Contacts of the helix formed by residues 29 - 39 (chain F) in PDB entry 1JB0
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 ALA 29 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23F ASN* 4.1 0.4 - - - -
27F ASP* 2.8 14.1 + - - +
28F PRO* 1.3 77.8 - - - +
30F SER* 1.3 56.2 + - - +
31F GLY 3.2 3.1 + - - -
32F GLN* 3.3 12.9 + - + +
33F LYS* 2.8 55.2 + - + +
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Residues in contact with SER 30 (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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23F ASN* 3.2 3.9 + - - -
24F THR* 3.3 29.8 - - - -
25F THR* 3.0 25.8 + - - -
27F ASP* 2.7 28.8 + - - +
29F ALA* 1.3 76.8 - - - +
31F GLY* 1.3 53.9 + - - +
33F LYS* 3.7 5.7 - - - +
34F ARG* 2.8 40.5 + - - +
34J PRO* 5.7 2.7 - - - -
35J ASP* 4.0 3.6 - - - +
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Residues in contact with GLY 31 (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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21F ALA* 3.5 20.2 - - - -
22F VAL 3.4 20.6 + - - -
23F ASN* 2.8 14.7 + - - -
30F SER* 1.3 79.4 - - - +
32F GLN* 1.3 62.3 + - - +
34F ARG* 3.2 4.5 + - - +
35F PHE* 2.9 27.5 + - - -
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Residues in contact with GLN 32 (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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18F ALA* 3.1 29.4 + - - +
19F ALA* 4.4 7.7 + - - +
21F ALA* 3.8 8.5 + - - +
23F ASN* 4.9 0.2 + - - -
28F PRO 5.9 0.9 - - - +
29F ALA* 3.3 14.5 + - + +
31F GLY* 1.3 73.3 - - - +
33F LYS* 1.3 53.0 + - + +
35F PHE* 3.2 6.1 + - - +
36F GLU* 2.7 56.4 + - + +
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Residues in contact with LYS 33 (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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27F ASP* 2.8 32.5 + - - +
29F ALA* 2.8 37.4 + - + +
30F SER* 3.7 5.4 - - - +
32F GLN* 1.3 73.2 - - + +
34F ARG* 1.3 63.2 + - - +
36F GLU* 3.1 18.0 + - - +
37F ARG* 2.9 26.9 + - - +
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Residues in contact with ARG 34 (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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451B THR* 4.0 8.1 - - - +
453B GLU* 2.6 30.1 + - + +
454B LYS* 3.8 10.3 - - - +
22F VAL* 2.4 41.2 + - - +
24F THR* 2.7 30.3 + - - -
30F SER 2.8 18.1 + - - +
31F GLY* 3.8 6.2 - - - -
33F LYS* 1.3 72.9 - - - +
35F PHE* 1.3 65.0 + - - +
37F ARG* 3.0 12.9 + - - +
38F TYR* 2.9 61.7 + - + -
35J ASP* 2.8 49.2 + - + +
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Residues in contact with PHE 35 (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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453B GLU* 3.4 46.9 - - + -
14F PHE* 3.3 39.6 - + + -
17F ARG* 3.7 25.6 - - + -
18F ALA* 3.5 34.5 - - + +
21F ALA* 3.1 38.1 - - + -
31F GLY 2.9 15.2 + - - +
32F GLN* 3.8 6.5 - - - +
34F ARG* 1.3 83.5 - - - +
36F GLU* 1.3 52.4 + - - +
38F TYR* 4.5 1.8 - - + -
39F SER* 2.6 33.6 + - - -
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Residues in contact with GLU 36 (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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32F GLN* 2.7 44.2 + - - +
33F LYS* 3.1 17.5 + - - +
35F PHE* 1.3 73.3 - - - +
37F ARG* 1.3 59.2 + - - +
39F SER* 2.8 24.8 + - - -
40F GLN* 4.5 0.5 + - - +
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Residues in contact with ARG 37 (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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33F LYS* 2.9 15.1 + - - +
34F ARG* 3.5 12.1 - - - +
36F GLU* 1.3 72.7 - - - +
38F TYR* 1.3 62.0 + - + +
39F SER 3.0 6.7 + - - -
40F GLN* 2.9 44.5 + - - +
33J TYR* 4.9 1.8 + - - +
34J PRO 2.7 29.3 + - - -
35J ASP* 3.8 17.8 + - - +
36J LEU* 3.7 21.4 - - - +
38J PHE* 3.6 11.7 - - + -
40J PRO* 3.8 25.4 - - - +
4015J BCR 4.3 21.6 - - - +
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Residues in contact with TYR 38 (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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453B GLU* 3.5 37.2 - - + -
454B LYS* 3.7 9.8 - - + +
1230B CLA 3.9 0.7 - - - -
8F CYS* 3.3 9.4 - - - -
14F PHE* 3.9 19.7 - + + -
34F ARG* 2.9 45.3 + - + +
35F PHE* 3.4 1.5 + - - -
37F ARG* 1.3 78.7 - - + +
39F SER* 1.3 57.8 + - - +
40F GLN 3.1 0.7 - - - -
41F ALA* 3.0 24.0 + - - +
49F PRO* 3.9 14.6 - - + -
35J ASP* 2.6 40.7 + - - +
37J LEU* 3.6 26.2 - - + +
38J PHE* 3.7 22.2 - + - -
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Residues in contact with SER 39 (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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7F PRO* 4.6 2.6 - - - +
8F CYS* 3.8 11.6 + - - +
9F LYS* 3.2 43.3 + - - +
14F PHE* 3.9 7.6 - - - -
15F GLN* 5.6 0.9 + - - -
35F PHE 2.6 22.9 + - - -
36F GLU* 2.8 17.6 + - - -
37F ARG 3.0 1.0 - - - -
38F TYR* 1.3 78.4 - - - +
40F GLN* 1.3 58.1 + - - +
41F ALA 3.2 2.7 + - - +
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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