Contacts of the helix formed by residues 48 - 70 (chain A) in PDB entry 1C1D
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 48 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A TYR* 3.7 8.0 - - - +
47A SER* 1.3 99.5 + - - +
49A LEU* 1.3 67.0 + - - +
50A ALA* 3.1 12.4 - - + +
51A ASP* 3.0 29.5 + - - +
52A ALA 3.6 2.4 + - - -
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Residues in contact with LEU 49 (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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2A ILE* 4.2 21.1 - - + -
15A THR* 5.8 6.5 - - + -
24A HIS* 3.7 55.0 - - + +
25A PHE 5.9 0.2 - - - +
26A VAL* 4.6 11.9 - - + -
46A TYR* 5.5 0.4 - - - -
48A ASN* 1.3 74.6 - - - +
50A ALA* 1.3 64.1 + - - +
52A ALA* 2.9 23.2 + - + +
53A LEU* 3.0 18.4 + - + +
82A ALA* 5.0 1.3 - - + -
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Residues in contact with ALA 50 (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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1A SER* 3.7 38.6 - - - +
2A ILE* 4.1 16.7 - - + +
5A ALA* 4.1 2.8 - - + +
48A ASN* 3.1 10.8 - - + +
49A LEU* 1.3 80.4 - - - +
51A ASP* 1.3 59.4 + - - +
53A LEU* 3.3 7.8 + - - +
54A THR* 2.9 33.3 + - - +
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Residues in contact with ASP 51 (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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46A TYR* 3.8 16.8 - - + -
47A SER* 3.9 13.0 + - - +
48A ASN* 3.0 32.3 + - - +
50A ALA* 1.3 81.1 - - - +
52A ALA* 1.3 58.3 + - - +
54A THR* 3.8 6.0 - - - -
55A ASP* 2.8 31.9 + - - +
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Residues in contact with ALA 52 (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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26A VAL* 4.4 10.8 - - + -
46A TYR* 3.7 31.1 - - + -
48A ASN 3.6 1.6 + - - -
49A LEU* 2.9 12.4 + - + +
51A ASP* 1.3 81.5 - - - +
53A LEU* 1.4 56.6 + - - +
55A ASP* 3.9 0.9 - - - +
56A ALA* 2.9 30.7 + - - +
80A VAL* 3.9 19.6 - - + +
82A ALA* 4.1 14.6 - - + -
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Residues in contact with LEU 53 (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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2A ILE* 3.8 29.4 - - + -
5A ALA* 3.9 18.8 - - + -
6A LEU* 4.3 14.1 - - + -
13A THR* 3.8 29.4 - - + -
15A THR* 4.0 12.8 - - + -
26A VAL* 3.8 19.7 - - + -
28A ARG* 2.9 21.3 + - - +
49A LEU* 3.0 19.7 + - + +
50A ALA* 3.4 6.3 - - - +
52A ALA* 1.4 74.7 - - - +
54A THR* 1.3 66.6 + - - +
56A ALA* 3.2 5.1 + - - +
57A GLY 2.9 19.2 + - - -
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Residues in contact with THR 54 (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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5A ALA* 4.0 14.6 - - - +
28A ARG* 4.4 4.9 - - - +
50A ALA* 2.9 17.6 + - - +
51A ASP* 3.8 7.2 - - - -
53A LEU* 1.3 76.0 - - - +
55A ASP* 1.3 65.1 + - - +
57A GLY* 3.2 1.9 + - - -
58A LYS* 3.0 46.0 + - + +
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Residues in contact with ASP 55 (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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42A ARG* 3.6 20.4 + - - -
46A TYR* 2.6 35.2 + - + +
51A ASP 2.8 19.4 + - - +
52A ALA 3.9 2.9 - - - +
54A THR* 1.3 76.7 - - - +
56A ALA* 1.3 65.3 + - - +
58A LYS* 3.1 8.9 + - - +
59A LEU* 2.8 44.3 + - + +
80A VAL* 4.8 0.4 - - + -
263A ASN* 4.7 4.0 - - - +
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Residues in contact with ALA 56 (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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26A VAL* 3.6 25.6 - - + -
28A ARG* 4.1 9.8 - - + +
52A ALA 2.9 19.6 + - - +
53A LEU 3.6 4.3 - - - +
55A ASP* 1.3 77.1 - - - +
57A GLY* 1.3 57.9 + - - +
59A LEU* 3.9 3.4 - - - -
60A ALA* 2.9 31.4 + - - +
78A LYS* 3.9 10.2 - - - +
80A VAL* 3.7 20.5 - - + +
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Residues in contact with GLY 57 (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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8A TRP* 3.8 28.6 + - - -
28A ARG* 3.6 19.7 - - - +
30A ASP* 4.9 0.2 - - - +
53A LEU 2.9 13.1 + - - -
54A THR 3.7 2.7 - - - -
56A ALA* 1.3 78.7 - - - +
58A LYS* 1.3 62.3 + - - +
60A ALA* 3.4 2.1 + - - +
61A GLY* 3.0 19.8 + - - -
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Residues in contact with LYS 58 (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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54A THR* 3.0 35.3 + - + +
55A ASP* 3.9 8.1 - - - +
57A GLY* 1.3 76.7 - - - +
59A LEU* 1.4 63.1 + - - +
61A GLY* 3.4 1.8 + - - -
62A ALA 3.1 17.8 + - - -
263A ASN* 3.2 32.3 + - + +
265A ILE 5.5 1.6 + - - -
266A ALA* 4.0 20.6 + - - +
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Residues in contact with LEU 59 (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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42A ARG* 3.8 31.9 - - - +
55A ASP* 2.8 46.0 + - - +
56A ALA 3.9 0.2 - - - +
58A LYS* 1.4 79.2 - - - +
60A ALA* 1.4 57.1 + - - +
62A ALA* 3.3 5.7 + - - +
63A MET* 3.0 30.5 + - - +
78A LYS* 3.5 35.4 + - + +
80A VAL* 4.4 5.2 - - + -
262A ASN* 3.5 29.9 - - + +
263A ASN* 3.1 22.2 - - - +
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Residues in contact with ALA 60 (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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8A TRP* 4.4 1.3 - - + -
28A ARG* 3.5 29.4 - - + +
30A ASP* 3.6 14.2 - - + +
56A ALA 2.9 19.0 + - - +
57A GLY 3.8 4.0 - - - +
59A LEU* 1.4 74.8 - - - +
61A GLY* 1.4 63.5 + - - +
63A MET* 3.1 12.3 + - - +
64A THR* 3.1 15.8 + - - -
76A GLY 3.8 1.7 - - - -
77A GLY* 3.9 19.7 - - - -
78A LYS* 3.8 0.8 - - - +
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Residues in contact with GLY 61 (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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30A ASP* 3.7 22.3 - - - +
57A GLY 3.0 14.8 + - - -
58A LYS* 3.4 3.3 + - - -
59A LEU 3.3 0.2 - - - -
60A ALA* 1.4 71.9 - - - +
62A ALA* 1.3 65.6 + - - +
64A THR* 3.2 4.3 + - - -
65A LEU* 3.2 30.0 + - - +
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Residues in contact with ALA 62 (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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58A LYS 3.1 13.8 + - - +
59A LEU* 3.4 10.5 - - - +
60A ALA 3.3 0.2 - - - -
61A GLY* 1.3 75.0 - - - +
63A MET* 1.4 60.1 + - + +
65A LEU* 3.3 7.2 + - - +
66A LYS* 2.8 32.4 + - - +
262A ASN* 4.3 17.5 - - - +
263A ASN* 3.8 17.0 - - - +
284A ASP* 5.8 2.5 - - - +
285A PHE* 3.9 15.5 - - + +
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Residues in contact with MET 63 (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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38A ALA 3.6 16.4 - - - +
39A GLY* 4.1 6.5 - - - -
59A LEU 3.0 18.3 + - - +
60A ALA 3.1 8.0 + - - +
62A ALA* 1.4 76.9 - - - +
64A THR* 1.4 62.7 + - - +
66A LYS* 3.6 30.9 - - + +
67A MET* 2.9 59.5 + - + +
76A GLY* 3.7 6.3 - - - -
77A GLY 3.3 19.7 - - - +
78A LYS* 4.3 8.7 - - + -
262A ASN* 5.2 1.6 - - - +
361A PHE* 3.7 34.3 - - + +
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Residues in contact with THR 64 (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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30A ASP* 2.7 39.0 + - - +
31A SER* 3.5 19.3 - - - +
34A LEU* 5.3 2.8 - - + +
60A ALA 3.1 4.9 + - - -
61A GLY 3.2 7.6 + - - -
63A MET* 1.4 77.1 - - - +
65A LEU* 1.3 63.0 + - + +
67A MET* 3.9 2.4 - - - +
68A ALA* 3.1 28.6 + - + +
74A MET 5.0 1.0 - - - +
75A GLY* 4.5 3.4 - - - -
76A GLY* 3.3 20.5 + - - +
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Residues in contact with LEU 65 (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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61A GLY 3.2 16.6 + - - +
62A ALA* 3.8 6.7 - - - +
64A THR* 1.3 83.4 - - + +
66A LYS* 1.3 62.2 + - - +
68A ALA* 3.8 3.7 - - + +
69A VAL* 2.8 34.7 + - - +
285A PHE* 3.5 32.3 - - + -
338A ARG* 3.7 51.4 - - + +
341A ALA* 4.0 20.0 - - + +
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Residues in contact with LYS 66 (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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62A ALA 2.8 18.2 + - - +
63A MET* 3.6 26.0 - - + +
65A LEU* 1.3 75.9 - - - +
67A MET* 1.4 62.3 + - - +
69A VAL* 3.7 0.6 - - - +
70A SER* 2.8 31.0 + - - -
72A LEU* 4.9 0.2 - - - +
262A ASN* 3.1 22.9 + - - -
285A PHE* 3.5 28.4 - - + +
288A ASN* 2.9 28.7 + - - +
289A ALA* 3.7 16.2 - - + -
292A ALA* 4.0 14.6 - - + -
360A NAI 3.8 0.8 - - - -
361A PHE* 2.6 34.2 + - - +
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Residues in contact with MET 67 (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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38A ALA* 3.9 22.0 - - + +
63A MET* 2.9 46.4 + - + +
64A THR 3.9 2.7 - - - +
66A LYS* 1.4 76.8 - - - +
68A ALA* 1.3 62.3 + - - +
70A SER 3.2 1.7 + - - -
71A ASN 3.1 3.8 + - - -
72A LEU* 2.9 62.1 + - - +
74A MET* 3.1 28.5 - - + +
75A GLY 3.6 13.5 - - - +
292A ALA* 4.2 4.7 - - + -
296A VAL* 3.9 11.2 - - + -
361A PHE* 3.7 18.8 - - + -
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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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34A LEU* 3.8 25.1 - - + +
64A THR* 3.1 17.4 + - + +
65A LEU* 3.8 4.7 - - + +
67A MET* 1.3 79.1 - - - +
69A VAL* 1.3 63.7 + - - +
71A ASN* 3.1 12.4 + - - +
72A LEU 5.2 0.2 - - - +
341A ALA* 3.8 24.5 - - + +
344A ARG* 3.5 16.3 - - - +
345A ALA* 4.2 7.3 + - + +
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Residues in contact with VAL 69 (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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65A LEU 2.8 23.2 + - - +
66A LYS 3.7 5.8 - - - +
68A ALA* 1.3 74.6 - - - +
70A SER* 1.3 65.7 + - - +
71A ASN 3.3 0.9 - - - -
285A PHE* 4.1 12.6 - - + +
286A VAL* 3.9 27.1 - - + -
318A THR* 4.0 20.0 - - + +
337A ALA* 4.0 8.7 - - - +
340A LEU* 4.1 12.8 - - + -
341A ALA* 3.8 28.2 - - + +
344A ARG* 2.7 33.4 + - - +
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Residues in contact with SER 70 (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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66A LYS 2.8 23.1 + - - -
67A MET 4.0 1.3 - - - -
68A ALA 3.1 1.2 - - - -
69A VAL* 1.3 80.7 - - - +
71A ASN* 1.3 72.3 + - - +
72A LEU* 3.2 22.8 + - - +
286A VAL 5.2 0.2 + - - -
289A ALA* 3.3 22.9 - - - +
293A ILE* 4.3 16.4 - - - +
311A ARG* 3.6 12.8 + - - -
315A ILE* 5.7 0.9 - - - +
318A THR* 5.9 0.4 - - - -
344A ARG* 4.8 1.6 - - - +
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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
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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