Contacts of the helix formed by residues 31 - 44 (chain A) in PDB entry 1J46
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 ARG 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ARG 4.5 4.4 + - - +
30A MET* 1.3 80.0 - - - +
32A ASN* 1.3 66.4 + - - +
33A SER* 2.9 14.6 + - - +
34A GLU* 3.0 25.5 + - + +
35A ILE* 3.0 10.7 + - - +
112B A 3.9 27.6 - - - +
113B C 3.4 45.2 + - - -
114B C 5.5 1.8 + - - -
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Residues in contact with ASN 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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20A ARG* 3.5 18.5 - - - +
24A ALA* 6.1 0.2 - - - +
30A MET 4.6 3.5 - - - +
31A ARG* 1.3 73.1 - - - +
33A SER* 1.3 55.6 + - - +
35A ILE* 4.2 14.4 - - - +
36A SER* 2.4 42.7 + - - +
110B A 3.2 24.8 + - + -
111B C 2.3 63.7 + - + +
112B A 4.3 4.6 + - - +
118C G 3.3 7.8 - - - +
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Residues in contact with SER 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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31A ARG* 2.9 12.0 + - - +
32A ASN* 1.3 79.7 - - - +
34A GLU* 1.3 64.8 + - - +
36A SER* 3.9 0.5 - - - -
37A LYS* 3.3 28.4 + - - +
112B A 5.2 2.9 - - - -
118C G 3.3 29.9 + - - +
119C T 3.7 30.9 - - - +
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Residues in contact with GLU 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 MET* 2.9 37.3 - - + +
31A ARG* 3.0 16.9 + - + +
33A SER* 1.3 81.7 - - - +
35A ILE* 1.3 66.7 + - - +
37A LYS* 2.9 26.0 + - + +
38A GLN* 3.0 17.9 + - + +
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Residues in contact with ILE 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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20A ARG* 5.0 10.5 - - + +
23A MET* 3.7 30.7 - - + -
24A ALA* 4.5 13.9 - - + +
27A ASN* 4.0 10.3 - - - +
30A MET* 3.4 42.4 - - + +
31A ARG 3.0 9.3 + - - +
32A ASN* 4.0 13.2 - - - +
34A GLU* 1.3 76.2 - - - +
36A SER* 1.3 65.6 + - - +
38A GLN* 3.0 8.1 + - - +
39A LEU* 2.8 48.4 + - + +
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Residues in contact with SER 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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12A PHE* 6.1 0.2 - - - -
20A ARG* 3.6 16.4 + - - +
32A ASN* 2.4 33.3 + - - +
33A SER 3.9 0.2 - - - -
35A ILE* 1.3 74.3 - - - +
37A LYS* 1.3 60.9 + - - +
39A LEU* 4.0 8.7 - - - +
40A GLY 3.2 13.5 + - - -
119C T 2.6 32.9 + - - -
120C T 3.0 39.1 + - - +
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Residues in contact with LYS 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 SER* 3.3 20.6 + - - +
34A GLU* 2.9 17.0 + - + +
36A SER* 1.3 76.6 - - - +
38A GLN* 1.3 66.9 + - + +
40A GLY* 3.4 1.6 + - - -
41A TYR* 3.1 21.0 + - - +
119C T 3.6 44.0 + - - +
120C T 3.9 13.8 - - - +
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Residues in contact with GLN 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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23A MET* 3.8 25.4 - - + +
27A ASN* 5.0 2.6 + - - -
30A MET* 3.9 26.2 - - - +
34A GLU* 3.0 12.4 + - + +
35A ILE* 3.0 7.8 + - - +
37A LYS* 1.3 74.2 - - + +
39A LEU* 1.3 62.1 + - - +
41A TYR* 3.0 8.6 + - + +
42A GLN* 2.7 37.6 + - + +
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Residues in contact with LEU 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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12A PHE* 4.6 5.4 - - + -
15A TRP* 3.6 16.0 - - + -
16A SER* 4.9 7.4 - - - -
19A GLN* 3.8 26.5 - - + -
20A ARG* 4.0 33.4 - - + +
23A MET* 4.3 23.8 - - + -
35A ILE* 2.8 39.7 + - + +
36A SER* 4.0 7.9 - - - +
38A GLN* 1.3 76.8 - - - +
40A GLY* 1.3 53.1 + - - +
42A GLN* 4.4 5.4 - - + -
43A TRP* 2.6 39.8 + - - +
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Residues in contact with GLY 40 (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 PHE* 4.5 1.9 - - - -
36A SER 3.2 9.1 + - - -
37A LYS 3.9 1.8 - - - -
38A GLN 3.2 0.8 - - - -
39A LEU* 1.3 78.2 - - - +
41A TYR* 1.3 63.3 + - - +
43A TRP* 3.7 1.7 - - - +
44A LYS* 3.0 29.8 + - - +
120C T 3.5 25.8 - - - -
121C T 3.7 18.8 - - - -
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Residues in contact with TYR 41 (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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37A LYS 3.1 13.3 + - - +
38A GLN* 3.0 12.0 + - + +
40A GLY* 1.3 78.5 - - - +
42A GLN* 1.3 84.1 + - + +
44A LYS* 3.4 11.4 + - + +
45A MET* 3.2 52.4 + - + +
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Residues in contact with GLN 42 (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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15A TRP* 4.9 7.6 - - + -
23A MET* 5.6 6.1 - - + -
38A GLN* 2.7 28.4 + - + +
39A LEU* 3.7 9.4 - - + +
41A TYR* 1.3 88.8 - - + +
43A TRP* 1.3 67.3 + - - +
45A MET* 2.9 24.5 + - - +
46A LEU* 3.5 14.1 + - + +
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Residues in contact with TRP 43 (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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11A ALA 4.0 15.3 - - - -
12A PHE* 3.6 23.6 - + + -
15A TRP* 3.2 57.6 - + + -
39A LEU 2.6 22.3 + - - +
40A GLY 3.7 3.1 - - - +
42A GLN* 1.3 73.5 - - - +
44A LYS* 1.3 67.9 + - + +
45A MET 3.1 0.7 + - - -
46A LEU* 3.3 40.1 + - + +
51A LYS* 3.6 33.0 + - + +
54A PHE* 4.3 11.9 - + + -
55A PHE* 3.9 18.6 - + - -
121C T 2.7 41.8 + - - -
122C G 2.7 12.6 + - - -
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Residues in contact with LYS 44 (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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40A GLY 3.0 18.2 + - - +
41A TYR* 3.8 9.4 - - + +
42A GLN 3.2 0.6 - - - -
43A TRP* 1.3 85.2 - - + +
45A MET* 1.3 66.2 + - + +
46A LEU 3.4 4.7 + - - +
51A LYS* 5.5 2.9 - - - +
121C T 3.2 33.9 + - - +
122C G 5.8 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