.6 - - + +
73S TRP* 2.8 57.7 + - + +
74S PHE* 3.6 1.9 - - - +
76S TYR* 1.3 74.8 - - + +
78S ALA* 1.3 58.1 + - - +
79S GLY 3.4 0.7 + - - -
91S PHE 5.3 0.2 + - - -
92S PHE* 3.4 24.9 - - + +
93S SER* 3.2 26.5 + - - +
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Residues in contact with ALA 78 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277R GLY* 5.3 1.1 - - - -
278R GLY 4.7 5.1 + - - -
74S PHE 3.0 15.4 + - - +
75S TRP* 3.0 10.7 + - - +
77S GLN* 1.3 78.7 - - - +
79S GLY* 1.3 61.9 + - - +
80S TRP* 4.3 1.3 - - - +
81S ASN* 3.1 21.2 + - - +
84S VAL* 3.7 16.0 - - + +
85S PHE* 3.9 23.6 - - + +
92S PHE* 3.6 16.2 - - + -
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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