Contacts of the helix formed by residues 9 - 26 (chain a) 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 a).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8a ARG* 1.3 74.4 - - - +
10a TYR* 1.3 60.9 + - - +
11a SER* 3.6 9.5 + - - -
12a GLN* 2.8 35.3 + - - +
13a ARG* 2.8 26.5 + - - +
53b THR* 4.3 3.8 - - - -
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Residues in contact with TYR 10 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9a SER* 1.3 73.4 - - - +
11a SER* 1.3 72.4 + - - +
13a ARG* 3.0 4.9 + - + -
14a TYR* 2.9 48.2 + + + +
45b PHE* 4.1 0.6 - + - -
46b GLN* 3.3 35.9 + - - +
49b VAL* 3.8 16.4 - - + -
50b PRO* 3.5 48.5 - - + -
53b THR* 3.5 32.0 - - + +
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Residues in contact with SER 11 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9a SER* 3.2 9.7 + - - -
10a TYR* 1.3 88.1 - - - +
12a GLN* 1.3 59.9 + - - +
14a TYR* 4.1 3.7 - - - +
15a ALA* 3.0 30.2 + - - +
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Residues in contact with GLN 12 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1887 T 4.5 3.4 + - - -
40Z VAL* 5.2 1.5 - - - +
43Z GLN* 5.3 8.2 - - + +
44Z ASN* 2.9 34.0 + - - +
47Z THR* 4.6 18.9 + - - +
48Z ASN* 5.2 1.6 - - - +
7a SER 4.2 5.4 + - - +
8a ARG* 3.6 29.5 - - - +
9a SER* 2.8 39.4 + - - +
11a SER* 1.3 77.4 - - - +
13a ARG* 1.3 66.9 + - - +
15a ALA* 3.7 5.1 - - - +
16a LYS* 3.2 23.7 + - - +
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Residues in contact with ARG 13 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1877 A 3.4 53.5 + - + +
1887 T 3.6 41.1 + - - -
1628 T 4.1 7.3 + - - -
1638 A 5.3 5.7 + - - -
8a ARG* 4.1 6.9 - - - +
9a SER 2.8 21.2 + - - +
10a TYR* 3.4 9.9 - - + +
12a GLN* 1.3 73.5 - - - +
14a TYR* 1.3 63.4 + - - +
17a TRP* 3.1 23.5 + - - +
45b PHE* 4.6 8.3 - - + -
49b VAL* 3.7 21.5 + - - +
52b PHE* 4.6 4.6 - - - +
53b THR* 2.8 43.5 + - - +
56b ASN* 4.3 10.5 - - - +
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Residues in contact with TYR 14 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10a TYR* 2.9 36.0 + + + +
11a SER* 4.1 3.1 - - - +
13a ARG* 1.3 75.9 - - - +
15a ALA* 1.3 68.5 + - - +
17a TRP* 3.1 16.6 + + - +
18a GLN* 2.7 56.9 + - + +
42b GLN* 3.7 8.6 + - - +
45b PHE* 3.4 35.9 - + + -
46b GLN* 2.9 37.1 + - + -
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Residues in contact with ALA 15 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40Z VAL* 4.0 20.9 - - + +
11a SER 3.0 20.8 + - - +
12a GLN* 3.7 7.6 - - - +
14a TYR* 1.3 82.6 - - - +
16a LYS* 1.3 62.8 + - - +
18a GLN* 3.3 6.1 + - - +
19a ALA* 3.2 19.2 + - - +
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Residues in contact with LYS 16 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1877 A 3.3 40.7 + - - +
1887 T 4.3 14.5 + - - +
1538 A 3.8 37.9 + - - +
1548 T 2.8 35.6 + - - +
37Z VAL* 4.9 8.1 - - + -
40Z VAL* 3.9 17.5 - - + +
44Z ASN* 5.0 2.9 - - - +
8a ARG* 6.0 0.2 - - - +
12a GLN 3.2 13.7 + - - +
15a ALA* 1.3 76.2 - - - +
17a TRP* 1.3 66.4 + - - +
19a ALA* 3.1 4.4 + - - +
20a LYS* 3.0 25.2 + - + +
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Residues in contact with TRP 17 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1857 A 5.3 0.4 - - - -
1867 T 3.6 18.8 + - + +
1877 A 3.5 27.5 - - - +
1648 T 2.9 36.8 + + + -
13a ARG 3.1 18.2 + - - +
14a TYR* 3.1 23.2 + + - +
16a LYS* 1.3 76.1 - - - +
18a GLN* 1.3 93.8 + - - +
20a LYS* 3.4 2.2 + - - +
21a PHE* 2.9 52.5 + + + +
41b ALA* 4.1 20.9 - - + -
42b GLN* 4.3 5.2 - - + -
45b PHE* 3.5 45.4 - + + -
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Residues in contact with GLN 18 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14a TYR* 2.7 53.7 + - + +
15a ALA* 3.5 7.2 - - - +
17a TRP* 1.3 88.6 - - - +
19a ALA* 1.3 63.0 + - - +
21a PHE* 3.2 6.3 + - - -
22a ASN* 2.9 63.7 + - - +
42b GLN* 3.2 36.0 - - - +
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Residues in contact with ALA 19 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36Z ASN* 3.4 34.7 - - - +
37Z VAL* 3.7 17.5 - - + -
40Z VAL* 4.3 7.0 - - + -
15a ALA 3.2 9.4 + - - +
16a LYS 3.1 9.1 + - - +
18a GLN* 1.3 81.0 - - - +
20a LYS* 1.3 58.3 + - - +
22a ASN* 3.6 8.8 - - - +
23a ALA* 3.1 27.0 + - - +
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Residues in contact with LYS 20 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1867 T 3.5 40.7 + - + +
1877 A 3.1 30.2 + - - +
1548 T 2.8 32.2 + - - +
1558 A 3.2 26.3 + - - -
33Z ILE* 4.0 20.9 - - + -
37Z VAL* 3.7 15.9 - - + -
16a LYS* 3.0 18.1 + - + +
17a TRP 3.9 3.4 - - - +
19a ALA* 1.3 73.2 - - - +
21a PHE* 1.3 65.6 + - - +
23a ALA* 3.3 4.1 + - + +
24a PHE* 3.0 25.1 + - - +
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Residues in contact with PHE 21 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1857 A 6.1 4.0 - + - -
1867 T 5.6 2.8 - - - +
1648 T 5.8 0.2 - - - -
1658 A 4.5 23.1 - - - -
17a TRP* 2.9 47.3 + + + +
18a GLN* 3.6 10.8 - - - +
20a LYS* 1.3 78.6 - - - +
22a ASN* 1.3 72.4 - - - +
24a PHE* 3.3 11.6 + + - +
25a SER* 3.1 23.0 + - - -
34b LEU* 4.1 31.6 - - + -
37b VAL* 4.6 4.9 - - + -
38b SER* 3.5 36.8 - - - -
41b ALA* 4.3 11.9 - - + -
42b GLN* 5.8 0.2 - - + -
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Residues in contact with ASN 22 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Z ASN* 4.0 11.3 - - - +
18a GLN* 2.9 51.9 + - - +
19a ALA* 3.6 8.3 - - - +
21a PHE* 1.3 80.8 - - - +
23a ALA* 1.3 63.1 + - - +
25a SER* 2.6 26.7 + - - -
26a ASN* 3.6 3.3 + - - +
38b SER* 5.5 2.9 + - - -
42b GLN* 4.7 2.9 + - - -
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Residues in contact with ALA 23 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Z THR* 3.6 15.4 - - + +
33Z ILE* 3.8 27.8 - - + -
36Z ASN* 3.4 16.4 - - - +
19a ALA 3.1 12.8 + - - +
20a LYS* 3.5 11.4 - - - +
21a PHE 3.2 0.2 - - - -
22a ASN* 1.3 78.2 - - - +
24a PHE* 1.3 63.8 + - - +
26a ASN* 3.1 22.2 + - - +
29a VAL* 3.5 9.7 - - - +
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Residues in contact with PHE 24 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1857 A 3.7 52.5 - - + -
1867 T 4.6 8.5 - - - +
20a LYS 3.0 17.0 + - - +
21a PHE* 3.7 12.3 - + - +
23a ALA* 1.3 76.3 - - - +
25a SER* 1.3 62.8 + - - +
26a ASN 3.0 1.4 + - - -
29a VAL* 4.0 6.1 - - - -
30a ALA* 3.3 44.4 + - + +
33a ILE* 4.3 13.9 - - + -
34a LEU* 4.0 22.2 - - + -
24b PHE* 4.4 8.3 - + - -
34b LEU* 3.4 31.2 - - + -
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Residues in contact with SER 25 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21a PHE* 3.1 14.8 + - - -
22a ASN* 2.6 23.4 + - - -
24a PHE* 1.3 76.8 - - - +
26a ASN* 1.3 61.2 + - - +
27a PRO* 3.2 4.0 - - - +
30a ALA* 5.0 0.4 - - - +
31b SER* 3.5 22.0 + - - +
34b LEU* 3.9 36.6 - - - -
35b SER* 4.6 6.0 - - - -
38b SER* 4.6 8.3 + - - -
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Residues in contact with ASN 26 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Z THR* 4.9 3.0 - - - +
32Z THR* 4.0 19.2 + - + +
22a ASN 3.6 2.0 + - - +
23a ALA 3.1 15.5 + - - +
24a PHE 3.0 0.8 + - - +
25a SER* 1.3 78.7 + - - +
27a PRO* 1.4 67.4 - - - +
28a THR* 2.7 31.6 + - - +
29a VAL* 2.7 35.5 + - + -
30a ALA* 2.9 11.5 + - - -
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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
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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