Contacts of the helix formed by residues 19 - 47 (chain A) in PDB entry 2R32
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 19 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A MET* 1.3 77.1 + - + +
21A LYS* 3.3 8.4 - - - +
22A GLN* 3.5 26.9 + - - +
23A ILE* 3.4 30.7 + - + +
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Residues in contact with MET 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG* 1.3 86.4 - - + +
21A LYS* 1.3 67.1 + - + +
22A GLN 3.3 0.2 + - - -
23A ILE* 3.3 18.4 + - + +
24A GLU* 3.0 41.2 + - + +
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Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG 3.3 5.6 - - - +
20A MET* 1.3 80.4 - - + +
22A GLN* 1.3 57.8 + - + +
24A GLU* 3.4 16.2 + - - +
25A ASP* 2.8 42.5 + - - +
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Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG* 3.5 27.6 + - - +
20A MET 3.2 0.8 - - - -
21A LYS* 1.3 78.2 - - + +
23A ILE* 1.3 52.3 + - + +
25A ASP* 3.0 8.7 + - - +
26A LYS* 2.8 56.1 + - - +
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Residues in contact with ILE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG* 3.4 20.2 + - + +
20A MET* 3.3 20.4 + - + +
22A GLN* 1.3 78.6 - - + +
24A GLU* 1.3 61.1 + - + +
26A LYS* 3.2 19.9 + - - +
27A ILE* 2.9 47.0 + - + +
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Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET* 3.0 35.3 + - + +
21A LYS* 3.7 18.7 + - - +
23A ILE* 1.3 80.1 - - + +
25A ASP* 1.3 60.6 + - - +
27A ILE* 3.5 11.4 + - + +
28A GLU* 3.1 26.7 + - - +
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Residues in contact with ASP 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 2.8 32.3 + - - +
22A GLN* 3.0 6.9 + - - +
24A GLU* 1.3 73.5 - - - +
26A LYS* 1.3 65.2 + - - +
28A GLU* 3.5 8.6 + - - +
29A GLU* 3.1 21.7 + - - +
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN* 2.8 38.7 + - - +
23A ILE* 3.2 21.4 + - - +
25A ASP* 1.3 75.3 - - - +
27A ILE* 1.3 60.1 + - + +
29A GLU* 3.1 9.2 + - + +
30A ILE* 2.9 42.1 + - + +
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 2.9 39.4 + - + +
24A GLU* 3.8 11.0 - - + +
26A LYS* 1.3 77.3 - - + +
28A GLU* 1.3 62.8 + - - +
30A ILE* 3.4 14.5 + - + +
31A LEU* 3.1 38.9 + - + +
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Residues in contact with GLU 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 GLU 3.1 16.8 + - - +
25A ASP* 3.7 9.9 - - - +
26A LYS 3.3 0.2 - - - -
27A ILE* 1.3 78.9 - - - +
29A GLU* 1.3 63.5 + - - +
31A LEU* 3.5 11.1 + - + +
32A SER* 3.3 24.4 + - - -
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Residues in contact with GLU 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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25A ASP 3.1 14.4 + - - +
26A LYS* 3.1 11.9 + - + +
28A GLU* 1.3 79.6 - - - +
30A ILE* 1.3 63.8 + - + +
32A SER* 3.3 8.0 + - - -
33A LYS* 3.1 40.2 + - - +
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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
----------------------------------------------------------
26A LYS* 2.9 30.2 + - + +
27A ILE* 3.6 12.8 - - + +
29A GLU* 1.3 73.9 - - + +
31A LEU* 1.3 70.6 + - + +
33A LYS* 3.1 18.9 + - + +
34A ILE* 2.9 42.7 + - + +
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Residues in contact with LEU 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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27A ILE* 3.1 38.0 + - + +
28A GLU* 3.7 11.7 - - + +
30A ILE* 1.3 80.3 - - + +
32A SER* 1.3 57.8 + - - +
34A ILE* 3.3 17.6 + - + +
35A TYR* 2.9 29.3 + - - +
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Residues in contact with SER 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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1A SO4 4.7 1.9 + - - -
28A GLU* 3.3 15.0 + - - -
29A GLU* 3.5 11.2 - - - -
30A ILE 3.2 0.4 - - - -
31A LEU* 1.3 79.6 - - - +
33A LYS* 1.3 59.0 + - - +
35A TYR* 3.4 7.4 + - - +
36A HIS* 3.0 26.2 + - - +
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Residues in contact with LYS 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 GLU* 3.1 26.5 + - - +
30A ILE* 3.1 18.9 + - + +
32A SER* 1.3 74.5 - - - +
34A ILE* 1.3 63.1 + - + +
36A HIS* 3.3 8.8 + - - +
37A ILE* 2.8 39.8 + - + +
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Residues in contact with ILE 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* 2.9 38.2 + - + +
31A LEU* 3.6 16.2 - - + +
32A SER 3.3 0.2 - - - -
33A LYS* 1.3 75.2 - - + +
35A TYR* 1.3 59.5 + - - +
37A ILE* 3.1 14.8 + - + +
38A GLU* 2.8 41.0 + - + +
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Residues in contact with TYR 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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1A SO4 3.8 12.3 - - - -
31A LEU 2.9 17.9 + - - +
32A SER* 3.6 7.4 - - - +
33A LYS 3.3 0.2 - - - -
34A ILE* 1.3 75.8 - - - +
36A HIS* 1.3 64.5 + - - +
38A GLU* 3.2 8.7 + - + +
39A ASN* 3.0 48.8 + - - +
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Residues in contact with HIS 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SO4 2.9 44.7 + - - +
32A SER 3.0 12.9 + - - +
33A LYS* 3.5 11.9 - - - +
35A TYR* 1.3 78.2 - - - +
37A ILE* 1.3 65.3 + - + +
39A ASN* 3.1 5.0 + - - +
40A GLU* 2.9 57.0 + - + +
43A ARG* 4.5 6.3 - - - -
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Residues in contact with ILE 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 LYS* 2.8 29.4 + - + +
34A ILE* 3.1 17.5 + - + +
36A HIS* 1.3 77.1 - - + +
38A GLU* 1.3 62.5 + - + +
40A GLU* 3.0 20.9 + - - +
41A ILE* 2.9 47.3 + - + +
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Residues in contact with GLU 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 ILE* 2.8 34.5 + - + +
35A TYR* 3.7 8.1 - - + +
37A ILE* 1.3 73.6 - - + +
39A ASN* 1.3 57.6 + - - +
41A ILE* 3.3 27.3 + - - +
42A ALA* 2.8 30.5 + - - +
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Residues in contact with ASN 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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1A SO4 2.8 42.1 + - - +
35A TYR* 3.0 32.7 + - - +
36A HIS 3.1 9.6 + - - +
38A GLU* 1.3 77.6 - - - +
40A GLU* 1.3 62.9 + - - +
42A ALA* 3.4 8.1 + - - +
43A ARG* 3.1 44.4 + - - +
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Residues in contact with GLU 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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36A HIS* 2.9 47.4 + - + +
37A ILE* 3.5 27.1 - - - +
39A ASN* 1.3 74.8 - - - +
41A ILE* 1.3 59.0 + - + +
43A ARG* 3.3 16.9 + - - +
44A ILE* 2.9 39.3 + - + +
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Residues in contact with ILE 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 ILE* 2.9 39.0 + - + +
38A GLU* 3.7 24.2 - - - +
39A ASN 3.2 0.2 - - - -
40A GLU* 1.3 75.0 - - + +
42A ALA* 1.3 66.8 + - - +
44A ILE* 2.9 14.2 + - + +
45A LYS* 2.8 45.9 + - + +
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Residues in contact with ALA 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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38A GLU 2.8 20.3 + - - +
39A ASN* 3.5 10.1 - - - +
41A ILE* 1.3 75.7 - - - +
43A ARG* 1.3 62.6 + - + +
45A LYS* 3.4 12.7 + - - +
46A LYS* 3.2 22.7 + - - +
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Residues in contact with ARG 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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1A SO4 3.6 21.2 + - - -
36A HIS* 4.5 5.1 - - - -
39A ASN* 3.1 30.8 + - - +
40A GLU* 3.7 34.2 - - - +
42A ALA* 1.3 76.6 - - + +
44A ILE* 1.3 65.8 + - + +
46A LYS* 3.3 21.5 + - - +
47A LEU* 3.1 35.9 + - + +
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Residues in contact with ILE 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 GLU* 2.9 28.0 + - + +
41A ILE* 2.9 15.0 + - + +
43A ARG* 1.3 76.4 - - + +
45A LYS* 1.3 64.7 + - + +
46A LYS 3.3 0.5 + - - -
47A LEU* 3.3 28.4 + - + +
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 2.8 41.9 + - + +
42A ALA* 3.6 11.7 - - - +
44A ILE* 1.3 76.0 - - + +
46A LYS* 1.3 63.9 + - - +
47A LEU 4.1 3.5 - - - +
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Residues in contact with LYS 46 (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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42A ALA 3.2 10.2 + - - +
43A ARG* 3.6 25.0 - - - +
44A ILE 3.2 0.2 - - - -
45A LYS* 1.3 81.6 - - - +
47A LEU* 1.3 75.7 + - - +
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Residues in contact with LEU 47 (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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43A ARG* 3.1 24.1 + - + +
44A ILE* 3.3 21.3 + - + +
45A LYS 4.1 3.7 - - - +
46A LYS* 1.3 96.2 - - + +
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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
------------------------------------------------------------
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