Contacts of the helix formed by residues 9 - 26 (chain j) 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 j).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53i THR* 4.2 5.4 - - - -
8j ARG* 1.3 76.1 - - - +
10j TYR* 1.3 65.5 + - - +
11j SER* 2.7 27.8 + - - -
12j GLN* 2.8 25.2 + - - +
13j ARG* 3.0 20.5 + - - +
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Residues in contact with TYR 10 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45i PHE* 5.3 0.2 - + - -
46i GLN* 5.2 14.1 + - - +
49i VAL* 4.6 7.2 - - + -
50i PRO* 3.7 40.6 - - + -
53i THR* 3.1 39.9 - - + +
9j SER* 1.3 76.7 - - - +
11j SER* 1.3 76.6 + - - +
13j ARG* 3.4 6.6 - - - +
14j TYR* 2.8 50.6 + + + -
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Residues in contact with SER 11 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9j SER* 2.7 21.7 + - - -
10j TYR* 1.3 103.2 - - - +
12j GLN* 1.3 60.4 + - - +
14j TYR* 3.9 4.2 - - - +
15j ALA* 2.9 29.2 + - - +
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Residues in contact with GLN 12 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2178 A 4.1 2.9 + - - -
7j SER 4.7 1.3 + - - +
8j ARG* 3.6 27.0 - - - +
9j SER* 2.8 39.7 + - - +
10j TYR 3.1 0.4 - - - -
11j SER* 1.3 84.7 + - - +
13j ARG* 1.3 63.0 + - - +
15j ALA* 3.7 5.4 - - - +
16j LYS* 3.1 26.2 + - - +
40k VAL* 5.0 2.6 - - + +
43k GLN* 5.3 7.4 - - + +
44k ASN* 2.9 32.5 + - - +
47k THR* 4.9 15.2 + - - +
48k ASN* 5.5 3.6 - - - +
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Residues in contact with ARG 13 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1337 A 3.9 15.0 + - - -
1347 T 4.8 5.5 + - - -
2168 T 3.8 32.0 + - + +
2178 A 3.6 57.8 + - - +
45i PHE* 4.5 8.1 - - + -
49i VAL* 3.8 19.9 + - + +
52i PHE* 4.5 4.4 - - - +
53i THR* 2.7 48.9 + - - +
56i ASN* 4.0 11.2 - - - +
8j ARG* 4.3 7.6 - - + -
9j SER 3.0 20.7 + - - +
10j TYR* 3.2 7.6 + - + +
12j GLN* 1.3 76.5 - - - +
14j TYR* 1.3 55.8 + - - +
17j TRP* 3.0 29.7 + - - +
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Residues in contact with TYR 14 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42i GLN* 3.9 9.9 + - - +
45i PHE* 3.5 33.6 - + + -
46i GLN* 3.4 40.9 + - + -
10j TYR* 2.8 36.1 + + + +
11j SER* 3.9 3.8 - - - +
13j ARG* 1.3 74.5 - - - +
15j ALA* 1.3 71.1 + - - +
17j TRP* 3.0 14.8 + + - +
18j GLN* 2.7 60.3 + - + +
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Residues in contact with ALA 15 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11j SER 2.9 20.2 + - - +
12j GLN* 3.3 8.0 + - - +
14j TYR* 1.3 84.0 - - + +
16j LYS* 1.3 62.3 + - - +
18j GLN* 3.3 5.3 + - - +
19j ALA* 3.1 19.6 + - - +
40k VAL* 4.1 21.2 - - + +
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Residues in contact with LYS 16 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247 T 3.7 33.4 + - - +
1257 A 2.8 32.4 + - - -
2168 T 3.3 33.7 + - - +
2178 A 3.9 21.5 + - - +
12j GLN 3.1 13.5 + - - +
15j ALA* 1.3 77.8 - - - +
17j TRP* 1.3 66.9 + - - +
19j ALA* 3.1 4.9 + - - +
20j LYS* 3.0 25.2 + - + +
37k VAL* 4.7 8.5 - - + -
40k VAL* 3.9 17.9 - - + +
44k ASN* 5.5 3.4 - - - +
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Residues in contact with TRP 17 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1357 A 3.8 34.0 + - + -
2158 A 3.8 27.5 + - + -
2168 T 3.8 18.5 - - - +
41i ALA* 4.1 21.3 - - + -
42i GLN* 4.2 7.0 - - + -
45i PHE* 3.5 53.8 - + + -
13j ARG 3.0 20.3 + - - +
14j TYR* 3.4 15.0 - + - +
16j LYS* 1.3 77.2 - - - +
18j GLN* 1.3 94.5 + - - +
20j LYS* 3.4 1.9 + - - +
21j PHE* 2.8 53.2 + + + +
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Residues in contact with GLN 18 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42i GLN* 3.2 39.8 - - - +
14j TYR* 2.7 57.1 + - + +
15j ALA* 3.5 6.5 - - - +
17j TRP* 1.3 82.3 - - - +
19j ALA* 1.3 63.2 + - - +
21j PHE* 3.2 6.1 + - - -
22j ASN* 2.9 62.7 + - - +
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Residues in contact with ALA 19 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15j ALA 3.1 9.6 + - - +
16j LYS* 3.1 10.6 + - - +
18j GLN* 1.3 79.9 - - - +
20j LYS* 1.3 58.2 + - - +
22j ASN* 3.5 9.7 + - - +
23j ALA* 3.0 27.0 + - - +
36k ASN* 3.4 34.2 - - - +
37k VAL* 3.7 16.4 - - + -
40k VAL* 4.5 4.7 - - + -
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Residues in contact with LYS 20 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1257 A 2.8 32.2 + - - +
1267 T 3.1 25.1 + - - -
2158 A 3.4 44.2 + - - +
2168 T 3.2 21.1 + - - +
16j LYS* 3.0 21.8 + - + +
17j TRP 3.9 3.6 - - - +
19j ALA* 1.3 74.8 - - - +
21j PHE* 1.3 66.3 + - - +
23j ALA* 3.3 3.9 + - + +
24j PHE* 3.0 24.4 + - - +
33k ILE* 3.9 19.5 - - + -
37k VAL* 3.6 17.3 - - + -
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Residues in contact with PHE 21 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1357 A 5.7 2.7 - + - -
1367 T 4.5 23.1 - - - -
2148 T 6.0 1.6 - - - -
2158 A 5.2 2.8 - - - -
34i LEU* 3.9 29.8 - - + -
37i VAL* 4.5 4.9 - - + -
38i SER* 3.5 37.5 - - - -
41i ALA* 4.5 9.6 - - + -
42i GLN* 5.8 0.2 - - + -
17j TRP* 2.8 48.8 + + + +
18j GLN* 3.2 11.9 + - - +
20j LYS* 1.3 76.1 - - - +
22j ASN* 1.3 72.4 + - - +
24j PHE* 3.3 11.6 + + - +
25j SER* 3.0 23.9 + - - -
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Residues in contact with ASN 22 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38i SER* 5.5 2.1 + - - -
42i GLN* 4.6 2.9 + - - -
18j GLN* 2.9 51.9 + - - +
19j ALA* 3.5 8.3 - - - +
21j PHE* 1.3 80.3 - - - +
23j ALA* 1.3 63.1 + - - +
25j SER* 2.6 25.6 + - - -
26j ASN* 3.6 4.0 + - - +
36k ASN* 4.0 12.3 - - - +
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Residues in contact with ALA 23 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19j ALA 3.0 13.8 + - - +
20j LYS* 3.5 9.4 - - + +
21j PHE 3.2 0.2 - - - -
22j ASN* 1.3 79.2 - - - +
24j PHE* 1.3 63.2 + - - +
26j ASN* 3.1 21.8 + - - +
29j VAL* 3.3 11.3 - - - +
32k THR* 3.6 15.3 - - + -
33k ILE* 3.8 27.1 - - + -
36k ASN* 3.5 15.9 - - - +
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Residues in contact with PHE 24 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2148 T 3.7 49.8 - - + +
2158 A 5.4 2.9 - - - +
24i PHE* 4.4 9.4 - + - -
34i LEU* 3.5 30.5 - - + -
20j LYS 3.0 16.5 + - - +
21j PHE* 3.3 11.4 + + - +
23j ALA* 1.3 77.5 - - - +
25j SER* 1.3 62.0 + - - +
26j ASN 3.0 1.4 + - - -
29j VAL* 3.8 6.3 - - + +
30j ALA* 3.3 44.8 + - - +
33j ILE* 4.2 19.3 - - + -
34j LEU* 4.0 25.6 - - + -
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Residues in contact with SER 25 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31i SER* 3.4 22.3 - - - +
34i LEU* 3.8 36.1 - - - -
35i SER* 4.5 6.5 - - - -
38i SER* 4.7 7.3 + - - -
21j PHE* 3.0 15.7 + - - -
22j ASN* 2.6 23.7 + - - -
24j PHE* 1.3 75.7 - - - +
26j ASN* 1.3 62.3 + - - +
27j PRO* 3.2 4.5 - - - +
30j ALA* 4.9 0.4 - - - +
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Residues in contact with ASN 26 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22j ASN 3.6 2.7 + - - +
23j ALA 3.1 15.4 + - - +
24j PHE 3.0 1.4 + - - -
25j SER* 1.3 78.2 + - - +
27j PRO* 1.4 67.1 - - - +
28j THR* 2.9 23.5 + - - -
29j VAL* 2.7 37.1 + - + -
30j ALA* 2.8 11.7 + - - -
32k THR* 4.0 19.1 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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