Contacts of the helix formed by residues 22 - 37 (chain A) in PDB entry 1WZN
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 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ARG* 3.4 17.5 + - - +
19A ARG* 3.7 31.3 + - - +
20A ILE 3.0 0.2 - - - -
21A GLU* 1.3 81.6 - - + +
23A VAL* 1.3 63.0 + - - +
24A LYS* 3.1 4.3 + - - +
25A ALA* 3.3 20.4 + - + +
26A GLU* 2.6 49.4 + - - +
113A PHE* 4.7 12.3 - - - -
242A ARG* 4.2 12.2 - - - +
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Residues in contact with VAL 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 ARG* 3.4 17.9 + - - +
20A ILE* 3.2 21.2 + - + +
21A GLU 3.6 0.2 - - - -
22A ARG* 1.3 77.0 - - - +
24A LYS* 1.3 70.7 + - + +
26A GLU* 3.2 7.5 + - + +
27A ILE* 2.9 30.6 + - + +
54A ILE* 3.8 20.2 - - + +
55A PRO* 3.7 30.7 - - + -
58A GLU* 3.9 17.5 - - + +
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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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21A GLU 5.7 3.8 - - - +
22A ARG* 3.1 1.4 - - - +
23A VAL* 1.3 85.7 - - + +
25A ALA* 1.3 61.9 + - - +
28A ASP* 3.1 15.9 + - - +
58A GLU* 3.0 37.9 + - - +
61A GLU* 3.7 18.8 + - - -
62A ARG* 2.9 29.0 + - - +
86A ARG* 5.5 0.8 - - - +
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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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22A ARG* 3.3 17.5 + - + +
24A LYS* 1.3 78.5 - - - +
26A GLU* 1.3 62.5 + - - +
28A ASP* 3.3 14.3 + - - +
29A PHE* 3.2 19.8 + - - +
232A LEU* 4.3 19.1 - - + +
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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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19A ARG* 3.2 31.3 + - - -
22A ARG* 2.6 40.6 + - + +
23A VAL* 3.2 9.9 + - + +
25A ALA* 1.3 80.0 - - - +
27A ILE* 1.3 63.0 + - + +
29A PHE* 3.2 6.2 + - - +
30A VAL* 3.0 29.3 + - + +
55A PRO* 5.6 1.1 - - + +
112A PHE* 5.1 2.8 - - + -
113A PHE* 6.1 0.7 - - - -
144A ASP* 5.4 0.9 - - - +
232A LEU* 4.2 15.0 - - + -
242A ARG* 2.8 39.1 + - - +
244A TRP* 4.5 12.1 - - + -
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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
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23A VAL* 2.9 18.2 + - + +
26A GLU* 1.3 76.9 - - + +
28A ASP* 1.3 59.6 + - - +
30A VAL* 4.0 18.6 - - + -
31A GLU* 2.8 31.1 + - + +
55A PRO* 4.1 19.3 - - + +
58A GLU* 3.4 32.1 - - + -
59A LEU* 3.8 36.1 - - + -
62A ARG* 3.5 32.3 - - - +
112A PHE* 4.2 6.7 - - + -
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Residues in contact with ASP 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 20.6 + - - +
25A ALA* 3.4 15.0 - - - +
27A ILE* 1.3 77.2 - - - +
29A PHE* 1.3 64.1 + - - +
31A GLU* 3.3 5.4 + - - +
32A GLU* 3.1 20.4 + - - +
62A ARG* 2.9 29.5 + - - +
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Residues in contact with PHE 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 3.2 4.3 + - - +
26A GLU 3.2 8.2 + - - +
27A ILE 3.2 0.2 - - - -
28A ASP* 1.3 77.5 - - - +
30A VAL* 1.3 67.1 + - - +
32A GLU* 3.0 15.4 + - - +
33A ILE* 3.0 39.0 + - + +
229A TYR* 4.0 13.0 - + + -
232A LEU* 3.4 44.2 - - + +
233A LYS* 3.3 39.7 - - - -
234A ARG* 3.6 14.1 - - + -
244A TRP* 3.6 40.8 - + - -
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Residues in contact with VAL 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 3.0 19.8 + - - +
27A ILE* 3.2 14.6 + - + +
29A PHE* 1.3 76.4 - - + +
31A GLU* 1.3 56.8 + - - +
33A ILE* 3.0 12.9 + - - +
34A PHE* 2.9 57.5 + - + -
59A LEU* 4.5 9.6 - - + -
110A THR* 5.0 0.7 - - + -
112A PHE* 3.7 36.1 - - + -
142A ILE* 4.0 11.0 - - + -
244A TRP* 4.4 12.1 - - + -
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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 ILE* 2.8 23.8 + - + +
28A ASP* 3.7 5.5 - - - +
29A PHE 3.2 0.2 - - - -
30A VAL* 1.3 73.4 - - - +
32A GLU* 1.3 59.5 + - - +
34A PHE* 3.3 11.9 + - + +
35A LYS* 2.9 29.3 + - - +
62A ARG* 2.6 40.6 + - - +
64A TYR* 2.7 39.7 + - + +
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Residues in contact with GLU 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 ASP 3.1 12.1 + - - +
29A PHE* 3.0 23.4 + - + +
31A GLU* 1.3 77.0 - - - +
33A ILE* 1.3 57.9 + - - +
35A LYS* 3.3 7.2 + - + +
36A GLU* 2.8 39.1 + - + +
232A LEU 5.0 2.1 - - - +
233A LYS* 5.1 0.7 - - - -
234A ARG* 3.5 33.3 + - - +
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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 PHE* 3.0 49.1 + - + +
30A VAL* 3.3 9.4 - - - +
32A GLU* 1.3 77.7 - - - +
34A PHE* 1.3 57.7 + - - +
37A ASP* 2.7 52.6 + - + +
38A ALA 3.3 1.7 + - - -
140A VAL* 4.8 3.8 - - + -
142A ILE* 3.6 35.4 - - + -
229A TYR* 4.5 3.4 - - + -
234A ARG* 4.5 2.2 - - + +
244A TRP* 5.0 0.9 - - + -
246A VAL* 3.8 35.9 - - + -
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Residues in contact with PHE 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 VAL* 2.9 33.8 + - + -
31A GLU* 3.5 10.8 - - - +
33A ILE* 1.3 77.4 - - - +
35A LYS* 1.3 61.5 + - - +
38A ALA* 3.1 28.5 + - - +
40A ARG 4.6 2.6 - - - +
42A VAL* 3.7 35.0 - - + +
45A VAL* 4.2 8.3 - - + -
59A LEU* 4.1 12.6 - - + -
64A TYR* 3.5 34.1 - + - +
108A ALA* 3.6 22.0 - - + -
110A THR* 4.8 6.3 - - + -
140A VAL* 4.0 12.1 - - + -
142A ILE* 3.6 22.0 - - + -
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Residues in contact with LYS 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 2.9 17.0 + - - +
32A GLU* 3.7 7.6 - - + +
34A PHE* 1.3 80.1 - - - +
36A GLU* 1.3 83.6 + - + +
38A ALA 4.6 4.5 - - - +
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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 GLU* 2.8 33.1 + - + +
35A LYS* 1.3 109.1 + - + +
37A ASP* 1.3 62.1 + - - +
38A ALA 4.5 2.3 - - - +
39A LYS* 4.9 8.3 + - - -
234A ARG* 3.3 36.7 + - - +
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Residues in contact with ASP 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 ILE* 2.7 35.9 + - + +
36A GLU* 1.3 72.3 - - - +
38A ALA* 1.3 64.2 + - - +
39A LYS* 3.7 9.6 + - - +
140A VAL* 4.1 2.5 - - + -
227A LYS* 3.2 18.1 - - - +
229A TYR* 2.8 34.2 + - - -
234A ARG* 2.8 33.8 + - - -
246A VAL* 4.3 6.1 - - + -
248A ILE* 3.6 30.7 - - + +
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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