Contacts of the helix formed by residues 9 - 26 (chain v) 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 v).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53u THR* 4.2 5.2 - - - -
8v ARG* 1.3 76.0 - - - +
10v TYR* 1.3 64.1 + - - +
11v SER* 2.7 28.7 + - - -
12v GLN* 2.8 23.6 + - - +
13v ARG* 3.0 21.9 + - - +
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Residues in contact with TYR 10 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45u PHE* 5.1 0.9 - + - -
46u GLN* 5.2 15.1 + - + +
49u VAL* 4.6 6.3 - - + -
50u PRO* 3.7 41.3 - - + -
53u THR* 3.1 38.8 - - + +
9v SER* 1.3 76.5 - - - +
11v SER* 1.3 76.8 + - - +
13v ARG* 3.5 6.5 - - - +
14v TYR* 2.8 50.0 + + + -
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Residues in contact with SER 11 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9v SER* 2.7 21.3 + - - -
10v TYR* 1.3 102.4 - - - +
12v GLN* 1.3 59.5 + - - +
14v TYR* 3.9 4.2 - - - +
15v ALA* 2.9 29.1 + - - +
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Residues in contact with GLN 12 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2898 A 4.1 3.5 + - - -
7v SER 4.7 1.5 + - - +
8v ARG* 3.6 28.0 - - - +
9v SER* 2.8 39.7 + - - +
10v TYR 3.1 0.2 - - - -
11v SER* 1.3 83.8 + - - +
13v ARG* 1.3 64.7 + - - +
15v ALA* 3.7 5.8 - - - +
16v LYS* 3.1 25.3 + - - +
40w VAL* 5.0 2.3 - - - +
43w GLN* 5.3 7.7 - - + +
44w ASN* 2.9 32.6 + - - +
47w THR* 4.9 15.8 + - - +
48w ASN* 5.5 3.4 - - - +
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Residues in contact with ARG 13 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617 A 3.9 15.4 + - - -
627 T 4.8 5.3 + - - -
2888 T 3.8 32.1 + - + +
2898 A 3.6 56.9 + - - +
45u PHE* 4.5 7.7 - - + -
49u VAL* 3.8 20.5 + - + +
52u PHE* 4.5 4.0 - - - +
53u THR* 2.7 48.8 + - - +
56u ASN* 4.0 11.2 - - - +
8v ARG* 4.3 8.3 - - + -
9v SER 3.0 20.4 + - - +
10v TYR* 3.5 6.1 - - + +
12v GLN* 1.3 77.2 - - - +
14v TYR* 1.3 57.7 + - - +
17v TRP* 3.0 29.7 + - - +
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Residues in contact with TYR 14 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42u GLN* 3.9 9.9 + - - +
45u PHE* 3.5 34.0 - + + -
46u GLN* 3.4 41.6 + - + -
10v TYR* 2.8 35.4 + + + +
11v SER* 3.9 5.2 - - - +
13v ARG* 1.3 74.7 - - - +
15v ALA* 1.3 70.7 + - + +
17v TRP* 3.0 14.2 + + - +
18v GLN* 2.7 59.4 + - + +
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Residues in contact with ALA 15 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11v SER 2.9 20.1 + - - +
12v GLN* 3.3 7.6 + - - +
14v TYR* 1.3 85.8 - - + +
16v LYS* 1.3 61.7 + - - +
18v GLN* 3.3 5.8 + - - +
19v ALA* 3.1 19.6 + - - +
40w VAL* 4.1 23.1 - - + +
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Residues in contact with LYS 16 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527 T 3.7 33.4 + - - +
537 A 2.8 32.1 + - - -
2888 T 3.3 32.1 + - - +
2898 A 3.9 21.7 + - - +
12v GLN 3.1 13.7 + - - +
15v ALA* 1.3 77.2 - - - +
17v TRP* 1.3 66.9 + - - +
19v ALA* 3.1 4.9 + - - +
20v LYS* 2.9 24.7 + - + +
37w VAL* 4.7 8.1 - - + -
40w VAL* 3.9 18.6 - - + -
44w ASN* 5.5 2.9 - - - +
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Residues in contact with TRP 17 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637 A 3.8 33.7 + - + -
2878 A 3.8 26.9 + - + -
2888 T 3.8 19.4 - - - +
41u ALA* 4.1 20.6 - - + -
42u GLN* 4.2 6.5 - - + -
45u PHE* 3.5 54.4 - + + -
13v ARG 3.0 19.9 + - - +
14v TYR* 3.4 14.8 - + - +
16v LYS* 1.3 76.1 - - - +
18v GLN* 1.3 92.4 + - - +
20v LYS* 3.4 2.1 + - - +
21v PHE* 2.9 53.2 + + + +
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Residues in contact with GLN 18 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42u GLN* 3.2 39.2 - - - +
14v TYR* 2.7 58.0 + - + +
15v ALA* 3.5 7.4 - - - +
17v TRP* 1.3 83.5 - - - +
19v ALA* 1.3 63.5 + - - +
21v PHE* 3.2 5.9 + - - +
22v ASN* 2.9 62.7 + - - +
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Residues in contact with ALA 19 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15v ALA 3.1 9.2 + - - +
16v LYS* 3.1 11.1 + - - +
18v GLN* 1.3 79.7 - - - +
20v LYS* 1.3 58.6 + - - +
22v ASN* 3.5 10.3 + - - +
23v ALA* 3.0 26.9 + - - +
36w ASN* 3.4 34.2 - - - +
37w VAL* 3.7 17.0 - - + -
40w VAL* 4.5 4.9 - - + -
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Residues in contact with LYS 20 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537 A 2.8 31.1 + - - +
547 T 3.1 25.3 + - - -
2878 A 3.4 45.0 + - + +
2888 T 3.2 21.5 + - - +
16v LYS* 2.9 22.2 + - + +
17v TRP 3.9 2.9 - - - +
19v ALA* 1.3 73.4 - - - +
21v PHE* 1.3 67.4 + - - +
23v ALA* 3.3 3.8 + - + +
24v PHE* 3.0 24.1 + - - +
33w ILE* 3.9 20.0 - - + -
37w VAL* 3.6 17.5 - - + -
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Residues in contact with PHE 21 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637 A 5.7 2.5 - + - -
647 T 4.5 24.2 - - - -
2868 T 6.0 1.3 - - - -
2878 A 5.2 3.1 - - - -
34u LEU* 3.9 30.7 - - + -
37u VAL* 4.5 5.2 - - + -
38u SER* 3.5 37.2 - - - -
41u ALA* 4.5 9.2 - - + -
42u GLN* 5.8 0.2 - - + -
17v TRP* 2.9 49.6 + + + +
18v GLN* 3.6 11.0 - - - +
20v LYS* 1.3 76.8 - - - +
22v ASN* 1.3 72.6 + - - +
24v PHE* 3.3 11.1 + + - +
25v SER* 3.0 23.2 + - - -
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Residues in contact with ASN 22 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38u SER* 5.5 2.3 + - - -
42u GLN* 4.6 3.3 + - - -
18v GLN* 2.9 52.0 + - - +
19v ALA* 3.5 7.9 - - - +
21v PHE* 1.3 80.0 - - - +
23v ALA* 1.3 63.1 + - - +
25v SER* 2.6 25.2 + - - -
26v ASN* 3.6 4.0 + - - +
36w ASN* 4.0 12.3 - - - +
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Residues in contact with ALA 23 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19v ALA 3.0 14.9 + - - +
20v LYS* 3.5 9.0 - - - +
22v ASN* 1.3 79.2 - - - +
24v PHE* 1.3 64.3 + - - +
26v ASN* 3.1 22.0 + - - +
29v VAL* 3.3 10.5 - - - +
32w THR* 3.6 14.4 - - + -
33w ILE* 3.8 27.6 - - + -
36w ASN* 3.5 15.8 - - - +
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Residues in contact with PHE 24 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657 A 6.0 0.2 - - - -
2868 T 3.7 52.3 - - + +
2878 A 5.4 3.1 - - - +
24u PHE* 4.4 9.2 - + - -
34u LEU* 3.5 30.1 - - + -
20v LYS 3.0 15.9 + - - +
21v PHE* 3.3 11.6 + + - +
23v ALA* 1.3 77.1 - - - +
25v SER* 1.3 62.7 + - - +
26v ASN 3.0 1.6 + - - -
29v VAL* 3.8 6.1 - - - -
30v ALA* 3.3 44.9 + - - +
33v ILE* 4.2 19.3 - - + -
34v LEU* 4.0 25.1 - - + -
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Residues in contact with SER 25 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31u SER* 3.4 22.0 + - - +
34u LEU* 3.8 36.6 - - - -
35u SER* 4.5 6.3 - - - -
38u SER* 4.7 7.3 + - - -
21v PHE* 3.0 15.3 + - - -
22v ASN* 2.6 24.2 + - - -
24v PHE* 1.3 75.9 - - - +
26v ASN* 1.3 60.7 + - - +
27v PRO* 3.2 4.3 - - - +
30v ALA* 4.9 0.7 - - - -
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Residues in contact with ASN 26 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22v ASN 3.6 2.7 + - - +
23v ALA 3.1 15.8 + - - +
24v PHE 3.0 0.8 + - - -
25v SER* 1.3 78.3 + - - +
27v PRO* 1.4 67.5 - - - +
28v THR* 2.9 24.7 + - - -
29v VAL* 2.7 37.1 + - + -
30v ALA* 2.8 11.9 + - - -
32w THR* 4.0 19.0 + - + +
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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