Contacts of the helix formed by residues 26 - 49 (chain n) 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 n).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22n ASN 4.5 2.2 - - - +
23n ALA 3.1 15.8 + - - +
24n PHE 3.0 1.0 + - - -
25n SER* 1.3 79.2 + - - +
27n PRO* 1.4 68.1 - - - +
28n THR* 2.9 23.8 + - - -
29n VAL* 2.7 36.8 + - + -
30n ALA* 2.8 11.9 + - - -
32o THR* 4.0 18.8 + - + +
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Residues in contact with PRO 27 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27m PRO* 3.5 32.6 - - + +
28m THR* 5.5 1.3 - - + -
31m SER* 3.5 19.1 - - - +
25n SER 3.2 7.1 - - - +
26n ASN* 1.4 91.9 - - - +
28n THR* 1.3 61.4 + - - +
30n ALA* 4.7 1.8 - - + -
31n SER* 2.8 30.2 + - - -
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Residues in contact with THR 28 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27m PRO* 5.7 0.4 - - - -
26n ASN* 2.8 13.9 + - - -
27n PRO* 1.3 74.5 - - - +
29n VAL* 1.3 60.4 + - - +
31n SER* 3.1 5.1 + - - -
32n THR* 2.5 47.4 + - - +
26o ASN* 4.8 4.0 - - - +
28o THR* 3.1 33.9 - - + +
29o VAL* 4.6 0.7 - - + -
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Residues in contact with VAL 29 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23n ALA 3.3 28.9 - - - +
24n PHE* 3.8 10.3 - - - +
26n ASN* 2.7 14.1 + - + +
28n THR* 1.3 70.7 - - - +
30n ALA* 1.3 64.7 + - - +
32n THR* 3.7 0.2 - - - -
33n ILE* 3.1 43.7 + - + +
28o THR* 4.3 1.3 - - - +
29o VAL* 3.9 30.3 - - + +
32o THR* 3.8 30.3 - - + +
33o ILE* 4.9 6.5 - - + -
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Residues in contact with ALA 30 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30m ALA* 3.6 29.6 - - + -
34m LEU* 4.6 2.5 - - + -
24n PHE* 3.3 35.4 + - + +
25n SER 4.9 0.9 - - - -
26n ASN 2.8 12.1 + - - +
27n PRO* 4.0 4.0 - - + +
29n VAL* 1.3 78.3 - - - +
31n SER* 1.3 57.3 + - - +
33n ILE* 4.0 0.3 - - - +
34n LEU* 2.9 37.8 + - + +
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Residues in contact with SER 31 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25m SER 3.5 24.0 - - - -
27m PRO* 3.5 24.7 - - - +
27n PRO 2.8 19.6 + - - -
28n THR* 3.1 8.1 + - - +
30n ALA* 1.3 77.6 - - - +
32n THR* 1.3 58.4 + - - +
34n LEU* 4.6 0.4 - - - -
35n SER* 2.6 42.6 + - - -
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Residues in contact with THR 32 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28n THR* 2.5 35.4 + - - +
29n VAL 3.7 3.1 - - - -
31n SER* 1.3 78.1 + - - +
33n ILE* 1.3 63.7 + - - +
35n SER* 3.2 3.9 + - - -
36n ASN* 3.1 34.8 + - - +
23o ALA* 3.6 35.4 - - + +
26o ASN* 4.0 15.5 + - + +
29o VAL* 3.7 14.3 - - + +
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Residues in contact with ILE 33 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027 T 5.7 2.2 - - - +
2388 T 3.7 37.5 - - - +
2398 A 4.7 5.8 - - - +
24n PHE* 4.2 14.8 - - + -
29n VAL* 3.1 33.6 + - + +
30n ALA 4.0 1.6 - - - +
32n THR* 1.3 79.0 - - - +
34n LEU* 1.3 58.4 + - - +
36n ASN* 3.1 2.9 + - - +
37n VAL* 3.0 29.5 + - + +
20o LYS* 4.0 24.5 - - + -
23o ALA* 3.8 20.9 - - + -
29o VAL* 4.9 7.9 - - + -
33o ILE* 5.3 5.4 - - + -
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Residues in contact with LEU 34 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2378 A 4.9 7.0 - - + -
2388 T 4.6 14.1 - - - +
21m PHE* 4.1 21.6 - - + -
24m PHE* 3.5 41.5 - - + +
25m SER* 3.9 25.4 - - - -
30m ALA* 4.5 0.4 - - + -
24n PHE* 4.0 23.1 - - + -
30n ALA* 2.9 27.1 + - + +
31n SER 4.3 0.4 - - - +
33n ILE* 1.3 76.8 - - - +
35n SER* 1.3 52.7 + - - +
37n VAL* 3.4 8.7 + - + +
38n SER* 2.6 37.1 + - - -
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Residues in contact with SER 35 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25m SER* 4.6 8.2 - - - -
31n SER* 2.6 27.0 + - - -
32n THR* 3.2 6.2 + - - -
34n LEU* 1.3 78.2 - - - +
36n ASN* 1.3 69.6 + - - +
38n SER* 3.3 20.1 + - - -
39n PRO* 4.1 3.6 - - - +
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Residues in contact with ASN 36 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32n THR* 3.1 23.8 + - - +
33n ILE 3.1 5.6 + - - +
35n SER* 1.3 86.7 + - - +
37n VAL* 1.3 58.5 + - - +
38n SER 3.3 0.7 + - - -
39n PRO* 3.6 12.3 - - - +
40n VAL* 4.3 2.3 - - - +
19o ALA* 3.4 30.2 + - + +
22o ASN* 4.0 9.5 - - - +
23o ALA* 3.4 31.3 - - + +
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Residues in contact with VAL 37 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2378 A 4.1 20.9 - - - +
2388 T 3.9 6.3 - - - +
21m PHE* 4.6 9.0 - - + -
33n ILE* 3.0 21.3 + - + +
34n LEU* 3.5 17.0 - - + +
36n ASN* 1.3 76.7 - - - +
38n SER* 1.3 64.4 + - - +
39n PRO* 3.5 1.3 - - - -
40n VAL* 3.3 9.1 + - + +
41n ALA* 2.8 23.0 + - + +
16o LYS* 4.9 8.1 - - + -
19o ALA* 3.7 22.7 - - + +
20o LYS* 3.7 27.1 - - + -
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Residues in contact with SER 38 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21m PHE* 3.6 21.8 - - - -
22m ASN* 5.5 2.5 + - - -
25m SER* 4.6 5.4 + - - -
34n LEU 2.6 21.3 + - - -
35n SER* 3.3 15.7 - - - -
37n VAL* 1.3 81.1 - - - +
39n PRO* 1.4 72.9 - - - +
41n ALA* 2.9 10.6 + - - +
42n GLN* 3.0 25.1 + - - +
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Residues in contact with PRO 39 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35n SER 4.1 4.3 - - - +
36n ASN 3.6 12.6 - - - +
37n VAL 3.5 1.6 - - - -
38n SER* 1.4 97.6 - - - +
40n VAL* 1.3 68.9 + - + +
42n GLN* 3.4 20.4 + - - +
43n GLN* 3.1 21.1 + - - +
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Residues in contact with VAL 40 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2378 A 4.8 1.8 - - - +
36n ASN 4.3 5.6 - - - +
37n VAL* 3.5 10.8 - - + +
38n SER 3.0 0.4 - - - -
39n PRO* 1.3 78.1 - - + +
41n ALA* 1.3 67.3 + - - +
43n GLN* 3.1 9.3 + - + +
44n ASN* 3.1 32.9 + - - +
12o GLN* 5.2 1.1 - - - +
15o ALA* 4.0 29.4 - - + +
16o LYS* 3.9 33.0 - - + +
19o ALA* 4.3 14.1 - - + -
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Residues in contact with ALA 41 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2368 T 4.2 2.5 - - - +
2378 A 3.7 35.6 - - - -
17m TRP* 4.1 17.0 - - + -
21m PHE* 4.3 11.4 - - + -
37n VAL 2.8 13.0 + - - +
38n SER 3.3 9.0 - - - +
40n VAL* 1.3 77.2 - - - +
42n GLN* 1.3 58.1 + - - +
44n ASN* 3.1 1.9 + - - +
45n PHE* 2.8 31.9 + - - +
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Residues in contact with GLN 42 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14m TYR* 3.7 12.2 + - - +
17m TRP* 4.3 10.3 - - + -
18m GLN* 3.2 41.1 - - - +
21m PHE* 5.8 0.4 - - + -
22m ASN* 4.7 2.2 + - - -
38n SER* 3.0 20.7 + - - +
39n PRO* 3.5 29.0 - - - +
40n VAL 3.1 0.2 - - - -
41n ALA* 1.3 76.0 - - - +
43n GLN* 1.3 57.1 + - - +
45n PHE* 3.7 0.9 - - - +
46n GLN* 2.9 43.9 + - - +
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Residues in contact with GLN 43 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J SER* 5.2 5.9 + - - -
12J GLN* 6.2 2.0 - - - +
43K GLN* 3.1 40.7 - - - +
39n PRO 3.1 9.6 + - - +
40n VAL* 3.1 12.4 + - - +
42n GLN* 1.3 80.4 - - - +
44n ASN* 1.3 59.7 + - - +
46n GLN* 3.4 14.6 + - - +
47n THR* 2.6 61.1 + - - +
12o GLN* 5.3 8.5 - - + +
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Residues in contact with ASN 44 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2368 T 3.5 29.6 - - - +
2378 A 3.0 21.2 + - - -
40n VAL* 3.1 24.0 + - - +
41n ALA 3.6 2.9 - - - +
43n GLN* 1.3 75.7 - - - +
45n PHE* 1.3 65.2 + - - +
47n THR* 3.4 4.5 + - - -
48n ASN* 3.1 22.7 + - - +
8o ARG* 3.6 24.9 - - - +
12o GLN* 2.9 33.7 + - - +
16o LYS* 5.0 4.4 - - - +
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Residues in contact with PHE 45 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1157 A 5.2 5.4 - - - -
2358 A 4.6 10.5 - + - -
2368 T 3.6 23.7 - - - -
10m TYR* 4.1 2.2 - + - -
13m ARG* 4.5 7.0 - - + -
14m TYR* 3.4 43.1 - + + -
17m TRP* 3.5 60.3 - + + -
41n ALA 2.8 16.8 + - - +
42n GLN 3.7 2.9 - - - +
44n ASN* 1.3 76.8 - - - +
46n GLN* 1.3 63.7 + - - +
49n VAL* 3.0 64.3 + - + +
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Residues in contact with GLN 46 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J SER* 4.3 26.5 + - - +
10m TYR* 3.3 21.1 + - - +
14m TYR* 2.9 38.7 + - + -
42n GLN* 2.9 34.9 + - - +
43n GLN* 3.7 14.8 + - - +
45n PHE* 1.3 77.7 - - - +
47n THR* 1.3 62.7 + - - +
50n PRO* 3.1 22.0 - - - +
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Residues in contact with THR 47 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J SER* 5.8 4.7 - - - -
11J SER* 5.0 5.7 + - - -
43n GLN* 2.6 43.0 + - - +
44n ASN* 3.7 6.2 - - - -
45n PHE 3.2 0.4 - - - -
46n GLN* 1.3 79.5 - - - +
48n ASN* 1.3 74.0 + - - +
50n PRO* 3.7 6.8 - - - +
51n LYS* 3.4 23.4 - - - +
12o GLN* 4.6 13.9 + - - +
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Residues in contact with ASN 48 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2358 A 3.8 20.4 - - - +
2368 T 3.1 20.8 + - - -
44n ASN 3.1 10.4 + - - +
47n THR* 1.3 86.4 - - - +
49n VAL* 1.3 62.6 + - - +
50n PRO* 3.4 1.8 - - - -
51n LYS* 3.0 33.8 + - + +
52n PHE* 3.1 27.1 - - + -
88n ASN* 4.9 4.7 + - - +
7o SER 3.9 14.6 + - - +
8o ARG* 3.4 14.8 - - - +
12o GLN* 5.2 2.4 - - - +
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Residues in contact with VAL 49 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2358 A 3.9 27.6 - - + +
2368 T 5.2 0.2 - - - -
10m TYR* 3.8 9.6 - - + -
13m ARG* 3.7 27.1 - - - +
45n PHE* 3.0 63.4 + - + +
48n ASN* 1.3 71.3 - - - +
50n PRO* 1.4 61.0 - - + +
51n LYS 3.0 4.0 - - - -
52n PHE* 2.8 30.4 + - - +
53n THR 3.2 6.6 + - - -
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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
------------------------------------------------------------
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