Contacts of the helix formed by residues 25 - 39 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LYS 4.7 0.7 - - - +
16B ALA* 4.9 3.2 + - - -
21B ASN* 4.1 23.7 + - - +
23B GLN 3.1 5.1 + - - +
24B GLU* 1.3 68.9 - - - +
26B TRP* 1.3 61.9 + - - +
27B GLU* 3.6 19.6 + - - +
28B TYR* 3.2 51.0 + - + +
29B ILE* 3.2 19.3 + - - +
64B GLN* 4.8 3.6 + - - -
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Residues in contact with TRP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLU* 3.5 38.5 + - + +
25B ASP* 1.3 69.8 + - - +
27B GLU* 1.3 64.6 + - + +
28B TYR 3.2 0.2 - - - -
29B ILE* 3.8 30.1 - - + -
30B ILE* 3.0 56.0 + - + +
67B THR* 5.0 11.0 - - - -
71B ALA* 4.4 11.2 - - + -
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 4.3 2.9 - - - -
25B ASP* 3.3 12.7 - - - +
26B TRP* 1.3 78.9 - - + +
28B TYR* 1.3 74.0 + - + +
30B ILE* 4.6 1.8 - - - +
31B GLY* 3.1 21.5 + - - -
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Residues in contact with TYR 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 3.9 25.8 - + + +
15B LYS* 3.6 56.0 + - + +
16B ALA* 3.8 21.4 - - - +
21B ASN* 5.8 1.8 - - - -
25B ASP* 3.2 40.0 + - - +
26B TRP 3.2 0.2 - - - -
27B GLU* 1.3 91.1 + - + +
29B ILE* 1.3 54.3 + - - +
31B GLY* 3.6 0.4 - - - +
32B PHE* 2.8 32.2 + - - +
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Residues in contact with ILE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ALA* 4.2 13.5 - - + +
24B GLU* 4.3 10.1 - - + -
25B ASP 3.2 19.9 + - - +
26B TRP* 3.8 39.7 - - + +
28B TYR* 1.3 73.4 - - - +
30B ILE* 1.3 67.3 + - + +
32B PHE* 2.9 16.4 + - - +
33B CYS* 3.0 13.5 + - - -
67B THR* 4.1 18.2 - - - +
68B VAL* 4.1 25.6 - - + -
71B ALA* 3.5 31.9 - - + -
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Residues in contact with ILE 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TRP* 3.0 44.5 + - + +
27B GLU* 4.6 2.2 - - - +
29B ILE* 1.3 79.0 - - + +
31B GLY* 1.3 58.1 + - - +
33B CYS* 3.2 6.9 + - + +
34B ASP* 2.8 46.4 + - - +
71B ALA* 5.2 3.4 - - + -
75B ASN* 4.6 27.1 - - - +
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 3.7 21.9 - - - -
27B GLU 3.1 22.2 + - - -
28B TYR 3.6 2.5 - - - -
29B ILE 3.0 1.0 - - - -
30B ILE* 1.3 77.7 - - - +
32B PHE* 1.3 60.4 + - - +
34B ASP* 3.4 11.5 + - - +
35B GLN* 3.2 26.3 + - - +
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Residues in contact with PHE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 3.3 45.3 - - + -
12B TRP* 3.9 16.7 - - + -
13B LEU* 4.0 26.9 - - + +
16B ALA* 5.0 2.5 - - + -
28B TYR 2.8 14.9 + - - +
29B ILE* 2.9 11.0 + - - +
31B GLY* 1.3 73.7 - - - +
33B CYS* 1.3 65.6 + - - +
35B GLN* 3.0 15.3 + - - +
36B ILE* 3.1 15.5 + - + +
46B ALA* 3.9 26.2 - - + -
49B LEU* 5.1 0.9 - - + -
50B LEU* 4.2 10.3 - - + -
68B VAL* 3.5 29.8 - - + -
72B CYS* 3.9 19.1 - - - -
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Residues in contact with CYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ILE* 3.0 17.4 + - - -
30B ILE* 3.5 11.9 - - + +
32B PHE* 1.3 76.0 - - - +
34B ASP* 1.3 61.8 + - - +
36B ILE* 3.1 8.1 + - - +
37B ASN* 3.0 27.8 + - - +
68B VAL 4.7 0.4 - - - -
71B ALA* 3.8 16.4 - - - -
72B CYS* 3.6 42.6 - - - -
75B ASN* 4.0 16.8 - - + +
76B CYS* 3.8 12.5 - - - -
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Residues in contact with ASP 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ILE* 2.8 31.2 + - - +
31B GLY* 3.5 12.0 - - - +
33B CYS* 1.3 76.6 - - - +
35B GLN* 1.3 68.4 + - - +
37B ASN* 3.1 14.7 + - - +
38B LYS* 3.1 33.3 + - - +
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Residues in contact with GLN 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B GLU* 4.7 3.3 - - - +
8B SER* 4.2 10.0 + - - -
9B LEU* 3.3 22.9 - - + +
12B TRP* 3.4 48.3 + - + +
31B GLY 3.2 11.4 + - - +
32B PHE* 3.0 7.2 + - - +
34B ASP* 1.3 81.8 - - - +
36B ILE* 1.3 62.5 + - - +
38B LYS* 3.6 32.7 + - - +
39B GLU* 3.2 30.7 + - - +
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Residues in contact with ILE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.8 19.7 - - + -
32B PHE* 3.1 22.5 + - + +
33B CYS* 3.1 12.8 + - - +
35B GLN* 1.3 77.4 - - - +
37B ASN* 1.3 60.3 + - - +
39B GLU 3.3 12.1 + - - +
42B GLY* 3.3 23.2 - - - +
43B PRO* 3.8 15.5 - - + -
46B ALA* 3.1 33.7 - - + -
72B CYS* 4.7 2.9 - - - -
76B CYS* 3.9 24.5 - - + -
79B ARG* 2.8 21.1 + - - +
80B PHE* 4.5 4.0 - - + -
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Residues in contact with ASN 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B CYS* 3.0 18.4 + - - +
34B ASP* 3.1 15.8 + - - +
36B ILE* 1.3 77.8 - - - +
38B LYS* 1.3 60.7 + - - +
39B GLU 3.6 0.2 + - - -
75B ASN* 3.4 20.5 + - - +
76B CYS* 3.4 28.2 - - - +
79B ARG* 3.8 17.7 + - - +
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Residues in contact with LYS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ASP* 3.1 26.4 + - - +
35B GLN* 3.6 36.1 - - - +
37B ASN* 1.3 76.6 - - - +
39B GLU* 1.3 69.7 + - - +
40B LEU 3.8 1.7 + - - -
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Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B GLU* 2.5 56.7 - - + +
35B GLN* 3.2 21.8 + - - +
36B ILE 3.3 3.1 + - - +
37B ASN 3.3 1.8 - - - -
38B LYS* 1.3 87.2 - - - +
40B LEU* 1.3 74.1 + - - +
41B GLU 4.0 3.4 - - - +
42B GLY* 2.8 25.2 + - - +
79B ARG* 3.0 15.2 + - - -
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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