Contacts of the helix formed by residues 73 - 94 (chain A) in PDB entry 2YF3
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 LEU 73 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 3.9 23.6 - - + -
68A LEU* 4.8 4.0 - - + -
69A SER 3.8 7.6 - - - +
70A ALA* 3.1 21.9 + - - +
72A ASP* 1.3 80.4 - - - +
74A ALA* 1.3 52.9 + - - +
75A PRO* 3.4 1.1 - - - -
76A LEU* 3.1 9.6 + - + +
77A ALA* 2.8 34.1 + - - +
29B PRO* 4.8 1.3 - - + -
30B THR 3.9 33.9 - - - +
31B PRO* 3.9 3.8 - - + -
32B PRO* 3.8 22.0 - - + -
94B LEU* 4.4 11.8 - - + +
96B ILE* 4.0 26.0 - - + -
138B ILE* 5.1 0.9 - - + -
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA 4.3 1.6 + - - -
71A GLY* 3.4 8.1 + - - +
73A LEU* 1.3 75.8 - - - +
75A PRO* 1.4 64.5 - - + +
77A ALA* 3.3 3.5 + - - +
78A HIS* 2.8 31.3 + - - +
134B VAL* 3.7 4.6 - - + +
135B ARG* 3.4 49.4 - - + +
138B ILE* 4.1 15.7 - - + +
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Residues in contact with PRO 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLU* 3.4 29.2 - - - +
71A GLY 4.4 2.0 - - - +
72A ASP* 3.4 17.5 - - - +
73A LEU 3.5 0.7 - - - -
74A ALA* 1.4 93.0 - - + +
76A LEU* 1.3 61.1 + - - +
78A HIS* 3.3 9.2 + - + +
79A GLU* 3.0 29.9 + - - +
135B ARG* 3.8 28.2 - - - +
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 3.9 21.3 - - + +
54A GLU* 3.8 17.7 - - + +
55A ILE* 3.6 26.9 - - + -
58A LEU* 3.8 28.7 - - + -
72A ASP 5.1 0.6 + - - +
73A LEU* 3.1 9.7 + - + +
75A PRO* 1.3 76.1 - - - +
77A ALA* 1.3 67.6 + - - +
79A GLU* 3.2 1.8 + - - -
80A LEU* 2.9 41.0 + - + +
37B LEU* 3.9 20.0 - - + -
94B LEU* 4.0 20.0 - - + -
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU 2.8 20.5 + - - +
74A ALA 3.6 4.0 - - - +
76A LEU* 1.3 73.6 - - - +
78A HIS* 1.3 62.0 + - - +
80A LEU* 3.3 3.7 + - - +
81A ALA* 3.0 23.7 + - - +
91B LEU* 4.0 24.8 - - + +
94B LEU* 5.4 1.0 - - - +
96B ILE* 4.1 18.4 - - + -
101B VAL* 3.8 5.7 - - + +
134B VAL* 4.0 13.5 - - + -
138B ILE* 4.2 8.3 - - + -
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Residues in contact with HIS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA 2.8 20.9 + - - +
75A PRO* 3.4 9.1 - - + +
77A ALA* 1.3 72.9 - - - +
79A GLU* 1.3 67.3 + - - +
81A ALA* 3.3 6.5 + - - +
82A ASP* 2.8 47.4 + - - -
105B VAL* 4.1 11.8 - - + +
132B ALA* 4.5 24.5 + - + +
134B VAL* 3.9 22.5 - - + +
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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
----------------------------------------------------------
47A GLU* 3.4 6.6 - - - +
50A GLU* 3.0 37.0 - - + +
51A VAL* 3.4 31.2 - - + +
54A GLU* 3.8 21.4 - - + +
75A PRO* 3.0 18.0 + - - +
76A LEU 3.2 3.3 + - - +
78A HIS* 1.3 85.1 + - - +
80A LEU* 1.3 61.2 + - - +
82A ASP* 3.1 18.6 + - - +
83A LEU* 2.8 23.6 + - - +
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Residues in contact with LEU 80 (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 VAL* 3.7 26.5 - - + -
55A ILE* 5.9 0.2 - - + -
76A LEU* 2.9 42.7 + - + +
77A ALA 3.7 4.0 - - - +
79A GLU* 1.3 74.4 - - - +
81A ALA* 1.3 58.1 + - - +
83A LEU* 3.2 2.0 + - - -
84A LEU* 3.0 24.6 + - - +
44B LEU* 4.2 15.3 - - + -
87B THR* 3.3 26.7 - - + +
90B ALA* 3.9 25.6 - - + -
91B LEU* 3.9 27.8 - - + -
94B LEU* 4.1 11.7 - - + -
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Residues in contact with ALA 81 (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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77A ALA 3.0 5.5 + - - -
78A HIS 3.5 8.3 - - - +
80A LEU* 1.3 74.3 - - - +
82A ASP* 1.3 59.5 + - - +
84A LEU* 3.2 14.7 + - + +
85A TYR* 2.8 28.4 + - - +
91B LEU* 4.5 3.6 - - + +
98B ALA 5.6 0.2 - - - +
101B VAL* 3.6 30.7 - - + -
102B PHE* 4.2 16.0 - - + +
105B VAL* 3.9 16.7 - - + +
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Residues in contact with ASP 82 (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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47A GLU* 3.2 29.7 - - - +
50A GLU* 4.2 2.6 - - - +
78A HIS* 2.8 34.5 + - - +
79A GLU* 3.1 26.0 + - - +
81A ALA* 1.3 72.9 - - - +
83A LEU* 1.3 61.9 + - - +
85A TYR* 3.1 8.8 + - - +
86A VAL* 3.1 26.7 + - - +
105B VAL* 3.6 19.1 - - - +
109B ASN* 5.3 1.9 + - - +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 4.1 17.7 - - + +
47A GLU* 4.0 19.0 - - + +
48A SER* 3.6 25.8 - - - +
51A VAL* 4.3 16.6 - - + -
79A GLU 2.8 14.6 + - - +
80A LEU* 3.4 9.2 - - + +
81A ALA 3.1 0.2 - - - -
82A ASP* 1.3 74.5 - - - +
84A LEU* 1.3 61.3 + - - +
86A VAL* 3.3 3.8 + - + +
87A THR* 2.7 42.9 + - - +
44B LEU* 3.7 20.2 - - + -
83B LEU* 4.2 9.4 - - + -
87B THR* 3.6 24.0 - - + +
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Residues in contact with LEU 84 (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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80A LEU 3.0 17.0 + - - +
81A ALA* 3.5 9.2 - - + +
83A LEU* 1.3 75.3 - - - +
85A TYR* 1.3 64.6 + - - +
87A THR* 4.3 3.8 - - - -
88A TYR* 2.8 34.5 + - + -
84B LEU* 3.9 19.3 - - + -
87B THR* 3.4 26.9 - - + -
88B TYR* 3.9 39.3 - - + +
91B LEU* 4.1 21.8 - - + -
98B ALA* 4.6 5.2 - - + +
102B PHE* 3.8 24.2 - - + -
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Residues in contact with TYR 85 (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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14A LEU* 3.6 30.7 - - + +
17A PHE* 3.3 39.9 - + - +
81A ALA 2.8 12.6 + - - +
82A ASP* 3.1 14.1 + - - +
84A LEU* 1.3 77.5 - - - +
86A VAL* 1.3 63.5 + - + +
89A GLY* 2.9 24.3 + - - -
102B PHE* 3.4 33.2 - + - -
105B VAL* 4.1 9.9 - - + -
106B HIS* 2.8 41.4 + - - -
109B ASN* 3.3 33.6 - - + +
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Residues in contact with VAL 86 (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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40A ARG* 3.0 30.7 + - - +
43A LEU* 4.0 32.3 - - + +
44A LEU* 4.2 19.0 - - + +
47A GLU* 3.8 29.6 - - + +
82A ASP 3.1 13.1 + - - +
83A LEU* 3.4 12.6 - - + +
85A TYR* 1.3 81.7 - - + +
87A THR* 1.3 61.6 + - - +
89A GLY 3.6 0.9 - - - -
90A ALA* 3.1 13.9 + - - +
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Residues in contact with THR 87 (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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44A LEU* 3.5 9.2 - - - +
83A LEU* 2.7 25.4 + - - +
84A LEU* 4.3 0.7 - - - -
86A VAL* 1.3 74.2 - - - +
88A TYR* 1.3 66.3 + - - +
89A GLY 3.1 0.4 - - - -
90A ALA* 3.1 13.2 + - - +
91A LEU* 3.2 14.6 + - - +
80B LEU* 3.3 44.3 - - + +
83B LEU* 3.5 25.1 - - + +
84B LEU* 3.6 23.1 - - + +
87B THR* 5.3 0.7 + - - -
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Residues in contact with TYR 88 (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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10A ASN* 3.5 17.5 + - + +
11A ALA* 3.7 28.0 - - + -
14A LEU* 3.7 20.1 - - + +
84A LEU* 2.8 29.0 + - + +
87A THR* 1.3 74.0 - - - +
89A GLY* 1.3 63.7 + - - +
91A LEU* 3.1 7.6 + - - +
92A ASP* 2.9 25.6 + - - +
98A ALA* 3.7 24.5 - - + +
99A ASP* 4.4 0.3 + - - -
10B ASN* 2.8 25.7 + - - -
84B LEU* 3.9 20.6 - - + +
88B TYR* 2.4 40.5 + + - -
102B PHE* 4.0 16.2 - + - -
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Residues in contact with GLY 89 (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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14A LEU* 3.6 18.1 - - - +
18A HIS* 3.4 6.6 - - - -
40A ARG* 3.4 20.9 - - - -
85A TYR 2.9 18.0 + - - -
87A THR 3.1 1.0 - - - -
88A TYR* 1.3 75.0 - - - +
90A ALA* 1.3 59.2 + - - +
93A GLN* 3.1 28.8 + - - +
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Residues in contact with ALA 90 (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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40A ARG* 3.4 33.3 - - + +
44A LEU* 5.1 3.4 - - + -
86A VAL 3.1 13.7 + - - +
87A THR 3.1 9.9 + - - +
89A GLY* 1.3 75.0 - - - +
91A LEU* 1.3 62.9 + - - +
93A GLN* 3.3 3.6 + - - +
94A LEU* 3.1 28.9 + - + +
55B ILE* 6.4 0.7 - - + -
76B LEU* 6.5 0.2 - - + -
80B LEU* 3.9 24.5 - - + -
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Residues in contact with LEU 91 (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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87A THR 3.2 9.3 + - - +
88A TYR 3.1 6.5 + - - +
90A ALA* 1.3 77.3 - - - +
92A ASP* 1.3 64.1 + - - +
94A LEU* 3.1 12.0 + - + +
96A ILE* 3.0 55.5 + - + +
98A ALA* 3.6 29.6 - - + +
101A VAL* 5.2 2.2 - - + -
77B ALA* 4.0 23.6 - - + +
80B LEU* 3.8 35.4 - - + -
81B ALA* 4.6 3.6 - - + +
84B LEU* 3.9 20.4 - - + -
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Residues in contact with ASP 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA 4.6 4.3 - - - +
14A LEU* 4.2 7.9 - - + -
15A HIS* 3.0 41.6 + - - +
18A HIS* 2.7 28.4 + - + +
25A THR* 2.7 28.0 + - - -
26A PRO 4.4 1.2 - - - +
88A TYR 2.9 15.5 + - - +
89A GLY 3.9 4.0 - - - +
91A LEU* 1.3 77.9 - - - +
93A GLN* 1.3 56.8 + - - +
95A GLY* 3.0 19.8 + - - -
96A ILE 4.2 5.1 + - - +
98A ALA* 5.7 0.4 - - - +
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Residues in contact with GLN 93 (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 HIS* 3.3 34.0 + - + +
21A ILE* 5.1 3.4 - - - +
23A ALA* 4.7 10.3 - - - +
25A THR* 3.9 15.4 - - + +
26A PRO* 4.0 12.0 - - - +
30A THR* 4.8 2.4 - - - +
32A PRO* 5.5 0.5 - - - +
36A LEU* 4.0 39.3 - - + +
39A LEU* 4.2 9.7 - - - +
40A ARG* 2.9 34.2 + - - +
89A GLY 3.1 17.0 + - - +
90A ALA 3.9 4.3 - - - +
91A LEU 3.3 0.2 - - - -
92A ASP* 1.3 74.7 - - - +
94A LEU* 1.3 59.0 + - - +
95A GLY 3.3 1.2 + - - -
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PRO* 3.4 2.9 - - - +
30A THR* 2.8 32.1 + - - +
32A PRO* 3.7 40.2 - - + -
36A LEU* 4.6 5.8 - - + -
37A LEU* 4.5 9.2 - - + -
40A ARG* 6.4 0.4 - - + -
90A ALA* 3.1 18.5 + - + +
91A LEU* 3.1 11.1 + - + +
93A GLN* 1.3 78.0 - - - +
95A GLY* 1.3 58.3 + - - +
96A ILE* 3.4 25.6 + - + +
73B LEU* 4.4 11.3 - - + +
76B LEU* 3.8 24.9 - - + -
77B ALA 5.4 0.7 - - - +
80B LEU* 4.2 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