Contacts of the helix formed by residues 67 - 89 (chain A) in PDB entry 5FSJ
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 ASP 67 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A TRP* 3.6 24.7 + - + -
57A ASP* 4.4 6.5 - - - +
61A GLN 4.1 3.5 - - - +
62A PHE* 3.2 41.4 - - + +
63A PHE 3.4 0.5 + - - -
64A ALA* 2.9 38.7 + - - +
66A TYR* 1.3 80.9 - - - +
68A ALA* 1.3 64.1 + - - +
69A PRO* 3.4 0.7 - - - -
70A ALA* 3.0 15.5 + - - +
71A VAL* 3.0 13.9 + - + +
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Residues in contact with ALA 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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11A ARG 3.4 22.0 - - - +
12A GLY 3.6 17.0 - - - +
13A VAL* 3.7 17.1 + - + +
64A ALA 3.4 4.7 + - - +
65A SER* 3.2 12.2 + - - +
67A ASP* 1.3 77.5 - - - +
69A PRO* 1.3 70.0 - - + +
70A ALA 3.3 0.2 + - - -
71A VAL* 3.3 3.1 + - - +
72A ASP* 3.2 18.4 + - - +
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Residues in contact with PRO 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.8 5.8 - - + -
65A SER 3.7 6.7 - - - +
66A TYR 3.6 11.7 - - - +
67A ASP 3.6 3.4 - - - -
68A ALA* 1.3 93.6 - - + +
70A ALA* 1.3 55.2 + - - +
73A ALA* 3.0 20.3 + - - +
104A VAL* 3.6 19.3 - - + +
105A HIS* 3.9 15.0 - - + -
122A TYR* 6.3 0.7 - - + -
123A GLY 6.0 0.2 - - - +
124A ASP* 4.1 4.7 - - - +
132A PRO* 3.6 33.2 - - + -
134A SER* 2.8 29.3 + - - +
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.6 17.5 - - + -
41A THR* 3.9 6.0 - - + +
55A TRP* 3.6 39.9 - - + -
62A PHE* 6.1 0.4 - - + -
67A ASP* 3.0 10.3 + - + +
69A PRO* 1.3 77.3 - - - +
71A VAL* 1.3 65.6 + - - +
73A ALA 3.4 0.5 + - - -
74A HIS* 3.0 27.0 + - - +
104A VAL* 3.9 13.9 - - + +
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLY* 4.5 2.2 - - - -
11A ARG 3.8 22.0 - - - +
12A GLY 4.1 0.9 - - - +
18A LYS* 3.8 31.4 - - + -
20A ILE* 4.0 20.1 - - + +
30A LEU* 5.2 0.4 - - - -
62A PHE* 3.6 40.8 - - + +
67A ASP* 3.0 18.1 + - + +
68A ALA 3.6 7.4 - - - +
70A ALA* 1.3 77.4 - - - +
72A ASP* 1.3 58.0 + - - +
74A HIS* 3.7 4.4 - - - +
75A TYR* 2.9 31.2 + - - +
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Residues in contact with ASP 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLY* 3.4 13.6 - - - -
13A VAL* 2.8 32.1 + - + +
14A LEU* 4.3 1.2 + - - +
16A ASP* 4.2 2.6 - - - +
18A LYS* 2.7 31.1 + - - +
68A ALA 3.2 7.5 + - - +
69A PRO 4.1 1.1 - - - +
71A VAL* 1.3 77.5 - - - +
73A ALA* 1.3 67.5 + - - +
75A TYR* 4.4 2.2 - - - +
76A TYR* 2.8 43.4 + - + +
134A SER* 3.3 20.0 - - - +
135A GLY* 3.5 7.2 - - - +
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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
----------------------------------------------------------
41A THR* 4.3 4.0 - - + -
69A PRO 3.0 18.8 + - - +
70A ALA 3.9 2.9 - - - +
72A ASP* 1.3 75.0 - - - +
74A HIS* 1.3 61.6 + - - +
77A ALA* 3.1 26.5 + - - +
102A SER* 4.3 12.7 + - - -
104A VAL* 3.6 20.6 - - + -
122A TYR* 4.0 13.8 + - + -
134A SER* 3.7 13.8 - - - -
140A VAL* 4.6 8.0 - - - +
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Residues in contact with HIS 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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20A ILE* 4.1 16.2 - - + -
21A ASN 2.8 30.3 + - - -
30A LEU* 3.3 37.8 - - + -
31A GLN 3.6 0.4 - - - -
32A ASP* 3.7 13.2 - - + +
35A ARG* 5.9 0.2 + - - -
39A ILE* 3.3 36.3 - - + +
41A THR* 2.8 26.7 + - - +
70A ALA 3.0 18.9 + - - +
71A VAL* 3.7 4.0 - - - +
73A ALA* 1.3 76.0 - - - +
75A TYR* 1.3 65.2 + - - +
77A ALA* 3.5 5.5 + - - +
78A GLY* 3.2 16.8 + - - -
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Residues in contact with TYR 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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18A LYS* 3.6 36.2 - - + +
19A ASN 3.3 26.9 - - - -
20A ILE* 4.1 8.7 - - + -
35A ARG* 6.3 0.2 - - - +
71A VAL 2.9 19.1 + - - +
72A ASP* 4.1 2.0 - - - +
74A HIS* 1.3 78.1 - - - +
76A TYR* 1.3 80.0 + + - +
78A GLY* 3.0 5.1 + - - -
79A VAL* 3.0 42.4 + - + +
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Residues in contact with TYR 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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14A LEU* 5.8 3.5 - - - +
16A ASP* 3.8 6.6 + - - -
18A LYS* 3.3 20.5 + - - -
72A ASP* 2.8 35.9 + - - +
75A TYR* 1.3 93.3 - + - +
77A ALA* 1.3 64.8 + - - +
79A VAL* 3.7 4.8 - - + +
80A THR* 2.9 29.3 + - - -
134A SER 3.3 26.9 - - - -
135A GLY 3.7 15.7 + - - -
137A ILE* 3.8 44.4 - - + +
140A VAL* 3.8 19.1 - - + -
180A ALA* 6.1 0.7 - - + -
182A LYS* 4.8 11.8 - - - -
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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
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39A ILE* 3.9 22.6 - - + +
73A ALA 3.1 21.8 + - - +
74A HIS 3.7 5.2 - - - +
76A TYR* 1.3 75.9 - - - +
78A GLY* 1.3 57.6 + - - +
80A THR* 3.3 5.2 + - - -
81A TYR* 2.9 29.5 + - - +
100A ILE* 4.3 16.7 - - + +
102A SER* 4.7 2.0 - - - +
120A MET* 4.3 11.0 - - + -
140A VAL* 3.8 7.9 - - + +
144A LEU* 4.5 5.1 - - - +
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Residues in contact with GLY 78 (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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32A ASP* 4.9 0.2 - - - -
35A ARG* 3.3 25.2 + - - -
39A ILE* 3.6 17.8 - - - +
74A HIS 3.2 9.3 + - - -
75A TYR* 3.0 9.2 + - - -
77A ALA* 1.3 73.9 - - - +
79A VAL* 1.3 64.7 + - - +
81A TYR* 3.4 1.2 + - - +
82A ASP* 2.9 27.7 + - - -
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 5.9 1.3 - - - +
75A TYR* 3.0 40.3 + - + +
76A TYR* 3.3 12.3 + - + +
78A GLY* 1.3 75.3 - - - +
80A THR* 1.3 58.7 + - - +
82A ASP* 3.2 10.1 + - - +
83A TYR* 2.9 26.5 + - - +
137A ILE* 3.8 24.9 - - + -
176A VAL* 4.1 8.3 - - + -
179A TYR* 4.1 13.9 - - + -
180A ALA* 4.1 15.0 - - + -
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Residues in contact with THR 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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76A TYR 2.9 19.2 + - - -
77A ALA* 3.7 4.5 - - - -
79A VAL* 1.3 74.5 - - - +
81A TYR* 1.3 65.2 + - - +
83A TYR* 3.2 3.5 + - - +
84A TYR* 3.1 43.3 + - + -
137A ILE* 5.0 0.9 + - - +
140A VAL* 4.3 1.5 - - - +
141A ALA* 3.5 39.0 + - + +
144A LEU* 3.6 26.9 - - + -
176A VAL* 3.8 13.6 - - + +
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Residues in contact with TYR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 3.8 29.8 - - + -
36A GLY* 3.3 19.6 + - - -
39A ILE* 4.3 2.0 - - + -
77A ALA 2.9 17.8 + - - +
78A GLY 3.6 4.3 - - - +
80A THR* 1.3 74.3 - - - +
82A ASP* 1.3 76.3 + - - +
84A TYR* 3.3 2.8 + - - +
85A LYS* 2.9 53.7 + - + +
90A ARG 4.7 0.5 - - - +
91A LEU* 4.0 3.4 - - - +
92A SER* 3.6 24.2 - - - -
97A ASN* 2.7 33.0 + - - -
100A ILE* 4.0 24.0 - - + -
144A LEU* 4.7 1.2 - - - +
1008A OXY 4.3 9.2 - - - -
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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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35A ARG* 2.8 41.5 + - - +
78A GLY 2.9 14.1 + - - +
79A VAL* 3.5 10.5 - - - +
81A TYR* 1.3 83.9 - - - +
83A TYR* 1.3 58.9 + - - +
85A LYS* 4.6 3.5 - - - +
86A ASN* 2.8 45.0 + - - +
179A TYR* 3.9 15.3 - - + +
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Residues in contact with TYR 83 (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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79A VAL 2.9 12.9 + - - +
80A THR 3.2 7.2 + - - +
82A ASP* 1.3 76.1 - - - +
84A TYR* 1.3 73.2 + + - +
87A VAL* 2.9 60.7 + - + +
88A HIS* 2.9 36.8 + + - -
172A PHE* 3.5 26.1 - + - -
175A LEU* 3.7 31.5 - - + +
176A VAL* 3.6 26.9 - - + -
179A TYR* 3.8 34.9 - + + -
264A GLY* 4.6 1.0 - - - -
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Residues in contact with TYR 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 THR* 3.1 39.5 + - + +
81A TYR 4.0 1.6 - - - +
83A TYR* 1.3 93.3 - + - +
85A LYS* 1.3 58.1 + - - +
88A HIS* 3.1 32.7 + + - +
90A ARG* 3.0 44.6 + - + +
144A LEU* 5.5 0.7 - - + -
145A THR* 2.7 37.7 + - - +
148A VAL* 4.0 21.0 - - + +
172A PHE* 3.3 22.6 - + + +
176A VAL* 5.0 1.6 - - + -
268A TYR* 4.3 20.6 - + - -
271A LEU* 5.8 0.6 - - + +
1008A OXY 3.5 22.2 - - - +
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Residues in contact with LYS 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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81A TYR* 2.9 43.5 + - + +
82A ASP* 4.0 3.6 - - - +
84A TYR* 1.3 76.9 - - - +
86A ASN* 1.3 71.6 + - - +
89A ASN* 3.0 29.5 + - - +
90A ARG 3.2 16.4 + - - +
91A LEU* 3.8 26.2 - - + -
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Residues in contact with ASN 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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82A ASP* 2.8 33.5 + - - +
85A LYS* 1.3 91.3 + - - +
87A VAL* 1.3 64.0 + - + +
89A ASN* 4.5 6.3 - - - +
179A TYR* 2.9 28.1 + - + +
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TYR* 2.9 44.6 + - + +
86A ASN* 1.3 82.0 - - + +
88A HIS* 1.3 81.7 + - + +
89A ASN* 3.7 3.5 + - - -
179A TYR* 4.0 21.3 - - + -
261A ASP* 6.1 4.9 - - - +
265A LYS* 4.0 19.4 + - + +
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Residues in contact with HIS 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TYR* 2.9 44.8 + + - -
84A TYR* 3.1 22.0 + + - +
87A VAL* 1.3 92.8 + - + +
89A ASN* 1.3 74.1 + - - +
90A ARG* 3.1 2.1 + - + +
172A PHE* 3.9 4.8 - - - -
264A GLY* 3.5 31.2 - - - -
265A LYS* 4.3 16.4 + - + +
268A TYR* 3.6 50.8 + + + +
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Residues in contact with ASN 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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85A LYS* 3.0 20.9 + - - +
86A ASN 4.5 6.3 - - - +
87A VAL 5.0 3.0 + - - -
88A HIS* 1.3 80.8 + - - +
90A ARG* 1.3 59.0 + - - +
91A LEU* 4.1 8.0 + - - +
265A LYS* 5.5 5.3 - - - +
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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