Contacts of the helix formed by residues 26 - 49 (chain t) 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 t).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22t ASN 4.5 2.0 - - - +
23t ALA 3.1 16.3 + - - +
24t PHE 3.0 1.6 + - - -
25t SER* 1.3 78.5 + - - +
27t PRO* 1.4 68.4 - - - +
28t THR* 2.9 24.5 + - - -
29t VAL* 2.7 36.8 + - + -
30t ALA* 2.8 11.0 + - - -
32u THR* 4.0 18.4 + - + +
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Residues in contact with PRO 27 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27s PRO* 3.5 33.6 - - + +
28s THR* 5.5 1.3 - - + -
31s SER* 3.5 18.8 - - - +
25t SER 3.2 6.6 - - - +
26t ASN* 1.4 93.2 - - - +
28t THR* 1.3 60.8 + - - +
30t ALA* 4.0 2.6 - - + +
31t SER* 2.8 30.1 + - - -
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Residues in contact with THR 28 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27s PRO* 5.7 0.4 - - - -
26t ASN* 2.8 13.9 + - - -
27t PRO* 1.3 74.4 - - - +
29t VAL* 1.3 60.6 + - - +
31t SER* 3.1 4.5 + - - -
32t THR* 2.5 47.1 + - - +
26u ASN* 4.8 4.0 - - - +
28u THR* 3.1 33.5 - - + +
29u VAL* 4.6 0.7 - - + -
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Residues in contact with VAL 29 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23t ALA 3.3 29.2 - - - +
24t PHE* 3.8 9.4 - - - -
26t ASN* 2.7 14.4 + - + +
28t THR* 1.3 70.4 - - - +
30t ALA* 1.3 66.7 + - - +
32t THR* 3.7 0.3 - - - -
33t ILE* 3.1 44.2 + - + +
28u THR 4.3 0.9 - - - +
29u VAL* 3.9 29.4 - - + +
32u THR* 3.8 31.2 - - + +
33u ILE* 4.9 6.3 - - + -
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Residues in contact with ALA 30 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30s ALA* 3.6 28.7 - - + -
34s LEU* 4.6 2.7 - - + -
24t PHE* 3.3 35.8 + - + +
25t SER 4.9 1.1 - - - -
26t ASN 2.8 12.6 + - - +
27t PRO* 4.0 3.8 - - + +
29t VAL* 1.3 78.9 - - - +
31t SER* 1.3 58.5 + - - +
33t ILE* 4.0 0.3 - - - +
34t LEU* 2.9 36.9 + - + +
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Residues in contact with SER 31 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25s SER 3.5 24.2 + - - -
27s PRO* 3.5 25.1 - - - +
27t PRO 2.8 21.2 + - - -
28t THR* 3.1 8.0 + - - -
30t ALA* 1.3 77.4 - - - +
32t THR* 1.3 58.2 + - - +
34t LEU* 4.5 0.7 - - - +
35t SER* 2.6 42.5 + - - -
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Residues in contact with THR 32 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28t THR* 2.5 34.3 + - - +
29t VAL 3.7 3.8 - - - -
30t ALA 3.3 0.2 - - - -
31t SER* 1.3 78.4 + - - +
33t ILE* 1.3 62.4 + - - +
35t SER* 3.2 3.5 + - - -
36t ASN* 3.1 35.4 + - - +
23u ALA* 3.6 34.8 - - + +
26u ASN* 4.0 15.4 + - + +
29u VAL* 3.7 15.6 - - + +
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Residues in contact with ILE 33 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667 T 5.7 2.5 - - - +
2748 T 3.7 37.5 - - - +
2758 A 4.7 7.2 - - - +
24t PHE* 4.2 14.1 - - + -
29t VAL* 3.1 35.0 + - + +
30t ALA 4.0 2.2 - - - +
32t THR* 1.3 77.9 - - - +
34t LEU* 1.3 59.4 + - - +
36t ASN* 3.1 3.1 + - - +
37t VAL* 3.0 29.8 + - + +
20u LYS* 4.0 22.9 - - + -
23u ALA* 3.8 22.9 - - + -
29u VAL* 4.9 7.9 - - + -
33u ILE* 5.3 5.4 - - + -
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Residues in contact with LEU 34 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2738 A 4.9 7.0 - - + -
2748 T 4.6 13.9 - - - +
21s PHE* 4.1 21.2 - - + -
24s PHE* 3.4 41.5 - - + +
25s SER* 3.9 25.8 - - - -
30s ALA* 4.5 0.4 - - + -
24t PHE* 4.0 22.4 - - + -
30t ALA* 2.9 27.1 + - + +
31t SER 4.3 0.4 - - - +
33t ILE* 1.3 78.5 - - - +
35t SER* 1.3 52.0 + - - +
37t VAL* 3.4 8.5 + - + +
38t SER* 2.6 37.1 + - - -
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Residues in contact with SER 35 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25s SER* 4.6 8.9 - - - -
31t SER* 2.6 26.8 + - - -
32t THR* 3.2 6.4 + - - -
34t LEU* 1.3 77.7 - - - +
36t ASN* 1.3 69.5 + - - +
38t SER* 3.4 20.3 + - - -
39t PRO* 4.1 3.5 - - - +
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Residues in contact with ASN 36 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32t THR* 3.1 24.4 + - - +
33t ILE 3.1 5.0 + - - +
35t SER* 1.3 85.7 + - - +
37t VAL* 1.3 59.0 + - - +
38t SER 3.3 0.8 + - - -
39t PRO* 3.6 12.5 - - - +
40t VAL* 4.3 1.7 - - - +
19u ALA* 3.4 29.8 + - + +
22u ASN* 4.0 10.3 - - - +
23u ALA* 3.4 30.8 - - + +
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Residues in contact with VAL 37 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2738 A 4.1 20.6 - - - +
2748 T 3.9 6.1 - - - +
21s PHE* 4.6 9.4 - - + -
33t ILE* 3.0 21.1 + - + +
34t LEU* 3.5 16.6 - - + +
36t ASN* 1.3 75.1 - - - +
38t SER* 1.3 65.0 + - - +
39t PRO* 3.5 1.3 - - - -
40t VAL* 3.3 10.0 + - + +
41t ALA* 2.8 23.1 + - + +
16u LYS* 4.9 7.6 - - + -
19u ALA* 3.7 22.4 - - + -
20u LYS* 3.7 28.0 - - + -
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Residues in contact with SER 38 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21s PHE* 3.6 21.8 - - - -
22s ASN* 5.5 2.5 + - - -
25s SER* 4.6 5.0 + - - -
34t LEU 2.6 20.7 + - - -
35t SER* 3.4 15.5 - - - -
37t VAL* 1.3 81.5 - - - +
39t PRO* 1.4 72.6 - - - +
41t ALA* 2.9 10.9 + - - +
42t GLN* 3.0 25.7 + - - +
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Residues in contact with PRO 39 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35t SER 4.1 4.3 - - - +
36t ASN 3.6 11.7 - - - +
37t VAL 3.5 2.2 - - - -
38t SER* 1.4 96.5 - - - +
40t VAL* 1.3 68.4 + - + +
42t GLN* 3.4 19.8 + - - +
43t GLN* 3.1 21.0 + - - +
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Residues in contact with VAL 40 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2738 A 4.8 1.3 - - - +
36t ASN 4.3 5.6 - - - +
37t VAL* 3.5 11.9 - - + +
38t SER 3.0 0.6 - - - -
39t PRO* 1.3 78.5 - - + +
41t ALA* 1.3 67.1 + - - +
43t GLN* 3.1 8.8 + - - +
44t ASN* 3.1 33.5 + - - +
12u GLN* 5.2 1.3 - - - +
15u ALA* 4.0 29.2 - - + +
16u LYS* 3.9 33.2 - - + +
19u ALA* 4.3 13.9 - - + -
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Residues in contact with ALA 41 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2728 T 4.2 2.7 - - - +
2738 A 3.7 35.6 + - - -
17s TRP* 4.1 17.4 - - + -
21s PHE* 4.3 11.4 - - + -
37t VAL 2.8 13.1 + - - +
38t SER 3.3 8.7 - - - +
40t VAL* 1.3 76.5 - - - +
42t GLN* 1.3 58.6 + - - +
44t ASN* 3.1 2.6 + - - +
45t PHE* 2.8 32.1 + - - +
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Residues in contact with GLN 42 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14s TYR* 3.7 11.9 + - - +
17s TRP* 4.3 11.0 - - + -
18s GLN* 3.2 41.5 - - - +
21s PHE* 5.8 0.6 - - + -
22s ASN* 4.7 1.8 + - - -
38t SER* 3.0 21.0 + - - +
39t PRO* 3.5 29.1 - - - +
40t VAL 3.1 0.2 - - - -
41t ALA* 1.3 76.4 - - - +
43t GLN* 1.3 57.8 + - - +
45t PHE* 3.4 1.2 + - - +
46t GLN* 2.9 42.8 + - - +
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Residues in contact with GLN 43 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P SER* 5.2 5.7 + - - -
12P GLN* 6.2 1.8 - - - +
43Q GLN* 3.1 40.0 - - - +
39t PRO 3.1 9.6 + - - +
40t VAL* 3.1 11.3 + - - +
42t GLN* 1.3 80.5 - - - +
44t ASN* 1.3 61.0 + - - +
46t GLN* 3.7 14.0 + - - +
47t THR* 2.6 61.0 + - - +
12u GLN* 5.3 8.1 - - + +
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Residues in contact with ASN 44 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687 T 5.5 0.2 + - - -
2728 T 3.5 29.9 - - - +
2738 A 3.0 21.2 + - - -
40t VAL* 3.1 22.9 + - - +
41t ALA 3.6 3.1 - - - +
43t GLN* 1.3 76.8 - - - +
45t PHE* 1.3 65.9 + - - +
47t THR* 3.4 4.7 + - - -
48t ASN* 3.1 22.5 + - - +
8u ARG* 3.6 24.5 - - - +
12u GLN* 2.9 34.0 + - - +
16u LYS* 5.0 4.9 - - - +
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Residues in contact with PHE 45 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797 A 5.2 5.4 - - - -
2718 A 4.6 10.3 - + - -
2728 T 3.6 23.4 - - - -
10s TYR* 4.1 1.8 - + - -
13s ARG* 4.5 6.7 - - + -
14s TYR* 3.4 43.1 - + + -
17s TRP* 3.5 60.3 - + + -
41t ALA 2.8 17.4 + - - +
42t GLN 3.7 3.4 - - - +
44t ASN* 1.3 76.1 - - - +
46t GLN* 1.3 65.0 + - - +
49t VAL* 3.0 64.5 + - + +
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Residues in contact with GLN 46 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P SER* 4.3 25.5 - - - +
10s TYR* 3.3 21.0 + - - +
14s TYR* 2.9 39.4 + - + -
42t GLN* 2.9 33.4 + - - +
43t GLN* 3.7 14.7 + - - +
45t PHE* 1.3 77.0 - - - +
47t THR* 1.3 62.7 + - - +
50t PRO* 3.1 21.8 - - - +
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Residues in contact with THR 47 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P SER* 6.0 1.3 - - - -
11P SER* 5.0 5.8 - - - -
43t GLN* 2.6 42.8 + - - +
44t ASN* 3.7 6.5 - - - -
46t GLN* 1.3 79.5 - - - +
48t ASN* 1.3 73.9 + - - +
50t PRO* 3.7 6.4 - - - +
51t LYS* 3.4 23.1 - - - +
12u GLN* 4.6 13.2 + - - +
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Residues in contact with ASN 48 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2718 A 3.8 20.0 - - - +
2728 T 3.1 20.6 + - - -
44t ASN 3.1 11.3 + - - +
47t THR* 1.3 86.9 - - - +
49t VAL* 1.3 62.9 + - - +
50t PRO* 3.4 1.6 - - - -
51t LYS* 3.0 33.9 + - + +
52t PHE* 3.1 27.5 - - + -
88t ASN* 4.9 4.7 + - - -
7u SER 3.9 14.6 + - - +
8u ARG* 3.4 14.6 - - - +
12u GLN* 5.2 2.0 - - - +
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Residues in contact with VAL 49 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2718 A 3.9 28.5 - - + +
10s TYR* 3.8 10.1 - - + -
13s ARG* 3.7 26.7 - - - +
45t PHE* 3.0 65.0 + - + +
48t ASN* 1.3 71.5 - - - +
50t PRO* 1.4 61.0 - - + +
51t LYS 3.0 4.0 - - - -
52t PHE* 2.8 30.9 + - - +
53t THR 3.2 7.1 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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