Contacts of the helix formed by residues 21 - 38 (chain E) in PDB entry 2ZHX
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 VAL 21 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18E LEU* 2.6 51.1 + - + +
20E PRO* 1.3 74.3 - - + +
22E ALA* 1.3 53.1 + - - -
23E ASP 3.4 2.2 - - - -
24E GLN* 2.8 20.3 + - + -
25E VAL* 2.7 36.4 + - + +
147E ALA* 3.5 32.5 - - + +
148E VAL* 3.8 17.9 - - + -
151E CYS* 3.5 14.1 - - + -
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Residues in contact with ALA 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E LEU* 3.9 20.0 - - + +
18E LEU 3.3 2.4 + - - -
19E GLU* 3.0 22.5 + - + +
20E PRO 3.3 1.0 - - - -
21E VAL* 1.3 74.9 - - - +
23E ASP* 1.3 62.0 + - - +
25E VAL* 3.1 11.1 - - - +
26E ALA* 2.9 29.3 + - - +
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Residues in contact with ASP 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E PRO 5.2 2.5 + - - +
21E VAL 3.4 0.4 - - - -
22E ALA* 1.3 78.7 - - - +
24E GLN* 1.3 51.6 + - - +
26E ALA* 3.4 7.7 + - - +
27E HIS* 2.8 33.8 + - - +
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Residues in contact with GLN 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E VAL* 2.8 32.9 + - + +
23E ASP* 1.3 71.7 - - - +
25E VAL* 1.3 57.4 + - - +
27E HIS* 3.5 20.5 - - - +
28E MET* 3.0 31.4 + - - +
144E GLY* 2.8 37.8 + - - -
147E ALA* 4.0 20.2 - - + +
148E VAL* 4.5 4.2 - - + +
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Residues in contact with VAL 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E LEU* 4.0 22.2 - - + -
9E LEU* 4.5 15.9 - - + -
18E LEU* 5.5 2.0 - - + -
21E VAL* 2.7 33.6 + - + +
22E ALA* 3.1 19.7 - - - +
24E GLN* 1.3 69.6 - - - +
26E ALA* 1.3 63.0 + - - +
28E MET* 3.4 9.4 - - - +
29E GLY* 3.1 17.2 + - - -
50E LEU* 4.4 25.1 - - + -
145E TRP* 5.1 5.0 - - + -
148E VAL* 4.3 18.3 - - + +
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Residues in contact with ALA 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ARG 5.2 10.3 - - - +
22E ALA 2.9 17.3 + - - +
23E ASP* 3.5 10.3 - - - +
25E VAL* 1.3 75.5 - - - +
27E HIS* 1.3 66.5 + - - +
29E GLY* 2.9 15.7 + - - -
30E GLN* 3.3 11.3 + - - +
33E ARG* 5.2 1.0 + - - -
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Residues in contact with HIS 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E ASP 2.8 21.3 + - - +
24E GLN* 3.3 23.5 + - - +
26E ALA* 1.3 70.9 - - - +
28E MET* 1.3 80.5 - - - +
29E GLY 2.7 1.7 + - - -
30E GLN* 2.8 40.0 + - + +
31E PHE* 3.1 18.4 + - + +
143E LYS 4.7 8.0 + - - -
144E GLY* 5.5 0.9 - - - -
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Residues in contact with MET 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E GLN* 3.0 16.9 + - - +
25E VAL* 3.4 10.3 - - - +
27E HIS* 1.3 87.7 - - - +
29E GLY* 1.3 63.7 + - - +
31E PHE* 3.2 25.0 + - + +
32E LEU* 3.0 27.2 + - - +
143E LYS 3.7 21.1 - - - +
144E GLY* 3.6 24.5 - - - +
145E TRP* 3.4 69.8 - - + +
148E VAL* 4.5 0.9 - - + -
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Residues in contact with GLY 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E VAL 3.1 7.4 + - - -
26E ALA* 2.9 9.3 + - - -
27E HIS 2.7 3.0 + - - -
28E MET* 1.3 78.1 - - - +
30E GLN* 1.3 60.9 + - - -
32E LEU* 3.1 19.5 + - - +
33E ARG* 3.1 28.4 + - - +
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Residues in contact with GLN 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ALA* 3.3 7.6 + - - +
27E HIS* 2.8 43.7 + - + +
29E GLY* 1.3 71.2 - - - -
31E PHE* 1.3 57.4 + - - +
33E ARG* 3.3 30.8 - - - +
34E ALA* 3.0 28.3 + - - +
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Residues in contact with PHE 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E HIS* 3.1 22.7 + - + +
28E MET* 3.4 29.4 - - + +
30E GLN* 1.3 75.7 - - - +
32E LEU* 1.3 78.2 + - + +
34E ALA* 3.1 10.3 + - + +
35E GLU* 2.8 61.1 + - + +
131E THR* 4.6 0.4 - - - -
140E HIS* 3.8 24.9 - + - -
143E LYS* 3.8 42.2 - - + -
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Residues in contact with LEU 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E MET 3.0 18.1 + - - +
29E GLY* 3.4 9.6 - - - +
31E PHE* 1.3 98.7 - - + +
33E ARG* 1.3 59.3 + - + +
35E GLU* 2.8 26.1 + - + +
36E ILE* 3.2 5.5 + - - +
42E TYR* 3.7 51.1 - - + +
49E VAL* 4.2 9.2 - - + -
131E THR* 3.7 36.1 - - + +
140E HIS* 4.4 2.9 - - + -
145E TRP* 4.5 9.4 - - + +
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Residues in contact with ARG 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ALA 5.2 0.8 + - - -
29E GLY* 3.1 24.7 + - - +
30E GLN* 3.3 31.6 - - - +
32E LEU* 1.3 74.8 - - + +
34E ALA* 1.3 58.1 + - - +
36E ILE* 3.1 17.0 + - + +
37E ALA* 3.0 27.3 + - - +
42E TYR* 6.2 0.2 - - - +
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Residues in contact with ALA 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E GLN 3.0 21.7 + - - +
31E PHE* 3.1 12.3 + - + +
33E ARG* 1.3 74.3 - - - +
35E GLU* 1.3 64.1 + - - +
37E ALA* 3.5 9.3 - - - +
38E ALA* 3.0 26.3 + - - +
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Residues in contact with GLU 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E PHE* 2.8 50.6 + - + +
32E LEU* 2.8 16.6 + - - +
34E ALA* 1.3 74.4 - - - +
36E ILE* 1.3 55.6 + - - +
38E ALA* 3.5 1.8 + - - -
39E GLY 3.5 2.8 + - - -
40E ARG* 2.7 82.4 + - - +
41E ARG 5.1 2.4 - - - +
42E TYR* 4.7 10.8 - - + +
133E ARG* 4.7 5.4 + - - +
140E HIS* 3.6 19.8 + - + +
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Residues in contact with ILE 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LEU 3.2 10.4 + - - +
33E ARG* 3.1 14.0 + - + +
35E GLU* 1.3 74.8 - - - +
37E ALA* 1.3 56.0 + - - +
39E GLY* 2.6 30.6 + - - +
40E ARG 3.3 10.1 - - - +
41E ARG* 5.2 6.7 - - + -
42E TYR* 4.1 28.3 - - + +
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Residues in contact with ALA 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ARG 3.0 12.2 + - - +
34E ALA* 3.5 14.8 - - - +
36E ILE* 1.3 77.3 - - - +
38E ALA* 1.3 57.3 + - - +
39E GLY* 3.1 3.9 + - - -
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Residues in contact with ALA 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ALA 3.0 17.8 + - - +
35E GLU 3.8 2.0 - - - +
36E ILE 3.2 0.2 - - - -
37E ALA* 1.3 73.7 - - - +
39E GLY* 1.3 55.1 + - - +
40E ARG* 3.4 44.4 + - - +
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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