Contacts of the helix formed by residues 60 - 83 (chain B) in PDB entry 3D5K
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 ASN 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ALA 2.9 23.0 + - - +
57B LEU 5.4 0.9 - - - +
58B GLU 4.0 0.9 - - - -
59B ASN* 1.3 71.5 - - - +
61B ARG* 1.3 58.6 + - - +
62B ASP* 2.9 37.3 + - - +
63B LEU* 3.2 12.0 + - + +
64B ARG* 3.2 24.4 + - - +
157B LEU* 3.4 29.4 - - + +
236B LEU 4.1 4.2 + - - -
237B LEU* 2.7 39.6 + - - +
238B LEU 3.5 4.5 + - - -
239B GLY* 4.3 4.3 - - - -
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Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ASN* 2.6 37.5 + - - +
60B ASN* 1.3 73.5 + - - +
62B ASP* 1.3 59.7 + - - +
64B ARG* 3.3 31.8 + - - +
65B VAL* 3.0 34.1 + - + +
236B LEU 6.0 0.2 + - - -
239B GLY 3.4 19.0 + - - -
13C PRO* 3.5 18.5 - - - +
356C ALA* 3.6 25.6 - - + +
359C GLU* 2.8 39.0 + - - -
360C LYS* 3.7 20.9 - - + +
363C GLN* 3.7 22.7 + - - +
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Residues in contact with ASP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ASN* 2.9 14.6 + - - +
61B ARG* 1.3 76.2 - - - +
63B LEU* 1.3 58.9 + - - +
65B VAL* 3.5 8.6 + - - +
66B ALA* 3.1 24.9 + - - +
153B ALA* 5.5 1.5 - - - +
237B LEU* 6.0 1.4 - - - +
360C LYS* 3.6 35.8 + - - +
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 3.9 37.7 - - + +
60B ASN* 3.2 10.0 + - - +
62B ASP* 1.3 76.9 - - - +
64B ARG* 1.3 60.0 + - - +
66B ALA* 3.3 5.3 + - + +
67B ALA* 2.9 28.0 + - + +
150B GLN* 3.9 22.9 - - + +
153B ALA* 4.2 9.4 - - + +
154B GLN* 3.9 39.5 - - + +
157B LEU* 3.7 31.9 - - + -
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Residues in contact with ARG 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 2.7 32.9 + - - +
59B ASN* 3.9 14.7 + - - +
60B ASN 3.2 12.8 + - - +
61B ARG* 3.5 46.9 - - - +
62B ASP 3.2 0.2 - - - -
63B LEU* 1.3 76.7 - - - +
65B VAL* 1.3 61.7 + - - +
67B ALA* 3.2 10.8 + - + +
68B LEU* 3.1 36.1 + - + +
356C ALA* 4.6 9.9 - - + -
359C GLU* 4.3 4.9 + - - -
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Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ARG 3.0 22.7 + - - +
62B ASP* 3.7 7.4 - - - +
63B LEU 3.4 0.2 - - - -
64B ARG* 1.3 75.0 - - - +
66B ALA* 1.3 57.3 + - - +
68B LEU* 3.2 10.0 + - - +
69B ASN* 3.0 40.2 + - - +
353C ILE* 4.0 30.7 - - + +
356C ALA* 3.8 20.9 - - + -
357C GLN* 4.1 19.1 - - + +
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP 3.1 14.7 + - - +
63B LEU* 3.4 10.3 - - + +
64B ARG 3.2 0.2 - - - -
65B VAL* 1.3 77.0 - - - +
67B ALA* 1.3 60.0 + - - +
68B LEU 3.3 0.5 + - - -
69B ASN* 3.5 10.4 + - - -
70B VAL* 3.4 10.2 - - - +
149B ALA 5.1 0.4 - - - +
150B GLN* 4.2 9.4 - - + -
153B ALA* 4.0 25.4 - - + -
478B NA 3.0 27.7 - - - -
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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
----------------------------------------------------------
63B LEU* 2.9 13.8 + - + +
64B ARG* 3.2 13.7 + - + +
66B ALA* 1.3 75.8 - - - +
68B LEU* 1.3 62.4 + - + +
70B VAL* 3.7 14.8 - - - +
71B GLU* 3.8 15.9 - - - +
150B GLN* 3.8 26.9 - - - +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ARG* 3.1 30.7 + - + +
65B VAL* 3.2 4.2 + - - +
66B ALA 3.2 0.4 - - - -
67B ALA* 1.3 76.5 - - + +
69B ASN* 1.3 60.5 + - - +
70B VAL 3.2 1.8 - - - -
71B GLU* 3.0 22.9 + - - +
72B ALA 2.9 23.6 + - - -
349C ILE* 3.4 22.5 - - + +
352C ASP* 3.7 49.1 - - + +
353C ILE* 3.6 22.4 - - + +
356C ALA* 5.0 1.3 - - + -
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Residues in contact with ASN 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 VAL* 3.0 31.6 + - - +
66B ALA* 3.8 10.2 - - - +
68B LEU* 1.3 75.9 - - - +
70B VAL* 1.3 57.1 + - - +
72B ALA* 3.1 6.5 + - - +
73B PHE* 2.9 44.7 + - + -
146B THR* 3.5 13.9 - - + -
478B NA 4.0 2.5 - - - -
350C GLN* 5.5 0.8 - - - +
353C ILE* 3.6 21.6 - - - +
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ALA 3.4 11.7 - - - +
67B ALA 3.7 7.2 - - - +
68B LEU 3.2 0.4 - - - -
69B ASN* 1.3 75.2 - - - +
71B GLU* 1.3 60.5 + - + +
73B PHE* 3.4 0.9 + - - -
74B ARG* 2.9 27.1 + - - +
143B TYR* 3.7 26.5 - - + +
146B THR* 3.4 33.6 - - - +
147B GLU* 3.9 18.4 - - + +
150B GLN* 3.3 25.6 - - + +
478B NA 4.0 0.2 - - - -
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA* 3.8 16.4 - - - +
68B LEU* 3.0 27.2 + - - +
70B VAL* 1.3 78.4 - - + +
72B ALA* 1.3 58.7 + - - +
74B ARG* 3.7 14.9 - - - +
75B ALA* 3.0 22.9 + - - +
78B ARG* 5.3 0.9 + - - -
349C ILE* 3.4 30.0 - - + +
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Residues in contact with ALA 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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68B LEU 2.9 11.5 + - - +
69B ASN* 3.1 14.6 + - - +
71B GLU* 1.3 77.9 - - - +
73B PHE* 1.3 61.3 + - + +
75B ALA 3.6 0.3 + - - -
76B GLN* 3.1 22.5 + - - +
346C TYR* 3.4 25.0 - - + -
349C ILE* 3.8 10.5 - - + +
350C GLN* 3.5 28.7 - - - +
353C ILE* 4.8 0.9 - - + -
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Residues in contact with PHE 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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69B ASN* 2.9 36.7 + - + +
70B VAL 3.9 2.7 - - - +
72B ALA* 1.3 78.8 - - + +
74B ARG* 1.3 61.0 + - - +
76B GLN* 3.7 9.0 - - + +
77B TYR* 3.0 27.4 + - - +
139B ALA 4.4 2.5 - - - +
142B GLN* 4.0 35.0 - - + -
143B TYR* 3.8 16.8 - - - +
146B THR* 3.3 31.9 - - + +
281B GLN* 5.8 3.1 - - - -
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Residues in contact with ARG 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 VAL* 2.9 17.9 + - - +
71B GLU* 3.7 15.0 - - - +
73B PHE* 1.3 77.4 - - - +
75B ALA* 1.3 58.0 + - - +
77B TYR* 3.4 10.9 + - + +
78B ARG* 3.0 56.3 + - + +
143B TYR* 3.8 31.3 - - + -
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Residues in contact with ALA 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 GLU 3.0 17.3 + - - +
72B ALA 3.8 5.8 - - - +
73B PHE 3.3 0.2 - - - -
74B ARG* 1.3 73.4 - - - +
76B GLN* 1.3 59.7 + - - +
78B ARG* 3.2 27.1 + - - +
79B ILE* 3.1 32.9 + - - +
342C ALA* 3.6 21.4 - - - +
346C TYR* 4.1 16.4 - - + +
349C ILE* 4.5 2.5 - - + -
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Residues in contact with GLN 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 ALA 3.1 16.8 + - - +
73B PHE* 3.7 12.8 - - + +
74B ARG 3.3 0.2 - - - -
75B ALA* 1.3 73.9 - - - +
77B TYR* 1.3 64.6 + - - +
79B ILE* 3.3 36.4 + - - +
80B GLN* 3.3 31.0 + - + +
139B ALA* 4.8 3.8 - - + -
346C TYR* 4.0 25.1 - - + -
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Residues in contact with TYR 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 PHE 3.0 14.5 + - - +
74B ARG* 3.4 18.6 - - + +
76B GLN* 1.3 76.1 - - - +
78B ARG* 1.3 62.9 + - + +
80B GLN* 3.2 3.5 + - - +
81B ARG* 2.9 61.9 + - + +
136B ARG* 3.7 30.3 + - + -
139B ALA* 3.9 20.7 - - + +
140B LEU* 3.7 54.0 - - + +
143B TYR* 4.7 5.2 - + + -
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Residues in contact with ARG 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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71B GLU 5.3 1.0 + - - -
74B ARG* 3.0 41.0 + - + +
75B ALA* 3.2 28.8 + - - +
77B TYR* 1.3 78.9 - - + +
79B ILE* 1.3 62.4 + - - +
81B ARG* 3.6 39.1 + - - +
82B ALA* 3.3 21.3 + - - +
337C ALA 4.8 1.4 - - - +
338C GLY 4.6 7.8 + - - +
341C ARG* 4.5 18.3 - - - +
342C ALA* 3.9 18.2 - - + +
345C ASP* 2.9 42.2 + - - +
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Residues in contact with ILE 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 ALA 3.1 16.4 + - - +
76B GLN* 3.6 37.5 - - - +
77B TYR 3.2 0.4 - - - -
78B ARG* 1.3 76.6 - - - +
80B GLN* 1.3 65.2 + - + +
82B ALA* 3.2 13.0 + - - +
83B ASP* 3.4 22.6 + - - +
339C SER* 4.0 17.5 + - - +
342C ALA* 3.7 15.9 - - + +
343C SER* 3.5 33.2 - - - +
346C TYR* 5.1 4.7 - - + -
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Residues in contact with GLN 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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76B GLN* 3.3 21.0 + - + +
77B TYR 3.2 7.7 + - - +
79B ILE* 1.3 75.1 - - + +
81B ARG* 1.3 64.3 + - - +
82B ALA 3.5 0.2 + - - -
83B ASP* 3.6 21.2 + - - +
84B LEU* 4.3 6.4 + - - +
132B LEU* 4.8 6.4 - - - +
135B LEU* 3.4 42.1 + - + +
136B ARG* 4.2 23.3 - - - +
138B GLN* 5.1 3.0 + - - -
139B ALA* 4.2 11.9 - - + +
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Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 2.9 48.2 + - + +
78B ARG* 3.6 39.5 + - - +
79B ILE 3.2 0.2 - - - -
80B GLN* 1.3 77.6 - - - +
82B ALA* 1.3 59.8 + - - +
83B ASP 3.6 0.3 + - - -
84B LEU* 3.7 12.0 + - - +
85B PHE* 3.7 20.5 - - + -
136B ARG* 3.8 26.6 - - + +
337C ALA 5.4 7.7 + - - -
338C GLY* 6.3 0.4 - - - -
341C ARG* 6.0 1.8 - - - +
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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
----------------------------------------------------------
78B ARG 3.3 13.7 + - - +
79B ILE 3.2 7.4 + - - +
81B ARG* 1.3 75.5 - - - +
83B ASP* 1.3 56.9 + - - +
84B LEU 3.1 5.6 - - - -
85B PHE* 3.0 30.6 + - - +
337C ALA* 3.3 38.4 + - + +
339C SER* 3.7 24.5 - - - +
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Residues in contact with ASP 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ILE* 3.4 24.2 + - - +
80B GLN* 3.6 17.1 + - - +
81B ARG 3.4 0.8 - - - -
82B ALA* 1.3 77.0 - - - +
84B LEU* 1.3 56.5 + - - +
85B PHE 3.2 9.3 + - - +
87B ARG* 5.5 6.9 + - - -
124B TRP* 5.0 5.0 - - - -
125B GLU 5.8 0.3 + - - -
132B LEU* 3.5 29.0 - - + +
339C SER* 4.7 6.1 + - - -
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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