Contacts of the helix formed by residues 9 - 26 (chain r) 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 r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53q THR* 4.2 5.2 - - - -
8r ARG* 1.3 76.1 - - - +
10r TYR* 1.3 66.4 + - - +
11r SER* 2.7 27.9 + - - -
12r GLN* 2.8 24.8 + - - +
13r ARG* 3.0 20.8 + - - +
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Residues in contact with TYR 10 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45q PHE* 5.1 0.7 - + - -
46q GLN* 5.2 14.1 + - + +
49q VAL* 4.6 6.1 - - + -
50q PRO* 3.7 42.0 - - + -
53q THR* 3.1 40.4 - - + +
9r SER* 1.3 75.2 - - - +
11r SER* 1.3 76.6 + - - +
13r ARG* 3.5 6.6 - - - +
14r TYR* 2.8 49.7 + + + -
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Residues in contact with SER 11 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9r SER* 2.7 22.0 + - - -
10r TYR* 1.3 101.6 - - - +
12r GLN* 1.3 59.2 + - - +
14r TYR* 3.9 3.9 - - - +
15r ALA* 2.9 29.5 + - - +
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Residues in contact with GLN 12 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2658 A 4.1 2.9 + - - -
7r SER 4.7 2.1 + - - +
8r ARG* 3.6 26.7 - - - +
9r SER* 2.8 38.5 + - - +
10r TYR 3.1 0.2 - - - -
11r SER* 1.3 82.8 + - - +
13r ARG* 1.3 65.4 + - - +
15r ALA* 3.7 5.8 - - - +
16r LYS* 3.1 25.5 + - - +
40s VAL* 5.0 2.8 - - - +
43s GLN* 5.3 7.6 - - + +
44s ASN* 2.9 33.0 + - - +
47s THR* 4.9 15.2 + - - +
48s ASN* 5.5 2.8 - - - +
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Residues in contact with ARG 13 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857 A 3.9 15.2 + - - -
867 T 4.8 5.1 + - - -
2648 T 3.8 30.7 + - + +
2658 A 3.6 57.1 + - - +
45q PHE* 4.5 9.2 - - + -
49q VAL* 3.8 20.3 + - + +
52q PHE* 4.5 4.4 - - - +
53q THR* 2.7 48.6 + - - +
56q ASN* 4.0 11.2 - - - +
8r ARG* 4.3 8.3 - - + -
9r SER 3.0 21.6 + - - +
10r TYR* 3.5 7.2 - - + +
12r GLN* 1.3 76.6 - - - +
14r TYR* 1.3 57.2 + - - +
16r LYS 3.7 0.2 + - - -
17r TRP* 3.0 29.4 + - - +
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Residues in contact with TYR 14 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42q GLN* 3.9 10.5 + - - +
45q PHE* 3.5 33.6 - + + -
46q GLN* 3.4 41.8 + - + -
10r TYR* 2.8 35.4 + + + +
11r SER* 3.9 4.9 - - - +
13r ARG* 1.3 75.5 - - - +
15r ALA* 1.3 71.5 + - - +
17r TRP* 3.0 13.9 + + - +
18r GLN* 2.7 59.5 + - + +
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Residues in contact with ALA 15 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11r SER 2.9 20.4 + - - +
12r GLN* 3.3 7.8 + - - +
14r TYR* 1.3 84.4 - - + +
16r LYS* 1.3 61.3 + - - +
18r GLN* 3.3 5.8 + - - +
19r ALA* 3.1 19.9 + - - +
40s VAL* 4.1 21.4 - - + +
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Residues in contact with LYS 16 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767 T 3.7 32.9 + - - +
777 A 2.8 31.3 + - - -
2648 T 3.3 32.4 + - - +
2658 A 3.9 21.9 + - - +
12r GLN 3.1 13.9 + - - +
15r ALA* 1.3 78.0 - - - +
17r TRP* 1.3 65.9 + - - +
19r ALA* 3.1 4.5 + - - +
20r LYS* 3.0 25.4 + - + +
37s VAL* 4.7 8.1 - - + -
40s VAL* 3.9 18.6 - - + +
44s ASN* 5.5 2.7 - - - +
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Residues in contact with TRP 17 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877 A 3.8 34.7 + - + -
2638 A 3.8 27.1 + - + -
2648 T 3.8 19.8 - - - +
41q ALA* 4.1 20.2 - - + -
42q GLN* 4.2 7.6 - - + -
45q PHE* 3.5 54.4 - + + -
13r ARG 3.0 20.8 + - - +
14r TYR* 3.0 15.5 + + - +
16r LYS* 1.3 75.3 - - - +
18r GLN* 1.3 93.2 + - - +
20r LYS* 3.4 2.5 + - - +
21r PHE* 2.9 53.6 + + + +
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Residues in contact with GLN 18 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42q GLN* 3.2 39.7 - - - +
14r TYR* 2.7 58.4 + - + +
15r ALA* 3.5 7.0 - - - +
17r TRP* 1.3 82.4 - - - +
19r ALA* 1.3 61.8 + - - +
21r PHE* 3.2 5.9 + - - +
22r ASN* 2.9 63.8 + - - +
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Residues in contact with ALA 19 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15r ALA 3.1 9.4 + - - +
16r LYS* 3.1 11.0 + - - +
18r GLN* 1.3 79.5 - - - +
20r LYS* 1.3 57.8 + - - +
22r ASN* 3.5 10.1 + - - +
23r ALA* 3.0 26.9 + - - +
36s ASN* 3.4 34.9 - - - +
37s VAL* 3.7 16.6 - - + -
40s VAL* 4.5 4.9 - - + -
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Residues in contact with LYS 20 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777 A 2.8 30.7 + - - +
787 T 3.1 26.1 + - - -
2638 A 3.4 45.4 + - + +
2648 T 3.2 21.4 + - - +
16r LYS* 3.0 21.6 + - + +
17r TRP 3.9 2.9 - - - +
19r ALA* 1.3 75.1 - - - +
21r PHE* 1.3 66.1 + - - +
23r ALA* 3.3 4.4 + - + +
24r PHE* 3.0 24.3 + - - +
33s ILE* 3.9 19.5 - - + -
37s VAL* 3.6 17.5 - - + -
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Residues in contact with PHE 21 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877 A 5.7 2.9 - + - -
887 T 4.5 22.9 - - - -
2628 T 6.0 2.0 - - - -
2638 A 5.2 2.6 - - - -
34q LEU* 3.9 29.8 - - + -
37q VAL* 4.5 4.9 - - + -
38q SER* 3.5 37.7 - - - -
41q ALA* 4.5 9.4 - - + -
42q GLN* 5.8 0.2 - - + -
17r TRP* 2.9 51.0 + + + +
18r GLN* 3.6 11.7 - - - +
20r LYS* 1.3 77.2 - - - +
22r ASN* 1.3 71.2 - - - +
24r PHE* 3.3 11.1 + + - +
25r SER* 3.0 24.2 + - - -
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Residues in contact with ASN 22 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38q SER* 5.5 2.1 + - - -
42q GLN* 4.6 3.5 + - - -
18r GLN* 2.9 52.5 + - - +
19r ALA* 3.5 8.7 - - - +
21r PHE* 1.3 79.5 - - - +
23r ALA* 1.3 62.3 + - - +
25r SER* 2.6 26.0 + - - -
26r ASN* 3.6 4.3 + - - +
36s ASN* 4.0 11.7 - - - +
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Residues in contact with ALA 23 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19r ALA 3.0 15.5 + - - +
20r LYS* 3.5 9.0 - - + +
22r ASN* 1.3 78.3 - - - +
24r PHE* 1.3 63.0 + - - +
26r ASN* 3.1 21.7 + - - +
29r VAL* 3.3 11.1 - - - +
32s THR* 3.6 15.0 - - + -
33s ILE* 3.8 27.1 - - + -
36s ASN* 3.5 15.9 - - - +
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Residues in contact with PHE 24 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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897 A 6.0 0.2 - - - -
2628 T 3.7 52.3 - - + +
2638 A 5.4 2.9 - - - +
24q PHE* 4.4 9.2 - + - -
34q LEU* 3.5 30.5 - - + -
20r LYS 3.0 17.4 + - - +
21r PHE* 3.7 11.7 - + - +
23r ALA* 1.3 77.4 - - - +
25r SER* 1.3 62.1 + - - +
26r ASN 3.0 1.6 + - - -
29r VAL* 3.8 6.1 - - - -
30r ALA* 3.3 44.1 + - - +
33r ILE* 4.2 19.5 - - + -
34r LEU* 4.0 25.4 - - + -
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Residues in contact with SER 25 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31q SER* 3.4 21.7 + - - +
34q LEU* 3.8 38.1 - - - -
35q SER* 4.5 5.7 - - - -
38q SER* 4.7 6.7 + - - -
21r PHE* 3.0 14.8 + - - -
22r ASN* 2.6 23.3 + - - -
24r PHE* 1.3 75.3 - - - +
26r ASN* 1.3 60.9 + - - +
27r PRO* 3.2 4.5 - - - +
30r ALA* 4.9 0.4 - - - -
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Residues in contact with ASN 26 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22r ASN 3.6 2.7 + - - +
23r ALA 3.1 15.1 + - - +
24r PHE 3.0 1.2 + - - -
25r SER* 1.3 78.6 + - - +
27r PRO* 1.4 67.2 - - - +
28r THR* 2.9 24.0 + - - -
29r VAL* 2.7 37.7 + - + -
30r ALA* 2.8 11.8 + - - -
32s THR* 4.0 18.6 + - + +
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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