Contacts of the helix formed by residues 41 - 65 (chain B) in PDB entry 3H90
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 ALA 41 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ILE* 5.5 0.6 - - + +
40B LEU* 1.3 74.0 - - - +
42B ALA* 1.3 54.2 + - - +
43B LEU* 2.8 18.4 + - - +
44B VAL* 3.1 28.0 + - + +
45B ASP* 3.8 2.4 + - - +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 4.3 13.5 + - - -
40B LEU* 3.4 15.2 - - + +
41B ALA* 1.3 74.7 - - - +
43B LEU* 1.3 57.4 + - - +
44B VAL 3.5 0.7 - - - -
45B ASP* 3.7 24.3 - - + +
46B SER* 4.0 5.2 + - - -
121B THR* 6.0 3.6 - - + -
160B MET* 4.7 19.7 - - + -
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 4.0 14.3 - - + +
31B TRP* 3.8 45.3 - - + +
40B LEU 3.2 24.1 + - - +
41B ALA* 2.8 4.2 - - - -
42B ALA* 1.3 78.4 - - - +
44B VAL* 1.3 74.6 + - + +
45B ASP 3.3 0.4 - - - -
46B SER* 3.6 8.8 + - - -
47B LEU* 3.2 28.7 + - + +
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Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ALA* 3.1 21.7 + - + +
43B LEU* 1.3 92.1 - - + +
45B ASP* 1.3 54.9 + - - +
46B SER 3.2 0.7 - - - -
47B LEU* 2.9 17.5 + - + +
48B VAL* 2.7 45.7 + - + +
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Residues in contact with ASP 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 5.0 5.5 + - - -
41B ALA 3.8 2.8 + - - +
42B ALA* 3.7 25.1 - - - +
44B VAL* 1.3 78.5 - - - +
46B SER* 1.3 56.7 + - - +
48B VAL* 3.5 8.0 - - - +
49B ASP* 2.8 31.4 + - - +
153B HIS* 4.0 6.1 - - - -
157B ASP* 3.7 10.4 - - - +
160B MET* 5.3 6.1 - - - +
291B ZN 2.3 34.2 - - - -
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Residues in contact with SER 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.5 32.0 - - - +
27B LYS* 4.0 21.7 + - - -
28B ILE* 3.5 25.9 + - - +
42B ALA 4.0 2.9 + - - -
43B LEU* 3.6 9.5 + - - -
44B VAL 3.2 0.4 - - - -
45B ASP* 1.3 77.0 - - - +
47B LEU* 1.3 62.6 + - - +
48B VAL 3.3 0.7 - - - -
49B ASP* 3.5 9.0 - - - +
50B ILE* 3.0 26.7 + - - +
291B ZN 4.6 0.2 - - - -
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 4.0 21.3 - - + -
43B LEU* 3.2 19.6 + - + +
44B VAL* 2.9 22.5 + - + +
46B SER* 1.3 76.2 + - - +
48B VAL* 1.3 64.4 + - - +
50B ILE* 3.0 31.4 - - + +
51B GLY* 3.6 2.3 + - - -
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Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 2.7 28.8 + - + +
45B ASP* 3.5 10.3 - - - +
47B LEU* 1.3 75.6 - - - +
49B ASP* 1.3 59.7 + - - +
51B GLY* 2.9 5.5 + - - -
52B ALA* 2.6 43.4 + - + +
89B PHE* 6.5 0.4 - - + -
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B SER 5.6 0.2 - - - -
24B LEU* 2.9 34.4 - - + +
45B ASP* 2.8 16.3 + - - +
46B SER 3.5 2.5 - - - +
47B LEU 3.4 0.2 - - - -
48B VAL* 1.3 80.5 - - - +
50B ILE* 1.3 57.6 + - - +
52B ALA* 4.0 8.2 - - - +
53B SER* 2.8 36.4 + - - -
153B HIS* 2.9 21.6 + - - -
154B TYR* 3.2 11.6 - - - +
157B ASP* 3.0 2.3 - - - +
291B ZN 2.2 32.7 - - - -
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Residues in contact with ILE 50 (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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21B SER 5.7 1.1 - - - -
22B LEU* 4.5 15.0 - - + +
24B LEU* 4.4 9.4 + - - +
25B LEU* 3.5 49.8 - - + +
28B ILE* 4.7 8.1 - - + -
46B SER 3.0 13.3 + - - +
47B LEU* 3.0 35.2 - - + +
48B VAL 3.1 0.4 + - - -
49B ASP* 1.3 74.7 - - - +
51B GLY* 1.3 63.2 + - - +
53B SER* 5.2 0.7 - - - -
54B LEU* 3.0 32.1 + - + +
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Residues in contact with GLY 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU 3.6 2.2 + - - -
48B VAL 2.9 6.4 + - - -
50B ILE* 1.3 82.9 - - - +
52B ALA* 1.3 58.4 + - - +
54B LEU* 3.2 10.3 + - - +
55B THR* 2.8 33.8 + - - -
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B VAL* 2.6 31.3 + - + +
49B ASP* 3.8 10.3 - - - +
51B GLY* 1.3 72.3 - - - +
53B SER* 1.3 63.2 + - - +
55B THR* 3.2 9.0 + - - -
56B ASN* 3.2 18.9 + - - +
86B GLN* 5.8 1.0 + - - -
150B ASP* 5.4 2.0 - - - +
153B HIS* 6.5 0.7 - - + -
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Residues in contact with SER 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ALA* 4.4 3.5 - - - +
21B SER* 3.5 18.6 - - - -
22B LEU* 3.7 12.1 - - - +
49B ASP* 2.8 18.3 + - - -
52B ALA* 1.3 76.2 - - - +
54B LEU* 1.3 56.8 + - - +
56B ASN* 3.3 10.9 + - - +
57B LEU* 3.0 24.6 + - - +
150B ASP* 3.2 22.6 + - - +
154B TYR* 2.6 26.4 + - - -
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 3.7 28.2 - - + +
50B ILE* 3.0 25.3 + - + +
51B GLY* 3.2 9.3 + - - +
53B SER* 1.3 74.9 - - - +
55B THR* 1.3 65.7 + - - +
57B LEU* 3.1 18.3 + - + +
58B LEU* 3.1 30.1 + - + +
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Residues in contact with THR 55 (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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51B GLY 2.8 18.7 + - - -
52B ALA* 3.4 8.7 + - - -
54B LEU* 1.3 74.7 - - - +
56B ASN* 1.3 55.9 + - - +
58B LEU* 2.8 37.1 + - + +
59B VAL* 2.8 25.6 + - + +
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Residues in contact with ASN 56 (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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18B ALA* 5.1 4.4 - - + +
52B ALA 3.2 9.4 + - - +
53B SER* 3.4 13.9 - - - +
55B THR* 1.3 79.1 - - - +
57B LEU* 1.3 56.9 + - - +
59B VAL* 4.5 4.5 - - - +
60B VAL* 2.9 50.3 + - - +
82B ALA* 4.3 11.7 - - - +
86B GLN* 3.0 31.6 + - - +
146B ALA* 3.4 15.6 + - - +
147B VAL* 4.8 2.4 - - - +
150B ASP* 3.3 27.8 + - - +
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA* 4.2 7.6 - - - +
18B ALA* 3.6 27.1 - - + +
19B MET* 4.3 20.2 - - + +
22B LEU* 4.5 8.7 - - + -
53B SER 3.0 11.5 + - - +
54B LEU* 3.3 27.6 - - + +
55B THR 3.1 0.4 - - - -
56B ASN* 1.3 78.1 - - - +
58B LEU* 1.3 58.7 + - + +
60B VAL* 3.2 11.8 - - + +
61B ARG* 2.9 69.8 + - - +
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Residues in contact with LEU 58 (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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54B LEU* 3.1 30.9 + - + +
55B THR* 2.8 26.9 + - + +
57B LEU* 1.3 75.1 - - + +
59B VAL* 1.3 58.9 + - + +
61B ARG* 3.4 8.0 + - - +
62B TYR* 3.0 24.4 + - - +
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B THR* 2.8 28.3 + - + +
56B ASN* 4.1 5.4 - - - +
58B LEU* 1.3 75.9 - - + +
60B VAL* 1.3 59.4 + - + +
61B ARG 3.1 1.1 - - - -
62B TYR* 3.2 8.4 + - + +
63B SER* 2.9 26.4 + - - -
78B ALA* 3.6 31.8 - - + +
79B GLU* 5.4 0.9 - - - -
82B ALA* 3.7 20.2 - - + -
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Residues in contact with VAL 60 (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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14B ILE* 3.5 24.2 - - + -
15B ALA* 4.5 7.4 - - + -
18B ALA* 4.2 16.2 - - + -
56B ASN* 2.9 39.9 + - - +
57B LEU* 3.2 21.1 - - + +
59B VAL* 1.3 72.4 - - + +
61B ARG* 1.3 65.7 + - - +
63B SER* 3.3 9.4 - - - -
64B LEU* 3.0 32.3 + - + +
79B GLU* 5.2 1.1 - - + +
146B ALA* 3.8 22.4 - - + -
147B VAL* 5.3 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
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15B ALA* 5.1 14.8 - - + +
19B MET* 3.4 34.2 - - - +
57B LEU* 2.9 42.2 + - - +
58B LEU* 3.5 7.9 - - - +
59B VAL 3.1 0.2 - - - -
60B VAL* 1.3 76.9 - - + +
62B TYR* 1.3 65.4 + - - +
64B LEU* 3.4 14.4 + - + +
65B GLN* 3.7 12.5 + - - +
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Residues in contact with TYR 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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58B LEU 3.0 13.9 + - - +
59B VAL* 3.2 12.8 + - + +
61B ARG* 1.3 76.1 - - - +
63B SER* 1.3 65.0 + - - +
64B LEU 3.0 1.7 + - - -
65B GLN* 3.1 48.0 + - - +
71B HIS* 3.2 30.1 + - - -
75B HIS* 3.3 30.5 + + + +
78B ALA* 4.0 16.2 - - + -
293B ZN 3.9 0.9 - - - -
203D GLN* 4.4 7.6 + - - -
206D LEU* 4.3 18.4 - - + -
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Residues in contact with SER 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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11B ARG* 4.8 0.2 + - - -
59B VAL 2.9 16.8 + - - -
60B VAL* 3.3 17.9 + - - +
62B TYR* 1.3 74.2 - - - +
64B LEU* 1.3 69.3 + - - +
65B GLN 3.5 2.8 + - - +
75B HIS* 3.3 34.1 + - - +
76B GLY* 3.9 7.2 + - - -
78B ALA* 4.3 5.2 - - - -
79B GLU* 3.3 34.2 + - - +
241B PRO* 5.2 1.9 - - - +
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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
----------------------------------------------------------
11B ARG* 4.4 37.5 - - + +
12B ALA* 5.9 0.4 - - - -
14B ILE* 4.0 23.6 - - + -
15B ALA* 4.7 12.1 - - + -
60B VAL 3.0 24.9 + - - +
61B ARG* 3.4 9.2 + - + +
62B TYR 3.0 1.6 + - - -
63B SER* 1.3 86.2 - - - +
65B GLN* 1.3 66.4 + - - +
66B PRO* 3.4 5.5 - - - +
241B PRO* 4.9 7.0 - - + -
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Residues in contact with GLN 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ARG 3.7 7.6 + - - +
62B TYR* 3.1 50.9 + - - +
63B SER 3.9 5.0 - - - +
64B LEU* 1.3 78.9 - - - +
66B PRO* 1.3 75.3 - - + +
68B ASP* 5.9 0.8 + - - -
74B GLY* 5.5 0.3 - - - -
75B HIS* 3.3 27.2 + - + +
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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