Contacts of the helix formed by residues 26 - 49 (chain D) in PDB entry 3J9X
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 26 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ASN 4.5 2.7 - - - +
23D ALA 3.1 15.4 + - - +
24D PHE 3.0 1.4 + - - -
25D SER* 1.3 78.6 + - - +
27D PRO* 1.4 66.8 - - - +
28D THR* 2.9 23.9 + - - -
29D VAL* 2.7 37.2 + - + -
30D ALA* 2.8 11.9 + - - -
32E THR* 4.0 19.7 + - + +
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Residues in contact with PRO 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PRO* 3.5 32.8 - - + +
28C THR* 5.5 1.3 - - + -
31C SER* 3.5 19.1 - - - +
25D SER 3.2 6.8 - - - +
26D ASN* 1.4 91.5 - - - +
28D THR* 1.3 61.9 + - - +
30D ALA* 4.0 2.9 - - + +
31D SER* 2.8 29.6 + - - -
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Residues in contact with THR 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PRO* 5.7 0.4 - - - -
26D ASN* 2.8 14.5 + - - -
27D PRO* 1.3 75.2 - - - +
29D VAL* 1.3 60.3 + - - +
31D SER* 3.1 4.7 + - - -
32D THR* 2.5 46.8 + - - +
26E ASN* 4.8 4.7 - - - +
28E THR* 3.1 34.2 - - + +
29E VAL* 4.6 0.2 - - + -
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Residues in contact with VAL 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ALA 3.3 29.2 - - - +
24D PHE* 3.8 9.6 - - - -
26D ASN* 2.7 15.4 + - + +
28D THR* 1.3 71.1 - - - +
30D ALA* 1.3 65.4 + - - +
32D THR* 3.4 0.3 + - - -
33D ILE* 3.1 43.8 + - + +
28E THR* 4.3 1.3 - - - +
29E VAL* 3.9 29.8 - - + +
32E THR* 3.8 29.6 - - + +
33E ILE* 4.9 6.5 - - + -
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Residues in contact with ALA 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ALA* 3.6 29.2 - - + -
34C LEU* 4.6 2.5 - - + -
24D PHE* 3.3 37.1 + - + +
25D SER 4.9 0.7 - - - -
26D ASN 2.8 11.8 + - - +
27D PRO* 4.0 4.0 - - + +
29D VAL* 1.3 78.0 - - - +
31D SER* 1.3 57.9 + - - +
33D ILE* 4.0 0.5 - - - +
34D LEU* 2.9 37.1 + - + +
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Residues in contact with SER 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C SER 3.5 23.8 - - - -
27C PRO* 3.5 24.2 - - - +
27D PRO 2.8 20.2 + - - -
28D THR* 3.1 8.1 + - - -
30D ALA* 1.3 77.0 - - - +
32D THR* 1.3 58.0 + - - +
34D LEU* 4.6 0.2 - - - -
35D SER* 2.6 42.6 + - - -
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Residues in contact with THR 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D THR* 2.5 35.0 + - - +
29D VAL 3.7 3.1 - - - -
31D SER* 1.3 78.2 + - - +
33D ILE* 1.3 65.0 + - - +
35D SER* 3.2 3.4 + - - -
36D ASN* 3.1 35.1 + - - +
23E ALA* 3.6 34.1 - - + +
26E ASN* 4.0 15.2 + - + +
29E VAL* 3.7 15.5 - - + +
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Residues in contact with ILE 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3187 T 5.7 2.2 - - - +
228 T 3.7 38.1 - - - +
238 A 4.7 6.7 - - - +
24D PHE* 4.2 15.3 - - + -
29D VAL* 3.1 33.7 + - + +
30D ALA 4.0 1.6 - - - +
32D THR* 1.3 78.6 - - - +
34D LEU* 1.3 59.0 + - - +
36D ASN* 3.1 3.3 + - - +
37D VAL* 3.0 29.9 + - + +
20E LYS* 4.0 22.9 - - + -
23E ALA* 3.8 21.8 - - + -
29E VAL* 4.9 7.9 - - + -
33E ILE* 5.3 5.2 - - + -
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Residues in contact with LEU 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218 A 4.9 7.0 - - + -
228 T 4.6 14.4 - - - +
21C PHE* 4.1 21.6 - - + -
24C PHE* 3.4 41.5 - - + +
25C SER* 3.9 26.9 - - - -
30C ALA* 4.5 0.4 - - + -
24D PHE* 4.0 22.7 - - + -
30D ALA* 2.9 27.7 + - + +
31D SER 4.3 0.4 - - - +
33D ILE* 1.3 77.0 - - - +
35D SER* 1.3 52.4 + - - +
37D VAL* 3.4 8.3 + - + +
38D SER* 2.6 37.3 + - - -
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Residues in contact with SER 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C SER* 4.6 8.9 - - - -
31D SER* 2.6 27.7 + - - -
32D THR* 3.2 6.4 + - - -
34D LEU* 1.3 78.4 - - - +
36D ASN* 1.3 69.9 + - - +
38D SER* 3.4 20.6 + - - -
39D PRO* 4.1 3.5 - - - +
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Residues in contact with ASN 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D THR* 3.1 23.3 + - - +
33D ILE 3.1 5.6 + - - +
35D SER* 1.3 86.1 + - - +
37D VAL* 1.3 59.7 + - - +
38D SER 3.3 1.1 + - - -
39D PRO* 3.6 12.0 - - - +
40D VAL* 4.3 1.9 - - - +
19E ALA* 3.4 30.5 + - + +
22E ASN* 4.0 10.3 - - - +
23E ALA* 3.4 31.1 - - + +
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Residues in contact with VAL 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218 A 4.1 20.9 - - - +
228 T 3.9 6.5 - - - +
21C PHE* 4.6 8.5 - - + -
33D ILE* 3.0 20.5 + - + +
34D LEU* 3.5 17.3 - - + +
36D ASN* 1.3 76.2 - - - +
38D SER* 1.3 65.3 + - - +
39D PRO* 3.5 1.3 - - - -
40D VAL* 3.9 7.6 - - + -
41D ALA* 2.8 23.8 + - + +
16E LYS* 4.9 7.9 - - + -
19E ALA* 3.7 22.4 - - + -
20E LYS* 3.7 27.4 - - + -
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Residues in contact with SER 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C PHE* 3.6 22.0 - - - -
22C ASN* 5.5 2.5 + - - -
25C SER* 4.6 5.2 + - - -
34D LEU 2.6 22.1 + - - -
35D SER* 3.4 15.5 - - - -
36D ASN 3.3 0.2 - - - -
37D VAL* 1.3 81.1 - - - +
39D PRO* 1.4 71.9 - - - +
41D ALA* 2.9 11.3 + - - +
42D GLN* 3.0 25.1 + - - +
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Residues in contact with PRO 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D SER 4.1 4.3 - - - +
36D ASN 3.6 13.0 - - - +
37D VAL 3.5 1.6 - - - -
38D SER* 1.4 98.0 - - - +
40D VAL* 1.3 68.3 + - + +
42D GLN* 3.4 20.3 + - - +
43D GLN* 3.1 21.7 + - - +
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Residues in contact with VAL 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218 A 4.8 1.8 - - - +
36D ASN 4.3 13.7 - - - +
37D VAL* 3.5 11.4 - - + +
38D SER 3.0 0.8 + - - -
39D PRO* 1.3 77.6 - - + +
41D ALA* 1.3 68.0 + - - +
43D GLN* 3.1 9.1 + - - +
44D ASN* 3.1 33.4 + - - +
12E GLN* 5.2 1.3 - - - +
15E ALA* 4.0 28.9 - - + +
16E LYS* 3.9 33.4 - - + +
19E ALA* 4.3 6.7 - - + -
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Residues in contact with ALA 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208 T 4.2 2.5 - - - +
218 A 3.7 35.6 - - - -
17C TRP* 4.1 17.8 - - + -
21C PHE* 4.3 11.7 - - + -
37D VAL 2.8 13.8 + - - +
38D SER 3.3 9.0 - - - +
40D VAL* 1.3 76.1 - - - +
42D GLN* 1.3 56.5 + - - +
44D ASN* 3.1 2.3 + - - +
45D PHE* 2.8 31.9 + - - +
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Residues in contact with GLN 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C TYR* 3.7 12.7 + - - +
17C TRP* 4.3 10.3 - - + -
18C GLN* 3.2 40.7 - - - +
21C PHE* 5.8 0.7 - - + -
22C ASN* 4.7 2.0 + - - -
38D SER* 3.0 20.8 + - - +
39D PRO* 3.5 29.3 - - + +
40D VAL 3.1 0.2 - - - -
41D ALA* 1.3 76.5 - - - +
43D GLN* 1.3 57.6 + - - +
45D PHE* 3.7 1.0 - - - +
46D GLN* 2.9 42.5 + - - +
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Residues in contact with GLN 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D PRO 3.1 9.6 + - - +
40D VAL* 3.1 12.0 + - - +
42D GLN* 1.3 78.9 - - - +
44D ASN* 1.3 60.8 + - - +
46D GLN* 3.4 15.4 + - - +
47D THR* 2.6 61.1 + - - +
12E GLN* 5.3 9.2 - - + +
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Residues in contact with ASN 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3207 T 5.5 0.2 + - - -
208 T 3.5 29.8 - - - +
218 A 3.0 21.4 + - - -
40D VAL* 3.1 23.0 + - - +
41D ALA 3.1 3.6 + - - +
43D GLN* 1.3 75.6 - - - +
45D PHE* 1.3 64.2 + - - +
47D THR* 3.4 4.6 + - - -
48D ASN* 3.1 22.3 + - - +
8E ARG* 3.6 24.3 - - - +
12E GLN* 2.9 33.9 + - - +
16E LYS* 5.0 4.8 - - - +
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Residues in contact with PHE 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3317 A 5.2 5.6 - - - -
198 A 4.6 10.1 - + - -
208 T 3.6 23.2 - - - -
10C TYR* 4.1 2.7 - + - -
13C ARG* 4.5 6.3 - - + -
14C TYR* 3.4 43.5 - + + -
17C TRP* 3.5 60.8 - + + -
41D ALA 2.8 15.7 + - - +
42D GLN 3.7 2.9 - - - +
44D ASN* 1.3 77.6 - - - +
46D GLN* 1.3 63.6 + - - +
49D VAL* 3.0 64.9 + - + +
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Residues in contact with GLN 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C TYR* 3.3 21.3 + - - +
14C TYR* 2.9 39.2 + - + -
42D GLN* 2.9 33.5 + - - +
43D GLN* 3.7 15.1 + - - +
45D PHE* 1.3 78.1 - - - +
47D THR* 1.3 62.9 + - - +
50D PRO* 3.1 21.5 - - - +
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Residues in contact with THR 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D GLN* 2.6 42.8 + - - +
44D ASN* 3.7 6.5 - - - -
45D PHE 3.2 0.4 - - - -
46D GLN* 1.3 80.4 - - - +
48D ASN* 1.3 74.2 + - - +
50D PRO* 3.7 6.1 - - - +
51D LYS* 3.4 23.4 - - - +
12E GLN* 4.6 14.1 + - - +
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Residues in contact with ASN 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198 A 3.8 20.4 - - - +
208 T 3.1 20.2 + - - -
44D ASN 3.1 11.0 + - - +
47D THR* 1.3 87.3 - - - +
49D VAL* 1.3 62.3 + - - +
50D PRO* 3.4 1.6 - - - -
51D LYS* 3.0 34.8 + - + +
52D PHE* 3.1 27.3 - - + -
88D ASN* 4.9 4.7 + - - -
7E SER 3.9 13.8 + - - +
8E ARG* 3.4 15.2 - - - +
12E GLN* 5.2 2.0 - - - +
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Residues in contact with VAL 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198 A 3.9 28.0 - - + +
10C TYR* 3.8 10.1 - - + -
13C ARG* 3.7 26.6 + - - +
45D PHE* 3.0 64.7 + - + +
48D ASN* 1.3 70.6 - - - +
50D PRO* 1.4 60.6 - - + +
51D LYS 3.0 4.5 - - - -
52D PHE* 2.8 30.5 + - - +
53D THR 3.2 6.4 + - - -
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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