Contacts of the helix formed by residues 9 - 26 (chain q) 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 SER 9 (chain q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47M THR* 5.5 12.1 - - - +
51M LYS* 6.0 5.2 - - - -
8q ARG* 1.3 75.5 - - - +
10q TYR* 1.3 60.5 + - - +
11q SER* 3.6 9.8 + - - -
12q GLN* 2.8 34.7 + - - +
13q ARG* 2.8 27.6 + - - +
53r THR* 4.3 3.4 - - - -
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Residues in contact with TYR 10 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M PRO* 4.9 12.1 - - + -
10N TYR* 2.8 44.6 + + - -
11N SER* 5.5 0.2 - - - -
9q SER* 1.3 73.6 - - - +
11q SER* 1.3 71.4 + - - +
13q ARG* 3.0 5.5 + - + -
14q TYR* 2.9 46.2 + + + +
45r PHE* 4.1 1.1 - + - -
46r GLN* 3.3 35.0 + - - +
49r VAL* 3.8 15.3 - - + -
50r PRO* 3.5 40.6 - - + -
53r THR* 3.5 31.8 - - + +
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Residues in contact with SER 11 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43M GLN* 5.1 9.6 - - - -
46M GLN* 2.8 46.9 + - - +
47M THR* 4.1 4.4 - - - -
50M PRO* 4.8 0.7 - - - +
10N TYR* 5.0 1.6 + - - -
9q SER* 3.2 9.9 + - - -
10q TYR* 1.3 88.2 - - - +
12q GLN* 1.3 60.0 + - - +
14q TYR* 4.1 3.4 - - - +
15q ALA* 3.0 30.5 + - - +
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Residues in contact with GLN 12 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927 T 4.5 3.9 + - - -
43M GLN* 6.1 2.7 - - - +
40p VAL* 5.2 1.9 - - - +
43p GLN* 5.3 9.1 - - + +
44p ASN* 2.9 34.1 + - - +
47p THR* 4.6 19.1 + - - +
48p ASN* 5.2 2.0 - - - +
7q SER 4.2 5.0 + - - +
8q ARG* 3.6 28.0 - - - +
9q SER* 2.8 41.0 + - - +
11q SER* 1.3 77.7 - - - +
13q ARG* 1.3 66.2 + - - +
15q ALA* 3.7 5.8 - - - +
16q LYS* 3.2 23.7 + - - +
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Residues in contact with ARG 13 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917 A 3.4 53.3 + - + +
927 T 3.6 40.8 + - - -
2588 T 4.1 7.3 + - - -
2598 A 5.3 6.1 + - - -
8q ARG* 4.1 6.1 - - + +
9q SER 2.8 22.3 + - - +
10q TYR* 3.0 10.1 + - + +
12q GLN* 1.3 72.4 - - - +
14q TYR* 1.3 63.6 + - - +
17q TRP* 3.1 23.3 + - - +
45r PHE* 4.6 7.6 - - + -
49r VAL* 3.7 21.0 + - - +
52r PHE* 4.6 5.1 - - - +
53r THR* 2.8 44.6 + - - +
56r ASN* 4.3 10.8 - - - +
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Residues in contact with TYR 14 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M GLN* 6.2 1.8 - - - -
10N TYR* 5.5 1.3 - - - -
10q TYR* 2.9 36.7 + + + +
11q SER* 4.1 3.1 - - - +
13q ARG* 1.3 76.6 - - - +
15q ALA* 1.3 69.0 + - - +
17q TRP* 3.1 17.4 + + - +
18q GLN* 2.7 57.1 + - + +
42r GLN* 3.7 8.5 + - - +
45r PHE* 3.4 34.5 - + + -
46r GLN* 2.9 36.8 + - + -
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Residues in contact with ALA 15 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40p VAL* 4.0 22.6 - - + +
11q SER 3.0 20.7 + - - +
12q GLN* 3.4 7.6 + - - +
14q TYR* 1.3 82.4 - - - +
16q LYS* 1.3 62.8 + - - +
18q GLN* 3.3 6.5 + - - +
19q ALA* 3.2 19.4 + - - +
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Residues in contact with LYS 16 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917 A 3.3 41.1 + - - +
927 T 4.3 14.1 + - - +
2498 A 3.8 38.1 + - - +
2508 T 2.8 35.6 + - - +
37p VAL* 4.9 7.6 - - + -
40p VAL* 3.9 19.5 - - + +
44p ASN* 5.0 2.5 - - - +
8q ARG* 6.0 0.4 - - - +
12q GLN 3.2 12.2 + - - +
15q ALA* 1.3 76.8 - - - +
17q TRP* 1.3 67.2 + - - +
19q ALA* 3.1 4.1 + - - +
20q LYS* 3.0 25.8 + - + +
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Residues in contact with TRP 17 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897 A 5.3 0.2 - - - -
907 T 3.6 18.9 + - + +
917 A 3.5 28.8 - - - +
2598 A 5.0 0.4 - + - -
2608 T 2.9 36.8 + - + -
2618 A 5.4 0.2 - - - -
13q ARG 3.1 18.9 + - - +
14q TYR* 3.1 21.4 + + - +
16q LYS* 1.3 75.7 - - - +
18q GLN* 1.3 95.9 + - - +
20q LYS* 3.4 2.0 + - - +
21q PHE* 2.9 51.1 + + + +
41r ALA* 4.1 22.0 - - + -
42r GLN* 4.3 5.2 - - + -
45r PHE* 3.5 42.7 - + + -
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Residues in contact with GLN 18 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14q TYR* 2.7 53.3 + - + +
15q ALA* 3.5 7.0 - - - +
17q TRP* 1.3 87.0 - - - +
19q ALA* 1.3 63.7 + - - +
21q PHE* 3.2 7.1 + - - +
22q ASN* 2.9 63.0 + - - +
42r GLN* 3.2 36.4 - - - +
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Residues in contact with ALA 19 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36p ASN* 3.4 35.0 - - - +
37p VAL* 3.7 17.5 - - + -
40p VAL* 4.3 6.7 - - + -
15q ALA 3.2 9.8 + - - +
16q LYS 3.1 9.1 + - - +
18q GLN* 1.3 80.7 - - - +
20q LYS* 1.3 58.4 + - - +
22q ASN* 3.5 8.4 + - - +
23q ALA* 3.1 25.8 + - - +
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Residues in contact with LYS 20 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907 T 3.5 39.6 + - + +
917 A 3.1 30.2 + - - +
2508 T 2.8 31.1 + - - +
2518 A 3.2 27.4 + - - -
33p ILE* 4.0 21.3 - - + -
37p VAL* 3.7 15.5 - - + -
16q LYS* 3.0 17.7 + - + +
17q TRP 3.9 3.1 - - - +
19q ALA* 1.3 73.7 - - - +
21q PHE* 1.3 66.5 + - - +
23q ALA* 3.3 3.8 + - - +
24q PHE* 3.0 24.8 + - - +
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Residues in contact with PHE 21 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897 A 6.1 3.8 - + - -
907 T 5.6 2.4 - - - +
2608 T 5.8 0.2 - - - -
2618 A 4.5 23.8 - - - -
17q TRP* 2.9 45.9 + + + +
18q GLN* 3.6 11.2 - - - +
20q LYS* 1.3 77.2 - - - +
22q ASN* 1.3 73.4 + - - +
24q PHE* 3.3 12.6 + + - +
25q SER* 3.1 23.2 + - - -
34r LEU* 4.1 31.4 - - + -
37r VAL* 4.6 4.9 - - + -
38r SER* 3.6 35.7 - - - -
41r ALA* 4.3 12.3 - - + -
42r GLN* 5.8 0.2 - - + -
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Residues in contact with ASN 22 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36p ASN* 4.0 11.7 - - - +
18q GLN* 2.9 50.2 + - - +
19q ALA* 3.6 7.5 - - - +
21q PHE* 1.3 81.3 - - - +
23q ALA* 1.3 62.1 + - - +
25q SER* 2.6 25.5 + - - -
26q ASN* 3.6 3.8 + - - +
38r SER* 5.5 2.6 + - - -
42r GLN* 4.7 3.1 + - - -
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Residues in contact with ALA 23 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32p THR* 3.6 15.7 - - + +
33p ILE* 3.8 28.5 - - + -
36p ASN* 3.4 16.4 - - - +
19q ALA 3.1 11.7 + - - +
20q LYS* 3.5 11.7 - - + +
22q ASN* 1.3 78.8 - - - +
24q PHE* 1.3 62.7 + - - +
26q ASN* 3.1 22.3 + - - +
29q VAL* 3.5 9.5 - - - +
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Residues in contact with PHE 24 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897 A 3.7 50.9 - - + -
907 T 4.6 8.5 - - - +
20q LYS 3.0 16.5 + - - +
21q PHE* 3.3 12.3 + + - +
23q ALA* 1.3 76.5 - - - +
25q SER* 1.3 62.0 + - - +
26q ASN 3.0 1.4 + - - -
29q VAL* 4.0 6.3 - - - -
30q ALA* 3.3 45.5 + - + +
33q ILE* 4.3 14.6 - - + -
34q LEU* 4.0 23.6 - - + -
24r PHE* 4.4 9.2 - + - -
34r LEU* 3.4 29.8 - - + -
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Residues in contact with SER 25 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21q PHE* 3.1 15.7 + - - -
22q ASN* 2.6 23.7 + - - -
24q PHE* 1.3 76.1 - - - +
26q ASN* 1.3 61.2 + - - +
27q PRO* 3.2 4.2 - - - +
30q ALA* 5.0 0.4 - - - -
31r SER* 3.5 21.7 - - - +
34r LEU* 3.9 35.0 - - - -
35r SER* 4.6 6.4 - - - -
38r SER* 4.6 8.3 + - - -
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Residues in contact with ASN 26 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28p THR* 4.9 3.0 - - - +
32p THR* 4.0 19.7 + - + +
22q ASN 3.6 2.2 + - - +
23q ALA 3.1 15.8 + - - +
24q PHE 3.0 1.4 + - - -
25q SER* 1.3 78.8 + - - +
27q PRO* 1.4 66.6 - - - +
28q THR* 2.7 33.9 + - - +
29q VAL* 2.7 33.7 + - + -
30q ALA* 2.9 12.3 + - - -
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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