Contacts of the helix formed by residues 18 - 30 (chain A) in PDB entry 1JXH
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 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ASP* 2.8 23.7 + - + +
17A GLY* 1.3 78.3 - - - +
19A GLY* 1.3 71.3 + - - +
21A GLN* 3.4 10.6 + - - +
22A ALA* 3.0 17.6 + - - -
209A HIS* 3.7 17.5 - - + +
210A GLY* 4.0 12.8 - - - -
213A CYS* 4.1 4.3 - - - -
2003A SO4 4.0 14.6 - - - +
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Residues in contact with GLY 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA* 4.9 2.7 - - - -
11A GLY 3.2 16.4 - - - -
12A THR* 4.5 2.5 - - - -
13A ASP* 4.3 0.2 - - - +
18A ALA* 1.3 78.7 - - - +
20A ILE* 1.3 62.3 + - - -
21A GLN* 4.5 2.0 - - - -
22A ALA* 3.0 3.5 + - - +
23A ASP* 3.0 29.5 + - - +
213A CYS* 3.5 6.8 - - - -
2003A SO4 3.0 20.2 + - - -
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Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A THR* 4.0 17.0 - - + +
10A ALA* 3.7 29.4 - - + +
11A GLY 2.8 18.5 + - - +
12A THR* 3.9 10.3 - - + -
19A GLY* 1.3 71.5 - - - -
21A GLN* 1.3 78.1 + - - +
23A ASP* 3.5 9.8 - - - +
24A LEU* 2.8 38.1 + - + +
36A SER* 4.0 18.4 - - - +
37A VAL 4.4 3.6 - - - +
38A ILE* 3.7 32.3 - - + -
20B ILE* 4.7 4.5 - - + -
21B GLN* 4.2 7.4 - - - +
24B LEU* 6.3 0.2 - - + -
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Residues in contact with GLN 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A THR* 3.5 11.4 - - - +
13A ASP 2.8 39.4 + - - +
16A GLY* 3.7 22.9 - - - +
18A ALA 3.4 7.1 - - - +
19A GLY 3.0 0.4 - - - -
20A ILE* 1.3 100.8 - - - +
22A ALA* 1.3 61.6 + - - +
24A LEU* 3.9 2.4 - - - +
25A LYS* 3.1 33.3 + - - +
20B ILE* 4.2 8.5 - - - +
24B LEU* 3.9 20.9 - - + +
36B SER* 2.9 28.7 + - - +
38B ILE* 4.7 2.0 - - - +
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLY 4.4 1.5 + - - -
17A GLY 3.2 27.6 - - - +
18A ALA* 3.0 20.3 + - - -
19A GLY 3.6 1.1 - - - +
21A GLN* 1.3 75.4 - - - +
23A ASP* 1.3 65.3 + - - +
25A LYS* 3.2 2.9 + - - +
26A THR* 2.9 29.1 + - - -
213A CYS* 4.3 7.9 - - + -
214A THR* 4.1 7.6 - - - +
217A ALA* 5.1 0.2 - - - -
261A HIS* 4.0 19.5 - - + -
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Residues in contact with ASP 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A THR* 2.5 37.7 + - - +
10A ALA* 3.8 4.3 - - - +
19A GLY* 3.0 23.7 + - - +
20A ILE* 3.5 9.3 + - - +
21A GLN 3.4 0.2 - - - -
22A ALA* 1.3 77.1 - - - +
24A LEU* 1.3 58.7 - - - +
26A THR* 3.2 1.6 + - - -
27A PHE* 2.9 37.5 + - + -
77A LYS* 2.7 36.4 + - - -
213A CYS* 3.3 11.8 - - - +
217A ALA* 3.5 12.3 - - + +
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A THR* 4.1 8.3 - - + -
20A ILE* 2.8 29.1 + - + +
21A GLN* 3.9 3.8 - - - +
23A ASP* 1.3 71.1 - - - +
25A LYS* 1.3 64.1 + - + +
27A PHE* 3.4 5.5 + - + +
28A SER* 2.9 30.5 + - - -
34A GLY* 3.9 23.9 - - - +
35A CYS 3.6 25.4 - - - +
36A SER* 3.9 17.5 - - - +
20B ILE* 6.3 0.2 - - + -
21B GLN* 3.9 24.9 - - + +
24B LEU* 5.1 15.3 - - + -
25B LYS* 4.9 14.1 - - + -
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Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLY* 3.0 21.6 + - - +
21A GLN* 3.1 22.5 + - - +
22A ALA 3.2 3.6 + - - +
24A LEU* 1.3 75.3 - - + +
26A THR* 1.3 57.5 + - - +
28A SER* 3.2 5.1 + - - -
29A ALA* 2.8 31.3 + - - +
261A HIS* 3.7 27.6 - - + -
262A PHE* 3.6 33.7 - - + -
24B LEU* 4.9 12.6 - - + -
28B SER* 4.1 8.1 - - - +
33B TYR* 3.4 21.8 - - + +
34B GLY* 2.9 41.4 + - - +
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Residues in contact with THR 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA 2.9 18.5 + - - -
23A ASP 3.5 4.5 - - - -
25A LYS* 1.3 74.0 - - - +
27A PHE* 1.3 65.7 + - - +
29A ALA 3.3 1.1 + - - +
30A LEU* 3.1 32.3 + - + +
214A THR* 3.4 15.2 - - - +
217A ALA* 3.8 6.5 - - - +
218A ALA* 3.4 39.9 - - + +
239A TRP* 3.9 16.6 - - + -
261A HIS* 3.4 15.6 + - - -
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Residues in contact with PHE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ALA* 3.7 41.1 - - + -
7A LEU 3.7 26.5 - - - -
8A THR* 3.8 21.8 - - + -
23A ASP* 2.9 23.1 + - + +
24A LEU* 3.7 11.0 - - + +
26A THR* 1.3 73.8 - - - +
28A SER* 1.3 64.2 + - - +
30A LEU* 3.0 12.5 + - - +
31A GLY 3.3 0.3 + - - -
32A ALA* 3.1 35.6 + - + +
34A GLY* 3.9 13.2 - - - -
35A CYS 4.2 0.4 - - - -
77A LYS* 4.2 8.1 - - + -
217A ALA* 3.5 32.8 - - + -
220A ALA* 4.4 7.4 - - + -
221A ALA* 3.9 10.5 - - + -
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Residues in contact with SER 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU 2.9 21.3 + - - -
25A LYS* 3.4 6.5 - - - -
27A PHE* 1.3 77.0 - - - +
29A ALA* 1.3 59.9 + - - +
30A LEU 3.2 0.3 + - - -
31A GLY 3.4 0.5 + - - -
32A ALA 3.8 9.1 + - - -
34A GLY 5.5 0.7 + - - -
262A PHE* 4.2 6.7 - - - -
265A TRP* 2.9 17.3 - - - -
25B LYS* 4.1 11.6 - - - +
28B SER* 5.4 0.2 - - - -
262B PHE* 3.1 42.8 - - - -
266B TRP* 3.0 17.5 + - - +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS 2.8 19.7 + - - +
26A THR 3.3 1.8 + - - +
28A SER* 1.3 72.9 - - - +
30A LEU* 1.3 63.3 + - - +
31A GLY 3.5 0.6 + - - -
239A TRP* 3.8 18.3 + - + +
261A HIS 3.3 26.2 - - - +
262A PHE* 3.9 10.5 - - + -
264A ALA* 6.0 1.6 - - - +
265A TRP* 3.1 28.4 - - + -
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR* 3.1 22.2 + - + +
27A PHE 3.0 6.7 + - - +
29A ALA* 1.3 81.0 - - - +
31A GLY* 1.3 60.8 + - - +
32A ALA* 3.6 1.8 - - - +
218A ALA* 3.7 36.6 - - + +
221A ALA* 4.1 10.4 - - + +
222A LEU* 3.7 38.5 - - + +
225A ARG* 4.6 10.2 + - - -
235A GLU* 5.0 4.5 - - - +
239A TRP* 3.6 41.3 - - + +
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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