Contacts of the helix formed by residues 25 - 39 (chain A) in PDB entry 1JPL
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 ASP 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LYS 5.3 0.2 - - - +
16A ALA* 5.0 1.1 + - - -
21A ASN* 4.7 18.0 - - - +
23A GLN 3.2 6.8 + - - +
24A GLU* 1.3 70.2 - - - +
26A TRP* 1.3 58.2 + - - +
27A GLU* 2.8 19.1 + - - +
28A TYR* 2.6 61.2 + - + +
29A ILE* 3.0 26.5 + - - +
64A GLN* 4.9 0.8 - - - +
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Residues in contact with TRP 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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24A GLU* 3.5 27.1 + - + +
25A ASP* 1.3 67.8 - - - +
27A GLU* 1.3 65.1 + - - +
28A TYR 3.1 2.0 - - - -
29A ILE* 3.6 38.6 - - + -
30A ILE* 3.1 43.9 + - + +
67A THR* 3.6 28.0 - - + -
70A GLU* 5.9 1.8 - - - -
71A ALA* 4.3 11.9 - - + -
74A LYS* 4.5 10.5 - - - -
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Residues in contact with GLU 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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12A TRP* 4.6 3.8 - - - -
25A ASP* 2.8 19.3 + - - +
26A TRP* 1.3 79.0 - - - +
28A TYR* 1.3 91.0 + - - +
30A ILE* 5.1 0.2 - - - +
31A GLY* 3.6 15.2 + - - -
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Residues in contact with TYR 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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12A TRP* 4.0 26.7 - + - +
15A LYS* 3.5 57.7 + - + +
16A ALA* 3.7 23.6 - - - +
21A ASN* 5.6 1.6 - - - -
25A ASP* 2.6 43.8 + - + +
27A GLU* 1.3 98.9 + - - +
29A ILE* 1.3 64.5 + - - +
30A ILE 3.5 0.2 - - - -
31A GLY* 3.5 0.5 + - - -
32A PHE* 3.2 22.2 + - - +
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Residues in contact with ILE 29 (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 ALA* 4.0 15.7 - - + +
24A GLU* 3.9 22.9 - - + -
25A ASP 3.0 21.0 + - - +
26A TRP* 3.5 39.9 + - + -
28A TYR* 1.3 74.9 - - - +
30A ILE* 1.3 63.2 + - + +
32A PHE* 3.2 18.7 + - - +
33A CYS* 3.5 8.5 + - - -
64A GLN* 6.1 1.6 - - + +
67A THR* 4.1 12.1 - - + -
68A VAL* 4.0 26.5 - - + +
71A ALA* 3.6 29.4 - - + -
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Residues in contact with ILE 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 TRP* 3.1 44.2 + - + +
27A GLU 5.1 0.2 - - - +
29A ILE* 1.3 76.9 - - + +
31A GLY* 1.3 62.2 + - - +
33A CYS* 2.9 24.2 + - + +
34A ASP* 3.0 29.4 + - - +
71A ALA* 4.6 1.1 - - + -
74A LYS* 4.6 4.7 - - - +
75A ASN* 3.9 27.4 - - - +
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Residues in contact with GLY 31 (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 TRP* 4.1 18.6 - - - -
27A GLU 3.6 14.2 + - - -
28A TYR 3.5 5.7 + - - -
29A ILE 3.3 0.8 - - - -
30A ILE* 1.3 79.3 - - - +
32A PHE* 1.3 60.6 + - - +
34A ASP* 3.5 13.3 + - - +
35A GLN* 3.1 29.1 + - - +
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Residues in contact with PHE 32 (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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9A LEU* 3.4 43.1 - - + -
12A TRP* 3.8 19.5 - - + +
13A LEU* 3.8 23.8 - - + -
16A ALA* 5.1 1.8 - - + -
28A TYR 3.2 12.0 + - - +
29A ILE* 3.3 10.3 - - - +
30A ILE 3.0 0.2 - - - -
31A GLY* 1.3 74.8 - - - +
33A CYS* 1.3 63.9 + - - +
35A GLN* 3.4 6.3 + - - +
36A ILE* 3.1 51.9 + - + +
46A ALA* 3.8 16.8 - - + -
49A LEU* 5.0 0.9 - - + -
50A LEU* 4.1 12.6 - - + -
68A VAL* 3.5 26.9 - - + -
72A CYS* 3.7 12.6 - - - -
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Residues in contact with CYS 33 (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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29A ILE 3.6 14.6 - - - -
30A ILE* 2.9 11.8 + - + +
32A PHE* 1.3 74.7 - - - +
34A ASP* 1.3 60.4 + - - +
36A ILE* 3.1 5.8 + - - +
37A ASN* 2.9 36.0 + - - +
71A ALA* 3.9 15.7 - - - -
72A CYS* 3.8 37.0 - - - -
75A ASN* 4.1 16.8 - - + +
76A CYS* 3.7 16.6 - - - -
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Residues in contact with ASP 34 (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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30A ILE* 3.0 30.6 + - - +
31A GLY* 3.5 15.1 - - - +
32A PHE 3.3 0.2 - - - -
33A CYS* 1.3 76.3 - - - +
35A GLN* 1.3 69.5 + - - +
37A ASN* 3.1 22.3 + - - +
38A LYS* 3.1 27.9 + - + +
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Residues in contact with GLN 35 (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 SER* 4.7 6.3 + - - +
9A LEU* 3.7 17.0 - - + -
12A TRP* 3.3 45.4 + - + +
31A GLY 3.1 14.6 + - - +
32A PHE* 3.6 8.3 - - - +
33A CYS 3.3 0.2 - - - -
34A ASP* 1.3 80.4 - - - +
36A ILE* 1.3 58.2 + - - +
38A LYS* 3.4 7.9 + - - +
39A GLU* 3.0 46.2 + - + +
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Residues in contact with ILE 36 (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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9A LEU* 4.1 10.8 - - + -
32A PHE* 3.1 45.7 + - + +
33A CYS* 3.4 7.9 - - - +
35A GLN* 1.3 78.9 - - - +
37A ASN* 1.3 60.7 + - - +
38A LYS 3.4 0.5 + - - -
39A GLU 3.4 10.2 - - - +
42A GLY* 3.7 25.9 - - - +
43A PRO* 3.8 14.1 - - + -
46A ALA* 3.4 20.2 - - + -
72A CYS* 3.7 16.4 - - - -
76A CYS* 4.2 15.5 - - + -
79A ARG* 2.9 21.2 + - - +
80A PHE* 4.4 6.1 - - + -
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Residues in contact with ASN 37 (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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33A CYS* 2.9 26.3 + - - +
34A ASP* 3.1 16.6 + - - +
36A ILE* 1.3 78.2 - - - +
38A LYS* 1.3 63.0 + - + +
75A ASN* 3.2 19.6 + - - +
76A CYS* 3.4 29.3 - - - +
79A ARG* 4.0 15.2 + - - +
123C MSE 5.4 3.5 - - - +
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Residues in contact with LYS 38 (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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34A ASP* 3.1 22.9 + - - +
35A GLN* 4.0 9.0 - - - +
37A ASN* 1.3 82.4 - - + +
39A GLU* 1.3 71.9 + - - +
40A LEU 3.7 1.7 + - - -
119C TYR* 3.3 22.7 + - + +
123C MSE 3.6 24.8 - - + +
132C LYS* 6.2 0.2 - - - -
147C ASP* 2.9 34.8 + - - +
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Residues in contact with GLU 39 (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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5A GLU* 3.2 36.4 - - + +
9A LEU* 4.9 13.2 - - + -
35A GLN* 3.0 32.1 + - + +
36A ILE 3.4 5.1 + - - +
38A LYS* 1.3 84.3 - - - +
40A LEU* 1.3 67.6 + - - +
41A GLU* 4.4 2.6 - - - +
42A GLY* 3.1 25.8 + - - +
45A ILE* 6.3 0.4 - - + -
79A ARG* 3.2 14.4 + - - -
136C HIS* 3.8 24.4 + - - -
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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