Contacts of the helix formed by residues 60 - 82 (chain B) in PDB entry 3LOC
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 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU* 4.6 3.4 - - - -
55B LEU* 4.6 4.3 - - - -
58B PHE 3.2 5.7 + - - +
59B PRO* 1.3 80.9 - - - +
61B LYS* 1.3 63.8 + - - +
62B GLU* 3.5 4.8 + - - +
63B ALA* 2.9 30.0 + - - +
64B LEU* 3.0 14.1 + - - +
194D ASN* 3.9 4.6 + - - -
198D GLU* 2.8 35.7 + - - -
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PHE* 3.9 18.2 - - + -
35B PHE* 2.8 51.4 + - + +
36B HIS* 3.9 13.3 + - - +
38B THR* 3.4 25.3 + - + +
40B LEU* 3.9 37.9 - - + +
60B SER* 1.3 71.3 - - - +
62B GLU* 1.3 57.7 + - - +
64B LEU* 3.1 3.4 + - - +
65B TYR* 2.8 31.9 + - - +
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PHE* 3.8 20.1 - - + -
60B SER* 3.6 8.7 - - - +
61B LYS* 1.3 78.1 - - - +
63B ALA* 1.3 61.4 + - - +
65B TYR* 3.9 1.2 - - - +
66B ILE* 3.0 49.2 + - + +
124B LEU* 3.5 27.1 - - + +
94D LYS* 5.7 2.4 + - - -
198D GLU* 3.5 25.8 - - - +
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B PHE* 4.6 5.6 - - + -
59B PRO* 3.9 26.2 - - + -
60B SER* 2.9 24.0 + - - +
62B GLU* 1.3 74.9 - - - +
64B LEU* 1.3 53.9 + - - +
66B ILE* 3.3 8.6 + - - +
67B ALA* 2.8 34.9 + - - +
194D ASN* 4.9 3.6 - - - +
198D GLU* 4.5 0.9 + - - +
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ILE* 4.1 3.8 - - + -
23B LEU* 3.9 13.0 - - + -
26B ALA* 3.7 16.4 - - + -
30B PHE* 4.1 2.9 - - + -
40B LEU* 4.1 15.0 - - + -
43B ILE* 3.4 38.8 - - + -
54B LEU* 4.4 11.0 - - + -
58B PHE* 3.4 46.4 - - + +
60B SER 3.0 6.6 + - - +
61B LYS* 3.5 8.7 - - - +
63B ALA* 1.3 76.0 - - - +
65B TYR* 1.3 61.4 + - - +
67B ALA* 2.9 5.0 + - - +
68B VAL* 2.8 31.4 + - - +
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Residues in contact with TYR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PHE* 3.5 40.4 - + + -
35B PHE* 3.8 27.6 + + + +
61B LYS 2.8 16.9 + - - +
62B GLU 3.9 2.7 - - - +
64B LEU* 1.3 76.9 - - - +
66B ILE* 1.3 65.7 - - + +
68B VAL* 3.2 6.3 + - - +
69B LEU* 3.1 40.6 + - + +
113B LEU* 4.2 29.9 + - + +
116B MSE 5.5 0.9 - - - +
117B GLU* 2.6 47.0 + - - +
124B LEU* 3.7 28.3 - - + -
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLU* 3.0 48.6 + - + +
63B ALA* 3.7 7.0 - - - +
65B TYR* 1.3 80.6 - - + +
67B ALA* 1.3 57.5 + - - +
69B LEU* 3.4 6.7 + - - +
70B ARG* 3.0 59.8 + - - +
124B LEU* 4.4 28.0 - - + +
125B LEU* 4.4 15.4 - - + +
128B GLU* 5.1 2.0 - - + -
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 3.8 11.3 - - + +
58B PHE* 3.7 28.9 - - + -
63B ALA 2.8 15.2 + - - +
64B LEU 2.9 11.2 + - - +
66B ILE* 1.3 75.1 - - - +
68B VAL* 1.3 62.4 + - - +
70B ARG* 3.5 8.4 + - - +
71B GLN* 3.2 22.5 + - - +
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 3.8 26.2 - - + +
26B ALA* 3.8 23.8 - - + -
27B LEU* 4.3 13.0 - - + +
30B PHE* 4.2 7.4 - - + -
64B LEU 2.8 16.7 + - - +
65B TYR* 3.6 8.1 - - - +
67B ALA* 1.3 77.8 - - - +
69B LEU* 1.3 66.1 + - + +
71B GLN* 3.3 11.4 + - - +
72B ILE* 3.2 23.9 + - + +
113B LEU* 3.5 31.4 - - + -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B TYR* 3.1 42.8 + - + +
66B ILE* 3.8 1.3 - - - +
67B ALA 3.3 0.2 - - - -
68B VAL* 1.3 82.6 - - + +
70B ARG* 1.3 63.5 + - - +
72B ILE* 3.3 10.7 + - + +
73B LEU* 3.2 25.4 + - - +
113B LEU* 4.2 20.2 - - + +
114B PHE* 3.9 38.5 - - + +
117B GLU* 3.7 17.9 - - + -
125B LEU* 3.6 35.4 - - + +
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ILE* 3.0 37.6 + - - +
67B ALA* 3.7 7.5 - - - +
68B VAL 3.2 0.2 - - - -
69B LEU* 1.3 75.3 - - - +
71B GLN* 1.3 60.4 + - - +
73B LEU* 3.1 14.0 + - + +
74B ASP* 2.9 42.7 + - - +
125B LEU* 5.0 1.8 - - - +
128B GLU* 2.4 59.7 + - - +
132B ASP* 4.6 2.2 + - - -
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Residues in contact with GLN 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LYS* 4.8 17.2 + - - +
23B LEU* 3.6 40.9 - - + +
24B SER* 5.3 1.6 + - - +
27B LEU* 5.1 10.7 - - - +
67B ALA 3.2 11.5 + - - +
68B VAL* 3.4 13.3 - - - +
70B ARG* 1.3 80.5 - - - +
72B ILE* 1.3 62.9 + - - +
74B ASP* 3.3 10.4 + - + +
75B ILE* 3.1 38.9 + - + +
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 4.4 15.9 - - + -
68B VAL* 3.2 15.6 + - + +
69B LEU* 3.6 23.3 - - + +
70B ARG 3.2 0.4 - - - -
71B GLN* 1.3 75.9 - - + +
73B LEU* 1.3 61.6 + - - +
75B ILE* 3.2 11.6 + - + +
76B TRP* 2.8 66.5 + - + +
103B VAL* 6.1 0.4 - - + -
110B ALA* 3.1 49.6 - - + +
113B LEU* 4.7 0.9 - - + -
114B PHE* 4.6 4.9 - - + +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A GLN* 4.8 1.8 - - - +
69B LEU 3.2 14.0 + - - +
70B ARG* 3.1 16.4 + - + +
72B ILE* 1.3 80.2 - - - +
74B ASP* 1.3 54.6 + - - +
76B TRP* 3.2 5.2 + - + -
77B LEU* 2.7 55.7 + - + +
114B PHE* 3.8 19.7 - - + -
125B LEU* 4.6 16.2 - - + -
128B GLU* 3.8 22.9 - - - +
129B LEU* 4.9 6.3 - - + -
133B LEU* 4.9 8.5 - - + -
212B URA 3.5 32.8 - - + -
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Residues in contact with ASP 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ARG* 2.9 30.2 + - - +
71B GLN* 3.6 10.8 - - + +
72B ILE 3.2 0.2 - - - -
73B LEU* 1.3 77.5 - - - +
75B ILE* 1.3 64.6 + - + +
77B LEU* 4.0 4.9 - - - +
78B ALA* 3.1 26.3 + - - +
81B LYS* 6.5 0.9 - - - -
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Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLN* 3.1 32.1 + - + +
72B ILE* 3.6 10.5 - - + +
74B ASP* 1.3 81.6 - - + +
76B TRP* 1.3 64.0 + - + +
78B ALA* 3.7 12.5 + - - +
79B PRO* 4.0 3.6 - - - +
103B VAL* 4.0 34.3 - - + +
107B TYR* 6.3 4.3 - - + -
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Residues in contact with TRP 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ILE* 2.8 36.2 + - + +
73B LEU* 3.6 8.5 - - + +
75B ILE* 1.3 75.1 - - + +
77B LEU* 1.3 58.9 + - - +
79B PRO* 3.3 18.2 - - - +
96B TYR* 4.1 13.3 - - - -
100B LYS* 3.2 30.9 + - + +
103B VAL* 3.4 34.0 - - + +
104B SER* 5.7 1.2 + - - +
110B ALA* 5.9 0.2 - - - +
111B SER* 3.8 26.9 - - - +
114B PHE* 3.6 40.8 - + + -
170B GLN* 3.4 27.7 - - + +
212B URA 3.3 51.8 - + + +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU* 2.7 39.7 + - + +
74B ASP* 4.5 4.5 - - - +
76B TRP* 1.3 72.3 - - - +
78B ALA* 1.3 65.4 + - - +
79B PRO* 3.4 0.9 - - - -
80B LEU* 3.0 28.6 + - + -
81B LYS* 2.8 40.2 + - + +
96B TYR* 5.0 1.6 - - - +
133B LEU* 3.9 29.4 - - + -
136B LEU* 4.5 12.1 - - + -
166B TRP* 4.4 2.9 - - + -
212B URA 3.8 25.4 - - + +
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ASP 3.1 18.1 + - - +
75B ILE* 3.8 6.5 - - - +
76B TRP 3.3 0.2 - - - -
77B LEU* 1.3 77.2 - - - +
79B PRO* 1.3 72.8 - - + +
81B LYS* 3.2 9.6 + - - +
82B ALA* 3.0 21.7 + - - +
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Residues in contact with PRO 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ILE 4.0 4.5 - - - +
76B TRP 3.3 16.6 - - - +
77B LEU 3.5 0.7 - - - -
78B ALA* 1.3 95.2 - - + +
80B LEU* 1.3 60.3 + - - +
82B ALA* 3.2 17.2 + - + +
83B PHE* 3.2 21.2 - - + -
96B TYR* 3.8 25.1 - - + -
99B LEU* 3.9 39.7 - - + -
100B LYS* 5.8 0.7 - - + -
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B LEU* 3.0 18.0 + - + +
79B PRO* 1.3 76.4 - - - +
81B LYS* 1.3 66.9 + - - +
82B ALA 3.0 1.1 - - - -
83B PHE* 3.1 51.0 + - + +
96B TYR* 3.7 35.0 - - + +
136B LEU* 4.0 8.3 - - + -
137B ILE* 3.8 29.4 - - + -
140B LYS* 3.5 29.3 - - + -
144B ILE* 5.5 1.6 - - + -
162B ILE* 4.7 16.6 - - + -
166B TRP* 4.8 0.2 - - + -
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ASP* 6.5 1.1 - - - -
77B LEU* 2.8 33.0 + - + +
78B ALA* 3.5 11.4 - - - +
80B LEU* 1.3 73.1 - - - +
82B ALA* 1.3 50.2 + - - +
84B ARG* 2.6 32.1 + - - -
136B LEU* 3.9 28.0 - - + -
140B LYS* 3.2 12.3 + - - +
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ALA 3.0 12.3 + - - +
79B PRO* 3.3 16.2 - - + +
80B LEU 3.0 1.0 - - - -
81B LYS* 1.3 74.5 - - - +
83B PHE* 1.3 65.6 + - - +
84B ARG* 3.8 12.1 + - - +
87B PHE* 3.0 23.2 - - + -
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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
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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