Contacts of the helix formed by residues 17 - 39 (chain A) in PDB entry 4X4U
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 17 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 3.5 4.1 + - - +
16A PRO* 1.3 76.0 - - - +
18A GLU* 1.3 65.0 + - - +
19A GLU* 3.3 29.9 - - - +
20A GLU* 3.0 25.5 + - - +
21A VAL* 3.2 9.7 + - - +
55A LYS* 3.4 19.5 + - - +
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Residues in contact with GLU 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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17A ASP* 1.3 75.0 - - - +
19A GLU* 1.3 62.7 + - - +
21A VAL* 3.8 9.0 - - - +
22A ARG* 3.2 31.8 + - - +
25A ARG* 5.4 0.2 + - - -
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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
----------------------------------------------------------
17A ASP* 3.1 19.9 + - - +
18A GLU* 1.3 79.1 - - - +
20A GLU* 1.3 60.9 + - - +
22A ARG* 4.2 19.3 + - - +
23A LYS* 3.5 19.9 + - - +
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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
----------------------------------------------------------
16A PRO* 3.5 26.1 - - + +
17A ASP* 3.0 20.8 + - - +
19A GLU* 1.3 77.9 - - - +
21A VAL* 1.3 65.7 + - - +
23A LYS* 3.4 14.4 - - + +
24A GLY* 3.3 14.4 + - - -
53A TRP* 3.9 6.6 + - - +
55A LYS* 4.0 6.6 + - - +
56A GLY* 3.4 28.7 + - - -
58A LEU* 3.6 37.8 - - + +
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Residues in contact with VAL 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PRO* 4.0 13.9 - - + +
17A ASP 3.2 16.0 + - - +
18A GLU* 3.4 9.8 + - - +
20A GLU* 1.3 74.5 - - - +
22A ARG* 1.3 55.2 + - - +
24A GLY* 2.7 6.8 + - - -
25A ARG* 2.6 51.0 + - + +
48A TYR* 4.7 2.1 + - + +
51A ASN* 5.9 0.7 - - - +
53A TRP* 4.5 27.8 - - + -
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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 GLU* 3.2 18.4 + - - +
19A GLU* 4.2 19.2 + - - +
21A VAL* 1.3 79.7 - - - +
23A LYS* 1.3 57.2 + - - +
25A ARG* 3.3 38.1 - - - +
26A GLU* 2.8 62.6 + - + +
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Residues in contact with LYS 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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19A GLU 3.5 14.6 + - - +
20A GLU* 3.4 19.8 - - + +
21A VAL 3.1 0.2 - - - -
22A ARG* 1.3 80.5 - - - +
24A GLY* 1.3 58.4 - - - +
26A GLU* 4.1 6.6 - - - +
27A ALA* 3.4 10.6 + - - +
58A LEU* 4.7 10.5 - - + +
105A LYS* 4.7 7.3 - - - +
106A GLY* 3.9 32.6 + - - -
107A VAL* 3.2 26.2 - - + +
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Residues in contact with GLY 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 3.3 6.1 + - - -
21A VAL 2.7 12.6 + - - -
23A LYS* 1.3 74.3 - - - +
25A ARG* 1.3 53.2 + - - -
26A GLU 3.3 0.2 - - - -
27A ALA* 3.5 2.0 - - - +
28A GLU* 2.8 30.0 + - - +
48A TYR* 2.8 21.8 + - - -
58A LEU* 4.4 6.1 - - - -
60A ILE* 3.5 9.2 - - - +
107A VAL* 4.0 11.4 - - - -
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Residues in contact with ARG 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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18A GLU 5.4 0.2 + - - -
21A VAL* 2.6 30.9 + - + +
22A ARG* 3.3 55.7 - - - +
24A GLY* 1.3 73.4 - - - +
26A GLU* 1.3 60.0 + - + +
28A GLU* 3.7 7.1 - - - +
29A GLU* 3.1 59.9 + - + +
48A TYR* 3.4 9.8 + - - +
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Residues in contact with GLU 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* 2.8 48.6 + - + +
23A LYS* 4.2 5.6 + - - +
25A ARG* 1.3 79.7 - - + +
27A ALA* 1.3 57.7 + - - +
29A GLU* 4.3 9.0 - - - +
30A GLU* 2.9 33.8 + - + +
105A LYS* 4.2 15.1 - - + +
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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 LYS 3.4 5.0 + - - +
24A GLY 3.2 4.6 + - - +
25A ARG 3.1 0.6 - - - -
26A GLU* 1.3 78.0 - - - +
28A GLU* 1.3 59.6 + - - +
31A LEU* 2.9 32.8 + - - +
60A ILE* 4.0 7.2 - - + -
104A VAL* 3.3 36.7 - - + +
105A LYS* 4.8 3.8 - - + -
107A VAL* 3.4 27.8 - - + -
109A VAL* 5.8 0.4 - - + -
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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 GLY 2.8 15.2 + - - +
25A ARG* 3.4 11.3 + - - +
27A ALA* 1.3 75.9 - - - +
29A GLU* 1.3 67.4 + - + +
31A LEU* 3.2 6.3 + - - +
32A ARG* 2.7 73.1 + - - +
44A PHE* 4.1 10.9 - - + -
48A TYR* 2.7 36.5 + - + +
60A ILE* 4.1 5.8 - - + +
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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 ARG* 3.1 44.7 + - + +
26A GLU* 4.7 8.6 - - - +
28A GLU* 1.3 81.1 - - + +
30A GLU* 1.3 66.5 + - + +
32A ARG* 3.5 11.6 + - - +
33A ARG* 3.3 29.6 + - + +
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Residues in contact with GLU 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 GLU* 2.9 27.2 + - + +
27A ALA* 4.1 3.6 - - - +
28A GLU 3.2 0.6 - - - -
29A GLU* 1.3 77.0 - - + +
31A LEU* 1.3 64.1 + - - +
32A ARG 3.3 0.2 - - - -
33A ARG* 2.6 44.7 + - - +
34A ARG* 3.3 39.1 + - - +
104A VAL* 4.9 6.7 - - + -
105A LYS* 3.7 32.9 + - + +
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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 ALA 2.9 20.9 + - - +
28A GLU 3.2 4.9 + - - +
30A GLU* 1.3 76.9 - - - +
32A ARG* 1.3 60.3 + - - +
34A ARG* 3.6 3.4 + - - +
35A LEU* 3.2 37.1 + - + +
44A PHE* 3.8 11.0 - - + -
60A ILE* 4.6 6.1 - - + -
62A VAL* 3.6 28.9 - - + -
86A VAL* 4.0 30.5 - - + +
87A LEU* 5.3 0.7 - - + -
104A VAL* 4.1 20.9 - - + -
109A VAL* 4.1 24.7 - - + -
111A VAL* 5.8 2.2 - - + -
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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 GLU* 2.7 51.1 + - - +
29A GLU* 3.8 10.4 - - - +
30A GLU 3.3 0.2 - - - -
31A LEU* 1.3 74.2 - - - +
33A ARG* 1.3 60.3 + - + +
34A ARG 3.1 2.0 - - - -
35A LEU* 3.0 4.5 + - - -
36A ASP* 2.9 40.3 + - - +
42A TYR* 3.7 17.6 - - - +
44A PHE* 3.4 48.8 - - + +
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Residues in contact with ARG 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* 3.3 15.3 + - + +
30A GLU* 2.6 44.4 + - - +
31A LEU 3.5 0.2 - - - -
32A ARG* 1.3 77.3 - - + +
34A ARG* 1.3 61.1 + - + +
36A ASP* 4.1 8.4 - - - +
37A GLU* 3.6 21.1 + - - +
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Residues in contact with ARG 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 GLU* 3.3 26.7 + - - +
31A LEU* 3.8 6.7 - - - +
32A ARG 3.1 0.6 - - - -
33A ARG* 1.3 78.8 - - + +
35A LEU* 1.3 64.3 + - - +
36A ASP 3.2 1.0 + - - -
37A GLU* 3.5 10.3 + - - +
38A LEU* 3.4 25.5 - - + +
85A ALA 5.6 0.7 - - - -
86A VAL* 3.2 46.6 + - + +
88A ASP* 3.3 26.0 + - - -
104A VAL* 3.8 20.6 - - - +
105A LYS* 4.8 17.0 - - - +
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Residues in contact with LEU 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 LEU* 3.2 38.2 + - + +
32A ARG 3.0 3.3 + - - +
34A ARG* 1.3 76.9 - - - +
36A ASP* 1.3 62.5 + - - +
38A LEU* 3.8 2.8 + - - +
39A GLY 3.6 12.5 + - - -
40A VAL* 3.7 27.4 + - + +
42A TYR* 3.6 41.7 - - + -
44A PHE* 4.2 2.9 - - + -
62A VAL* 4.0 14.4 - - + -
64A LEU* 4.5 11.0 - - + -
82A ILE* 4.4 15.7 - - + -
86A VAL* 3.9 27.1 - - + -
111A VAL* 6.0 2.2 - - + -
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Residues in contact with ASP 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* 2.9 25.7 + - - +
33A ARG* 4.1 8.3 + - - +
35A LEU* 1.3 75.0 - - - +
37A GLU* 1.3 64.5 + - - +
38A LEU 3.1 2.5 - - - -
39A GLY* 3.1 15.3 + - - +
40A VAL 5.8 0.2 - - - -
42A TYR* 2.8 29.1 + - - -
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Residues in contact with GLU 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 ARG 3.6 15.1 + - - +
34A ARG* 3.5 9.2 + - - +
35A LEU 3.5 0.6 - - - -
36A ASP* 1.3 78.2 - - - +
38A LEU* 1.3 67.0 + - + +
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Residues in contact with LEU 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 ARG* 3.4 16.5 + - + +
35A LEU* 4.1 8.1 - - - +
36A ASP 3.1 0.6 - - - -
37A GLU* 1.3 89.5 - - + +
39A GLY* 1.3 59.9 + - - +
40A VAL* 4.6 8.1 - - + +
82A ILE* 3.7 34.8 - - + -
85A ALA* 4.5 19.5 - - + -
86A VAL* 4.5 9.0 - - + -
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Residues in contact with GLY 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 LEU 3.6 1.8 + - - -
36A ASP* 3.1 16.4 + - - -
37A GLU 4.7 0.2 - - - -
38A LEU* 1.3 79.8 - - - +
40A VAL* 1.3 61.3 + - - +
41A GLU* 4.3 0.9 + - - +
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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