Contacts of the helix formed by residues 9 - 26 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ARG* 1.3 75.1 - - - +
10E TYR* 1.3 59.8 + - - +
11E SER* 3.6 9.5 + - - -
12E GLN* 2.8 35.4 + - - +
13E ARG* 2.8 26.3 + - - +
53F THR* 4.3 3.6 - - - -
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Residues in contact with TYR 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E SER* 1.3 73.3 - - - +
11E SER* 1.3 71.3 + - - +
13E ARG* 3.0 5.5 + - + -
14E TYR* 2.9 47.5 + + + +
45F PHE* 4.1 1.3 - + - -
46F GLN* 3.3 35.7 + - - +
49F VAL* 3.8 16.4 - - + -
50F PRO* 3.5 47.6 - - + -
53F THR* 3.5 32.3 - - + +
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Residues in contact with SER 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E SER* 3.2 9.7 + - - -
10E TYR* 1.3 87.1 - - - +
12E GLN* 1.3 60.0 + - - +
14E TYR* 4.1 3.6 - - - +
15E ALA* 3.0 30.4 + - - +
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Residues in contact with GLN 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3207 T 4.5 3.5 + - - -
40D VAL* 5.2 1.8 - - - +
43D GLN* 5.3 8.9 - - + +
44D ASN* 2.9 34.3 + - - +
47D THR* 4.6 18.7 + - - +
48D ASN* 5.2 1.8 - - - +
7E SER 4.2 4.9 + - - +
8E ARG* 3.6 28.4 - - - +
9E SER* 2.8 39.7 + - - +
11E SER* 1.3 77.8 - - - +
13E ARG* 1.3 66.6 + - - +
15E ALA* 3.7 5.6 - - - +
16E LYS* 3.2 23.6 + - - +
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Residues in contact with ARG 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3197 A 3.4 53.2 + - + +
3207 T 3.6 40.2 + - - -
308 T 4.1 7.7 + - - -
318 A 5.3 5.7 + - - -
8E ARG* 4.1 6.1 - - + +
9E SER 2.8 22.7 + - - +
10E TYR* 3.0 10.5 + - + +
12E GLN* 1.3 72.3 - - - +
14E TYR* 1.3 63.2 + - - +
16E LYS 3.7 0.2 + - - -
17E TRP* 3.1 23.0 + - - +
45F PHE* 4.6 7.0 - - + -
49F VAL* 3.7 20.6 + - + +
52F PHE* 4.6 4.9 - - - +
53F THR* 2.8 45.2 + - - +
56F ASN* 4.3 10.4 - - - +
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Residues in contact with TYR 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E TYR* 2.9 36.7 + + + +
11E SER* 4.1 2.9 - - - +
13E ARG* 1.3 76.5 - - - +
15E ALA* 1.3 68.1 + - - +
17E TRP* 3.1 15.5 + + - +
18E GLN* 2.7 58.1 + - + +
42F GLN* 3.7 9.2 + - - +
45F PHE* 3.4 35.7 - + + -
46F GLN* 2.9 36.5 + - + -
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Residues in contact with ALA 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D VAL* 4.0 22.2 - - + +
11E SER 3.0 20.7 + - - +
12E GLN* 3.4 7.6 + - - +
14E TYR* 1.3 81.7 - - - +
16E LYS* 1.3 62.4 + - - +
18E GLN* 3.3 6.7 + - - +
19E ALA* 3.2 20.3 + - - +
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Residues in contact with LYS 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3197 A 3.3 42.4 + - - +
3207 T 4.3 15.4 + - - +
218 A 3.8 37.4 + - - +
228 T 2.8 35.4 + - - +
37D VAL* 4.9 7.9 - - + -
40D VAL* 3.9 19.5 - - + +
44D ASN* 5.0 2.5 - - - +
8E ARG* 6.0 0.2 - - - +
12E GLN 3.2 12.8 + - - +
15E ALA* 1.3 77.0 - - - +
17E TRP* 1.3 66.7 + - - +
19E ALA* 3.1 4.1 + - - +
20E LYS* 3.0 25.9 + - + +
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Residues in contact with TRP 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3177 A 5.3 0.2 - - - -
3187 T 3.6 18.8 + - + +
3197 A 3.5 28.4 - - - +
318 A 5.0 0.2 - + - -
328 T 2.9 37.8 + - + -
13E ARG 3.1 19.1 + - - +
14E TYR* 3.1 21.9 + + - +
16E LYS* 1.3 75.3 - - - +
18E GLN* 1.3 94.8 + - - +
20E LYS* 3.4 1.8 + - - +
21E PHE* 2.9 52.0 + + + +
41F ALA* 4.1 21.8 - - + -
42F GLN* 4.3 5.4 - - + -
45F PHE* 3.5 44.9 - + + -
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Residues in contact with GLN 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E TYR* 2.7 54.2 + - + +
15E ALA* 3.5 7.4 - - - +
16E LYS 3.1 0.2 - - - -
17E TRP* 1.3 86.8 - - - +
19E ALA* 1.3 63.2 + - - +
21E PHE* 3.2 6.5 + - - +
22E ASN* 2.9 63.3 + - - +
42F GLN* 3.2 35.9 - - - +
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Residues in contact with ALA 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ASN* 3.4 35.0 - - - +
37D VAL* 3.7 17.0 - - + -
40D VAL* 4.3 7.4 - - + -
15E ALA 3.2 8.8 + - - +
16E LYS 3.1 9.3 + - - +
18E GLN* 1.3 80.7 - - - +
20E LYS* 1.3 57.5 + - - +
22E ASN* 3.5 9.2 + - - +
23E ALA* 3.1 26.2 + - - +
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Residues in contact with LYS 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3187 T 3.5 40.6 + - + +
3197 A 3.1 30.8 + - - +
228 T 2.8 31.3 + - - +
238 A 3.2 27.2 + - - -
33D ILE* 4.0 21.8 - - + -
37D VAL* 3.7 15.5 - - + -
16E LYS* 3.0 20.9 + - + +
17E TRP 3.9 2.7 - - - +
19E ALA* 1.3 73.2 - - - +
21E PHE* 1.3 66.1 + - - +
23E ALA* 3.3 4.3 + - - +
24E PHE* 3.0 24.6 + - - +
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Residues in contact with PHE 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3177 A 6.1 3.8 - + - -
3187 T 5.6 3.0 - - + +
328 T 5.8 0.4 - - - -
338 A 4.5 24.2 - - - -
17E TRP* 2.9 46.1 + + + +
18E GLN* 3.2 10.3 + - - +
20E LYS* 1.3 76.6 - - - +
22E ASN* 1.3 73.4 + - - +
24E PHE* 3.3 12.6 + + - +
25E SER* 3.1 23.1 + - - -
34F LEU* 4.1 31.4 - - + -
37F VAL* 4.6 4.5 - - + -
38F SER* 3.6 35.7 - - - -
41F ALA* 4.3 12.1 - - + -
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Residues in contact with ASN 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ASN* 4.0 12.6 - - - +
18E GLN* 2.9 50.9 + - - +
19E ALA* 3.6 7.5 - - - +
21E PHE* 1.3 80.9 - - - +
23E ALA* 1.3 62.5 + - - +
25E SER* 2.6 25.2 + - - -
26E ASN* 3.6 3.6 + - - +
38F SER* 5.5 2.8 + - - -
42F GLN* 4.7 3.3 + - - -
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Residues in contact with ALA 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D THR* 3.6 15.2 - - + +
33D ILE* 3.8 28.5 - - + +
36D ASN* 3.4 16.7 - - - +
19E ALA 3.1 11.7 + - - +
20E LYS* 3.5 11.2 - - - +
22E ASN* 1.3 78.5 - - - +
24E PHE* 1.3 64.3 + - - +
26E ASN* 3.1 22.0 + - - +
29E VAL* 3.5 9.9 - - - +
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Residues in contact with PHE 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3177 A 3.7 51.8 - - + -
3187 T 4.6 8.3 - - - +
338 A 6.3 0.2 - - - -
20E LYS 3.0 17.0 + - - +
21E PHE* 3.7 12.8 - + - +
23E ALA* 1.3 76.7 - - - +
25E SER* 1.3 62.2 + - - +
26E ASN 3.0 1.6 + - - -
29E VAL* 4.0 6.3 - - - -
30E ALA* 3.3 44.5 + - + +
33E ILE* 4.3 14.6 - - + -
34E LEU* 4.0 22.9 - - + -
24F PHE* 4.4 8.7 - + - -
34F LEU* 3.4 30.7 - - + -
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Residues in contact with SER 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E PHE* 3.1 15.7 + - - -
22E ASN* 2.6 23.3 + - - -
24E PHE* 1.3 76.6 - - - +
26E ASN* 1.3 60.0 + - - +
27E PRO* 3.2 4.3 - - - +
30E ALA* 5.0 0.4 - - - -
31F SER* 3.5 21.7 - - - +
34F LEU* 3.9 35.2 - - - -
35F SER* 4.6 5.8 - - - -
38F SER* 4.6 9.4 + - - -
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Residues in contact with ASN 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D THR* 4.9 3.2 - - - +
32D THR* 4.0 19.2 + - + +
22E ASN 3.6 2.0 + - - +
23E ALA 3.1 15.8 + - - +
24E PHE 3.0 0.8 + - - -
25E SER* 1.3 77.9 + - - +
27E PRO* 1.4 66.6 - - - +
28E THR* 2.7 34.0 + - - +
29E VAL* 2.7 33.5 + - + -
30E ALA* 2.9 12.2 + - - -
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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