Contacts of the helix formed by residues 22 - 43 (chain A) in PDB entry 4RWN
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 ASN 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LEU 3.6 1.4 + - - -
21A PRO* 1.3 74.4 - - - +
23A THR* 1.3 65.4 + - - +
24A CYS* 3.3 16.2 + - - +
25A PHE* 3.1 23.3 + - - +
26A ARG* 3.3 21.4 + - - +
70A ARG* 3.8 27.0 - - - +
5B U 5.6 1.3 - - - -
6B U 4.2 4.3 - - - -
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Residues in contact with THR 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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22A ASN* 1.3 75.0 - - - +
24A CYS* 1.3 64.3 + - - +
26A ARG* 3.6 8.4 - - - +
27A THR* 2.7 41.7 + - - +
5B U 3.4 14.4 + - - -
6B U 2.8 25.7 + - - +
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Residues in contact with CYS 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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22A ASN* 3.3 14.6 - - - +
23A THR* 1.3 81.6 - - - +
25A PHE* 1.3 59.7 + - - +
27A THR* 3.9 3.1 - - - -
28A GLN* 2.9 41.0 + - + +
141A GLN* 5.7 8.3 - - - +
142A GLN* 4.4 5.2 - - - +
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Residues in contact with PHE 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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21A PRO* 4.3 9.9 - - + -
22A ASN* 3.1 22.8 + - - +
24A CYS* 1.3 80.1 - - - +
26A ARG* 1.3 63.3 + - + +
28A GLN* 3.8 1.6 - - - +
29A VAL* 3.1 54.5 + - + +
68A THR* 4.4 17.9 - - + -
69A LEU 3.9 7.2 - - - -
70A ARG* 4.1 8.7 - - + -
71A GLY* 3.4 44.0 - - - +
73A SER* 3.7 28.7 - - - -
142A GLN* 3.7 27.3 - - - +
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Residues in contact with ARG 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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21A PRO* 4.4 14.1 - - + -
22A ASN 3.3 13.6 + - - +
23A THR* 3.6 11.5 - - - +
25A PHE* 1.3 85.5 - - + +
27A THR* 1.3 66.3 + - - +
29A VAL* 3.5 6.3 + - - +
30A LYS* 3.1 55.1 + - + +
68A THR* 6.0 0.2 - - - +
6B U 2.7 44.0 + - - -
7B U 3.7 33.8 + - - +
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Residues in contact with THR 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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23A THR* 2.7 32.8 + - - +
24A CYS* 3.9 3.8 - - - -
26A ARG* 1.3 82.7 + - - +
28A GLN* 1.3 64.0 + - - +
30A LYS* 3.3 10.2 + - - +
31A GLU* 3.0 31.3 + - + +
7C A 4.7 10.7 + - - +
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Residues in contact with GLN 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 CYS* 2.9 29.3 + - + +
25A PHE 3.8 1.3 - - - +
27A THR* 1.3 81.8 - - - +
29A VAL* 1.3 60.9 + - - +
31A GLU* 3.3 18.2 + - - +
32A ALA* 3.1 19.9 + - - +
139A GLN 4.7 3.0 + - - -
140A LEU* 3.3 24.3 - - + +
141A GLN* 2.7 59.1 + - + +
142A GLN* 3.7 31.9 + - + +
144A VAL* 4.2 3.2 - - + +
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Residues in contact with VAL 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 PHE* 3.1 50.0 + - + +
26A ARG* 3.8 6.1 - - - +
27A THR 3.3 0.2 - - - -
28A GLN* 1.3 75.4 - - - +
30A LYS* 1.3 58.9 + - + +
32A ALA* 3.2 3.8 + - - +
33A ILE* 2.9 44.8 + - + +
63A SER* 4.6 10.5 - - - +
73A SER 4.8 3.6 - - - +
74A ASP 5.3 1.6 - - - +
75A ALA* 4.5 7.0 - - + -
142A GLN* 5.2 1.6 - - - +
144A VAL* 4.1 31.4 - - + -
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Residues in contact with LYS 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 ARG* 3.1 41.3 + - + +
27A THR* 3.6 7.0 - - - +
29A VAL* 1.3 78.0 - - + +
31A GLU* 1.3 56.4 + - - +
33A ILE* 3.2 9.9 + - + +
34A ASP* 2.9 25.3 + - - +
59A LYS* 4.3 11.0 - - - +
6C A 3.5 38.9 - - - +
7C A 3.1 39.9 + - - +
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Residues in contact with GLU 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 THR* 3.0 16.5 + - + +
28A GLN* 3.5 28.0 + - - +
29A VAL 3.2 0.2 - - - -
30A LYS* 1.3 76.0 - - - +
32A ALA* 1.3 63.7 + - - +
34A ASP* 3.4 9.6 + - + +
35A ILE* 3.0 32.9 + - + +
139A GLN* 3.5 30.8 - - - +
140A LEU* 3.7 15.0 - - + +
6C A 5.4 2.0 - - - -
7C A 5.4 0.2 + - - -
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Residues in contact with ALA 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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28A GLN 3.1 6.4 + - - +
29A VAL 3.2 8.0 + - - +
31A GLU* 1.3 75.3 - - - +
33A ILE* 1.3 64.0 + - - +
35A ILE* 3.2 9.1 + - - +
36A VAL* 3.0 26.9 + - - +
135A LEU* 4.6 2.6 - - + +
140A LEU* 3.7 20.1 - - + +
144A VAL* 3.7 26.9 - - + -
146A PHE* 3.6 19.3 - - + -
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Residues in contact with ILE 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 VAL* 2.9 35.7 + - + +
30A LYS* 3.5 10.1 - - + +
32A ALA* 1.3 76.3 - - - +
34A ASP* 1.3 56.9 + - - +
36A VAL* 3.3 2.0 + - - +
37A CYS* 2.8 38.0 + - - -
59A LYS* 3.6 28.9 - - + +
63A SER* 5.0 1.8 - - - -
75A ALA* 3.8 25.6 - - + -
77A LEU* 4.2 13.5 - - + -
146A PHE* 4.0 9.9 - - + -
5C U 3.6 28.0 - - - +
6C A 4.3 4.5 - - - +
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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 LYS 2.9 12.3 + - - +
31A GLU* 3.5 12.3 - - - +
32A ALA 3.3 0.2 - - - -
33A ILE* 1.3 75.5 - - - +
35A ILE* 1.3 61.0 + - - +
37A CYS* 3.9 1.1 - - - +
38A ARG* 2.9 64.7 + - - +
15B A 5.9 1.6 - - - -
5C U 4.0 12.4 + - - +
6C A 3.6 37.6 + - - +
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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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31A GLU* 3.0 27.3 + - + +
32A ALA* 3.2 14.8 + - - +
34A ASP* 1.3 79.9 - - - +
36A VAL* 1.3 61.0 + - + +
38A ARG* 3.9 20.4 + - - +
39A PHE* 3.0 26.7 + - - +
114A PHE* 3.9 30.2 - - + -
135A LEU* 4.6 10.1 - - + -
137A SER* 4.0 27.8 - - - +
139A GLN* 5.4 3.8 - - + -
140A LEU* 4.3 11.4 - - + -
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Residues in contact with VAL 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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32A ALA 3.0 18.7 + - - +
33A ILE 3.8 3.8 - - - +
35A ILE* 1.3 75.2 - - + +
37A CYS* 1.3 62.2 + - - +
39A PHE* 3.2 12.1 + - + +
40A LEU* 2.8 42.2 + - + +
77A LEU* 3.8 19.7 - - + -
105A LEU* 6.0 4.0 - - + -
114A PHE* 6.5 0.2 - - - -
133A PHE* 4.5 13.0 - - + -
135A LEU* 4.6 10.1 - - + -
146A PHE* 3.6 30.5 - - + -
148A VAL* 4.6 11.2 - - + -
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Residues in contact with CYS 37 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ILE* 2.8 29.8 + - - +
34A ASP* 3.9 3.1 - - - +
36A VAL* 1.3 74.5 - - - +
38A ARG* 1.3 60.0 + - - +
40A LEU* 3.1 8.2 + - - +
41A LYS* 2.9 52.4 + - + +
57A VAL* 3.7 29.8 - - - -
77A LEU* 4.3 4.3 - - - -
5C U 3.6 35.7 - - - +
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Residues in contact with ARG 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* 2.9 46.6 + - - +
35A ILE* 3.9 19.3 + - - +
37A CYS* 1.3 75.4 - - + +
39A PHE* 1.3 54.8 + - - +
41A LYS* 4.8 8.0 - - - +
42A GLU* 2.7 71.9 + - - +
43A ARG 3.9 0.2 + - - -
16B U 6.2 0.9 - - - -
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Residues in contact with PHE 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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35A ILE 3.0 16.0 + - - +
36A VAL* 3.3 16.6 - - + +
38A ARG* 1.3 77.2 - - - +
40A LEU* 1.3 70.2 + - + +
43A ARG* 3.1 17.0 + - + -
44A CYS* 2.8 61.4 + - + -
101A ILE* 4.0 4.9 - - + -
104A GLN* 3.7 26.7 - - + -
105A LEU* 3.5 46.7 - - + -
108A CYS* 3.8 22.0 - - - -
114A PHE* 4.3 13.9 - + + -
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Residues in contact with LEU 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 VAL* 2.8 40.3 + - + +
37A CYS* 3.1 5.1 + - - +
39A PHE* 1.3 93.1 - - + +
41A LYS* 1.3 60.0 + - - +
44A CYS* 4.0 9.7 + - - +
45A PHE* 3.7 19.5 + - + +
54A VAL* 3.4 20.9 - - + +
57A VAL* 4.0 36.1 - - + -
77A LEU* 4.9 1.1 - - + -
79A VAL* 4.3 13.7 - - + -
101A ILE* 4.4 28.7 - - + -
148A VAL* 4.8 9.6 - - + -
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Residues in contact with LYS 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 CYS* 2.9 32.7 + - + +
38A ARG* 4.8 6.4 - - - +
40A LEU* 1.3 80.6 - - - +
42A GLU* 1.3 60.3 + - + +
43A ARG 3.7 0.9 - - - -
46A GLN* 3.5 15.0 + - - +
54A VAL* 4.3 15.7 - - + -
56A LYS* 6.5 0.2 - - - -
57A VAL* 4.4 15.5 - - + +
15B A 5.2 0.4 - - - -
16B U 3.2 41.5 + - - +
17B G 3.5 46.9 - - - +
4C A 4.4 7.6 - - + +
5C U 3.5 24.4 + - - -
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Residues in contact with GLU 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 ARG* 2.7 56.5 + - - +
41A LYS* 1.3 74.5 - - + +
43A ARG* 1.3 60.6 + - + +
46A GLN* 3.1 21.6 + - - +
16B U 2.8 54.4 + - - +
17B G 5.0 2.0 - - - +
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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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39A PHE* 3.1 18.2 + - + +
42A GLU* 1.3 81.8 - - + +
44A CYS* 1.3 69.2 + - - +
45A PHE 3.3 0.9 + - - -
46A GLN* 3.1 21.6 + - - +
47A GLY 4.7 1.0 + - - -
104A GLN* 4.4 13.8 + - - +
107A ALA* 4.6 11.1 - - - +
108A CYS* 4.0 26.8 - - - -
111A GLU* 2.7 42.2 + - - -
113A LYS* 3.7 10.5 - - - +
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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