Contacts of the helix formed by residues 16 - 37 (chain A) in PDB entry 3ZO7
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 16 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASN 3.5 5.0 + - - +
15A LEU* 1.3 76.0 - - - +
17A PRO* 1.3 75.6 - - + +
18A ARG* 3.2 10.2 + - - +
19A GLU* 2.8 57.2 + - - +
20A GLU* 3.1 10.3 + - - -
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Residues in contact with PRO 17 (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 LEU 4.6 0.9 - - - +
16A ASP* 1.3 89.7 - - + +
18A ARG* 1.3 57.3 + - + +
20A GLU* 3.2 9.9 + - + +
21A GLU* 2.8 29.7 + - - +
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Residues in contact with ARG 18 (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 ASP* 3.2 8.3 + - - +
17A PRO* 1.3 75.5 - - + +
19A GLU* 1.3 61.9 + - + +
21A GLU* 3.1 38.7 + - - +
22A ARG* 2.9 65.5 + - - +
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Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN 3.9 4.0 - - - +
15A LEU* 3.4 22.4 - - + -
16A ASP* 2.8 50.3 + - - +
18A ARG* 1.3 76.7 - - - +
20A GLU* 1.3 58.1 + - - +
22A ARG* 3.9 26.9 + - - +
23A LEU* 3.0 29.6 + - - +
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Residues in contact with GLU 20 (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 LEU* 3.2 31.3 - - + +
15A LEU* 3.2 20.6 - - + +
16A ASP 3.1 7.6 + - - +
17A PRO* 3.7 10.9 - - + +
18A ARG 3.2 0.2 - - - -
19A GLU* 1.3 76.1 - - - +
21A GLU* 1.3 60.4 + - - +
23A LEU* 3.2 6.3 + - + +
24A LYS* 2.9 43.7 + - - +
50A TYR* 3.4 23.3 + - - +
73A PHE* 5.3 1.5 - - + -
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Residues in contact with GLU 21 (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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17A PRO 2.8 18.3 + - - +
18A ARG* 3.1 37.8 + - - +
20A GLU* 1.3 76.4 - - - +
22A ARG* 1.3 61.9 + - - +
24A LYS* 3.4 8.7 + - - +
25A ALA* 3.1 23.6 + - + +
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Residues in contact with ARG 22 (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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18A ARG* 2.9 42.0 + - - +
19A GLU* 3.9 36.6 + - - +
21A GLU* 1.3 74.4 - - - +
23A LEU* 1.3 60.5 + - - +
25A ALA* 3.4 5.5 + - - +
26A SER* 3.0 40.1 + - - +
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Residues in contact with LEU 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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11A LEU* 4.3 2.2 - - + -
15A LEU* 4.2 15.7 - - + -
19A GLU 3.0 18.3 + - - +
20A GLU* 3.2 7.6 + - - +
22A ARG* 1.3 78.7 - - - +
24A LYS* 1.3 55.0 + - - +
26A SER* 3.3 6.6 + - - -
27A ALA* 2.9 30.8 + - - +
72A PRO* 3.7 30.4 - - + +
73A PHE* 3.7 31.6 - - + -
76A TYR* 3.6 30.1 - - + -
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Residues in contact with LYS 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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20A GLU* 2.9 34.6 + - - +
21A GLU* 3.6 8.5 - - - +
23A LEU* 1.3 76.7 - - - +
25A ALA* 1.3 57.2 + - - +
27A ALA* 3.5 2.1 + - - +
28A LYS* 3.1 29.5 + - + +
50A TYR* 3.7 22.9 + - - +
73A PHE* 4.2 13.2 - - + -
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Residues in contact with ALA 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 GLU* 3.1 17.3 + - + +
22A ARG* 3.4 6.7 + - - +
24A LYS* 1.3 73.2 - - - +
26A SER* 1.3 66.0 + - - +
28A LYS* 3.6 7.3 + - - +
29A ALA* 3.1 23.9 + - - +
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Residues in contact with SER 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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22A ARG* 3.0 26.7 + - - +
23A LEU* 3.3 8.0 + - - -
25A ALA* 1.3 74.7 - - - +
27A ALA* 1.3 59.6 + - - +
29A ALA* 3.3 6.4 + - - +
30A ARG* 2.9 30.3 + - - +
72A PRO* 3.7 18.1 - - - +
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Residues in contact with ALA 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 LEU 2.9 15.3 + - - +
24A LYS 3.8 2.9 - - - +
25A ALA 3.4 0.2 - - - -
26A SER* 1.3 75.3 - - - +
28A LYS* 1.3 59.2 + - - +
30A ARG* 3.2 1.9 + - - +
31A SER* 2.8 33.8 + - - -
72A PRO* 3.6 18.5 - - + +
73A PHE* 3.6 30.5 - - + -
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Residues in contact with LYS 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 LYS* 3.1 19.9 + - + +
25A ALA* 3.8 7.6 - - - +
27A ALA* 1.3 75.9 - - - +
29A ALA* 1.3 58.0 + - - +
31A SER* 3.0 19.3 + - - -
32A ARG* 3.0 20.8 + - + +
88D PRO* 3.7 26.8 + - + +
89D ALA* 4.2 21.1 - - + +
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Residues in contact with ALA 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 ALA 3.1 18.2 + - - +
26A SER* 3.6 6.3 - - - +
28A LYS* 1.3 75.8 - - - +
30A ARG* 1.3 65.1 + - - +
32A ARG* 3.3 9.9 + - - +
33A THR* 3.2 24.4 + - - -
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Residues in contact with ARG 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 SER 2.9 16.8 + - - +
27A ALA 3.2 3.8 + - - +
29A ALA* 1.3 76.0 - - - +
31A SER* 1.3 63.7 + - - +
33A THR* 3.3 20.6 + - - +
34A LEU* 3.1 57.2 + - + +
37A GLN* 5.3 1.4 + - - -
67A ILE* 4.7 9.5 - - - +
70A SER* 3.3 30.0 + - - +
71A LEU* 4.1 15.1 - - + +
72A PRO* 4.1 17.0 - - + -
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Residues in contact with SER 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 ALA 2.8 15.1 + - - -
28A LYS* 3.0 20.3 + - - -
30A ARG* 1.3 74.8 - - - +
32A ARG* 1.3 65.8 + - - +
34A LEU* 3.2 0.9 + - - +
35A GLN* 2.9 44.0 + - - +
40A TRP* 3.4 39.2 - - - -
43A LEU* 5.0 1.6 - - - -
89D ALA* 3.8 12.5 - - - +
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Residues in contact with ARG 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 LYS* 3.0 21.7 + - + +
29A ALA* 3.5 9.6 - - - +
30A ARG 3.3 0.2 - - - -
31A SER* 1.3 74.8 + - - +
33A THR* 1.3 63.6 + - - +
35A GLN* 3.8 1.9 - - - +
36A GLU* 2.7 68.8 + - - +
89D ALA 5.1 1.1 - - - +
90D ARG 5.8 0.4 + - - -
91D VAL* 3.9 41.6 - - + +
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Residues in contact with THR 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 ALA 3.2 12.6 + - - -
30A ARG* 3.5 24.8 - - - +
31A SER 3.2 0.2 - - - -
32A ARG* 1.3 79.4 - - - +
34A LEU* 1.3 62.8 + - - +
36A GLU* 3.2 12.5 + - - +
37A GLN* 3.0 45.9 + - + +
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Residues in contact with LEU 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 ARG* 3.1 57.2 + - + +
31A SER 3.2 3.1 + - - +
33A THR* 1.3 79.2 - - - +
35A GLN* 1.3 59.1 + - - +
37A GLN* 3.5 8.3 + - - +
38A GLY 3.2 2.9 + - - -
39A GLN* 3.1 50.9 + - + +
40A TRP* 3.1 36.6 + - + +
56A PHE* 5.1 0.7 - - + -
67A ILE* 3.8 34.8 - - + -
71A LEU* 4.0 4.3 - - + -
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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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31A SER* 2.9 36.1 + - - +
32A ARG 3.8 4.8 - - - +
34A LEU* 1.3 73.6 - - - +
36A GLU* 1.3 61.7 + - - +
37A GLN 3.1 0.2 - - - -
38A GLY* 3.0 18.4 + - - -
40A TRP* 3.3 34.7 - - + +
41A ARG* 5.8 0.2 - - - -
43A LEU* 4.0 10.3 - - - +
89D ALA 3.0 24.9 + - - -
90D ARG* 3.0 27.0 + - - +
91D VAL* 2.9 36.1 + - + +
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Residues in contact with GLU 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 ARG* 2.7 61.3 + - + +
33A THR* 3.6 9.5 - - - +
35A GLN* 1.3 75.8 - - - +
37A GLN* 1.3 61.4 + - + +
38A GLY* 3.3 0.6 + - - -
91D VAL* 4.5 14.3 - - + +
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Residues in contact with GLN 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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30A ARG* 5.3 1.0 + - - -
33A THR* 3.0 37.5 + - + +
34A LEU* 3.9 12.4 - - - +
35A GLN 3.1 0.4 - - - -
36A GLU* 1.3 79.4 - - + +
38A GLY* 1.3 60.0 + - - +
39A GLN* 3.3 28.7 + - + +
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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