Contacts of the helix formed by residues 9 - 26 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E THR* 4.2 4.9 - - - -
8F ARG* 1.3 76.9 - - - +
10F TYR* 1.3 64.8 + - - +
11F SER* 2.7 28.8 + - - -
12F GLN* 2.8 24.3 + - - +
13F ARG* 3.0 21.0 + - - +
47j THR* 5.8 6.3 - - - -
50j PRO* 6.4 2.9 - - - -
51j LYS* 6.4 2.5 - - - -
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Residues in contact with TYR 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E PHE* 5.1 0.7 - + - -
46E GLN* 5.2 12.6 + - + +
49E VAL* 4.6 6.3 - - + -
50E PRO* 3.7 35.4 - - + -
53E THR* 3.1 39.0 - - + +
9F SER* 1.3 75.2 - - - +
11F SER* 1.3 75.9 + - - +
13F ARG* 3.5 6.8 - - - +
14F TYR* 2.8 50.3 + + + -
10i TYR* 2.8 47.1 + + - -
11i SER* 5.0 3.6 + - - -
14i TYR* 5.5 2.1 - - - -
50j PRO* 4.1 17.0 - - + -
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Residues in contact with SER 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F SER* 2.7 21.7 + - - -
10F TYR* 1.3 102.0 - - - +
12F GLN* 1.3 59.3 + - - +
14F TYR* 3.9 4.0 - - - +
15F ALA* 2.9 29.3 + - - +
43j GLN* 5.2 5.9 + - - -
46j GLN* 4.3 39.7 + - - +
47j THR* 5.0 3.8 + - - -
50j PRO* 5.7 0.4 - - - -
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Residues in contact with GLN 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378 A 4.1 3.1 + - - -
7F SER 4.7 2.3 + - - +
8F ARG* 3.6 27.6 - - - +
9F SER* 2.8 39.7 + - - +
10F TYR 3.1 0.4 - - - -
11F SER* 1.3 83.3 + - - +
13F ARG* 1.3 64.0 + - - +
15F ALA* 3.7 6.0 - - - +
16F LYS* 3.1 25.6 + - - +
40G VAL* 5.0 1.9 - - - +
43G GLN* 5.3 7.0 - - + +
44G ASN* 2.9 33.1 + - - +
47G THR* 4.9 15.4 + - - +
48G ASN* 5.5 3.0 - - - +
43j GLN* 6.2 1.6 - - - +
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Residues in contact with ARG 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3137 A 3.9 15.0 + - - -
3147 T 4.8 5.1 + - - -
368 T 3.8 31.5 + - + +
378 A 3.6 56.7 + - - +
45E PHE* 4.5 7.9 - - + -
49E VAL* 3.8 20.7 + - + +
52E PHE* 4.5 4.2 - - - +
53E THR* 2.7 49.4 + - - +
56E ASN* 4.0 11.0 - - - +
8F ARG* 4.3 7.9 - - + -
9F SER 3.0 20.9 + - - +
10F TYR* 3.5 6.7 - - + +
12F GLN* 1.3 76.7 - - - +
14F TYR* 1.3 56.9 + - - +
17F TRP* 3.0 29.9 + - - +
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Residues in contact with TYR 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E GLN* 3.9 10.1 + - - +
45E PHE* 3.5 34.0 - + + -
46E GLN* 3.4 42.0 + - + -
10F TYR* 2.8 34.6 + + + +
11F SER* 3.9 4.9 - - - +
13F ARG* 1.3 75.1 - - - +
15F ALA* 1.3 70.2 + - - +
17F TRP* 3.0 13.1 + + - +
18F GLN* 2.7 59.3 + - + +
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Residues in contact with ALA 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F SER 2.9 20.7 + - - +
12F GLN* 3.3 7.2 + - - +
14F TYR* 1.3 83.7 - - + +
16F LYS* 1.3 63.0 + - - +
18F GLN* 3.3 5.5 + - - +
19F ALA* 3.1 20.1 + - - +
40G VAL* 4.1 23.1 - - + +
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Residues in contact with LYS 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3047 T 3.7 33.0 + - - +
3057 A 2.8 32.1 + - - -
368 T 3.3 33.0 + - - +
378 A 3.9 21.9 + - - +
12F GLN 3.1 12.8 + - - +
15F ALA* 1.3 77.2 - - - +
17F TRP* 1.3 65.3 + - - +
19F ALA* 3.1 5.2 + - - +
20F LYS* 3.0 25.8 + - + +
37G VAL* 4.7 8.3 - - + -
40G VAL* 3.9 19.0 - - + +
44G ASN* 5.5 2.7 - - - +
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Residues in contact with TRP 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3157 A 3.8 33.4 + - + -
358 A 3.8 27.6 + - + -
368 T 3.8 19.8 - - - +
41E ALA* 4.1 20.6 - - + -
42E GLN* 4.2 6.5 - - + -
45E PHE* 3.5 54.5 - + + -
13F ARG 3.0 21.0 + - - +
14F TYR* 3.4 14.8 - + - +
16F LYS* 1.3 75.9 - - - +
18F GLN* 1.3 93.3 + - - +
20F LYS* 3.4 2.5 + - - +
21F PHE* 2.9 53.9 + + + +
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Residues in contact with GLN 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E GLN* 3.2 39.7 - - - +
14F TYR* 2.7 57.7 + - + +
15F ALA* 3.5 7.2 - - - +
17F TRP* 1.3 83.0 - - - +
19F ALA* 1.3 62.6 + - - +
21F PHE* 3.2 5.8 + - - +
22F ASN* 2.9 63.4 + - - +
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Residues in contact with ALA 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F ALA 3.1 8.8 + - - +
16F LYS* 3.1 10.8 + - - +
18F GLN* 1.3 80.6 - - - +
20F LYS* 1.3 58.3 - - - +
22F ASN* 3.5 9.8 + - - +
23F ALA* 3.0 26.5 + - - +
36G ASN* 3.4 34.6 - - - +
37G VAL* 3.7 16.6 - - + -
40G VAL* 4.5 4.7 - - + -
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Residues in contact with LYS 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3057 A 2.8 31.4 + - - +
3067 T 3.1 25.7 + - - -
358 A 3.4 43.6 + - + +
368 T 3.2 21.8 + - - +
16F LYS* 3.0 21.2 + - + +
17F TRP 3.9 3.1 - - - +
19F ALA* 1.3 74.5 - - - +
21F PHE* 1.3 66.9 + - - +
23F ALA* 3.3 3.9 + - + +
24F PHE* 3.0 24.4 + - - +
33G ILE* 3.9 20.6 - - + -
37G VAL* 3.6 16.6 - - + -
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Residues in contact with PHE 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3157 A 5.7 2.9 - + - -
3167 T 4.4 24.2 - - - -
348 T 6.0 1.6 - - - -
358 A 5.2 2.8 - - - -
34E LEU* 3.9 30.5 - - + -
37E VAL* 4.5 4.9 - - + -
38E SER* 3.5 37.2 - - - -
41E ALA* 4.5 9.4 - - + -
42E GLN* 5.6 0.4 - - + -
17F TRP* 2.9 50.3 + + + +
18F GLN* 3.6 11.7 - - - +
20F LYS* 1.3 76.4 - - - +
22F ASN* 1.3 72.9 + - - +
24F PHE* 3.3 11.7 + + - +
25F SER* 3.0 23.5 + - - -
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Residues in contact with ASN 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E SER* 5.5 2.3 + - - -
42E GLN* 4.6 3.5 + - - -
18F GLN* 2.9 51.0 + - - +
19F ALA* 3.5 8.9 - - - +
21F PHE* 1.3 80.4 - - - +
23F ALA* 1.3 62.6 + - - +
25F SER* 2.6 25.9 + - - -
26F ASN* 3.6 4.3 + - - +
32G THR* 5.2 0.2 - - - +
36G ASN* 4.0 12.4 - - - +
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Residues in contact with ALA 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F ALA 3.0 14.0 + - - +
20F LYS* 3.5 9.9 - - + +
22F ASN* 1.3 78.7 - - - +
24F PHE* 1.3 63.3 + - - +
26F ASN* 3.1 22.2 + - - +
29F VAL* 3.3 10.6 - - - +
32G THR* 3.6 14.1 - - + -
33G ILE* 3.8 28.3 - - + -
36G ASN* 3.5 16.5 - - - +
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Residues in contact with PHE 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3177 A 6.0 0.2 - - - -
348 T 3.7 51.8 - - + +
358 A 5.4 2.7 - - - -
24E PHE* 4.4 9.6 - + - -
34E LEU* 3.5 30.1 - - + -
20F LYS 3.0 17.6 + - - +
21F PHE* 3.7 12.8 - + - +
23F ALA* 1.3 76.9 - - - +
25F SER* 1.3 62.5 + - - +
26F ASN 3.0 1.0 + - - -
29F VAL* 3.8 5.6 - - - -
30F ALA* 3.3 45.9 + - - +
33F ILE* 4.2 19.3 - - + -
34F LEU* 4.0 24.7 - - + -
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Residues in contact with SER 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E SER* 3.4 22.0 - - - +
34E LEU* 3.8 37.7 - - - -
35E SER* 4.5 6.3 - - - -
38E SER* 4.7 7.3 + - - -
21F PHE* 3.0 14.6 + - - -
22F ASN* 2.6 23.1 + - - -
24F PHE* 1.3 76.1 - - - +
26F ASN* 1.3 59.7 + - - +
27F PRO* 3.2 4.2 - - - +
30F ALA* 4.9 0.4 - - - -
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Residues in contact with ASN 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F ASN 3.6 2.4 + - - +
23F ALA 3.1 15.6 + - - +
24F PHE 3.0 0.8 + - - -
25F SER* 1.3 78.5 + - - +
27F PRO* 1.4 67.8 - - - +
28F THR* 2.9 24.6 + - - -
29F VAL* 2.7 37.4 + - + -
30F ALA* 2.8 11.7 + - - -
32G 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
------------------------------------------------------------
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