Contacts of the helix formed by residues 23 - 40 (chain O) in PDB entry 2HQT
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 THR 23 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21O SER 4.6 3.4 - - - +
22O PHE* 1.3 76.2 - - - +
24O LYS* 1.3 66.2 + - - +
25O GLU* 3.3 8.4 + - - +
26O GLN* 2.9 39.0 + - - +
27O SER* 3.0 20.7 + - - -
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Residues in contact with LYS 24 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23O THR* 1.3 75.1 - - - +
25O GLU* 1.3 64.4 + - - +
27O SER* 3.4 8.1 + - - -
28O ALA* 3.1 29.1 + - + +
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Residues in contact with GLU 25 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23O THR* 3.1 7.6 + - - +
24O LYS* 1.3 84.0 - - - +
26O GLN* 1.3 57.2 + - + +
28O ALA* 3.2 8.1 + - - +
29O GLN* 3.0 29.7 + - - +
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Residues in contact with GLN 26 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20O VAL* 5.8 1.3 - - - +
21O SER 3.8 3.8 - - - +
22O PHE* 3.4 23.1 - - + -
23O THR* 2.9 44.1 + - - +
25O GLU* 1.3 76.7 - - + +
27O SER* 1.3 50.7 + - - +
29O GLN* 3.4 2.6 + - - -
30O ALA* 2.8 32.6 + - - +
60O VAL* 2.8 48.2 + - + +
61O SER* 2.9 23.6 + - - -
62O THR* 3.9 9.3 - - - +
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Residues in contact with SER 27 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22O PHE* 3.4 32.0 + - - +
23O THR 3.0 11.2 + - - -
24O LYS* 3.5 12.1 - - - -
26O GLN* 1.3 74.3 - - - +
28O ALA* 1.3 57.6 + - - +
30O ALA* 3.2 3.6 + - - +
31O ALA* 2.9 30.1 + - - +
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Residues in contact with ALA 28 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24O LYS* 3.1 21.3 + - + +
25O GLU* 3.2 10.3 + - - +
27O SER* 1.3 75.3 - - - +
29O GLN* 1.3 59.7 + - - +
31O ALA* 3.3 6.7 + - - +
32O GLN* 2.8 29.8 + - - +
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Residues in contact with GLN 29 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25O GLU 3.0 13.6 + - - +
26O GLN* 3.6 11.0 - - - +
28O ALA* 1.3 72.1 - - - +
30O ALA* 1.3 65.9 + - - +
32O GLN* 3.3 14.4 + - - +
33O TRP* 3.0 56.5 + - + +
52O VAL* 3.6 24.2 - - - +
59O ILE 3.2 26.8 + - - +
60O VAL* 4.3 12.1 - - + -
61O SER* 6.1 0.2 - - - -
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Residues in contact with ALA 30 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22O PHE* 3.8 20.9 - - + -
26O GLN 2.8 20.3 + - - +
27O SER* 3.7 4.3 - - - +
29O GLN* 1.3 72.6 - - - +
31O ALA* 1.3 58.0 + - - +
33O TRP* 3.4 2.7 + - - +
34O GLU* 3.0 27.6 + - - +
60O VAL* 4.5 3.8 - - + -
68O THR* 3.6 32.0 - - + +
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Residues in contact with ALA 31 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27O SER 2.9 16.5 + - - +
28O ALA* 3.7 7.0 - - - +
30O ALA* 1.3 74.7 - - - +
32O GLN* 1.3 63.9 + - - +
34O GLU* 3.4 16.4 + - - +
35O SER* 3.0 23.7 + - - -
38O LYS* 5.4 0.7 + - - -
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Residues in contact with GLN 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28O ALA 2.8 15.3 + - - +
29O GLN* 3.4 19.4 - - - +
31O ALA* 1.3 75.5 - - - +
33O TRP* 1.3 105.2 + - - +
35O SER* 3.1 8.5 + - - -
36O VAL* 3.1 36.8 + - + +
45O HIS* 4.4 1.7 + - + -
48O GLN* 3.5 30.5 + - - -
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Residues in contact with TRP 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29O GLN* 3.0 50.1 + - + +
30O ALA* 4.0 4.5 - - - +
31O ALA 3.4 0.2 - - - -
32O GLN* 1.3 99.8 + - - +
34O GLU* 1.3 57.0 + - - +
36O VAL* 3.3 14.7 + - + +
37O LEU* 2.8 36.7 + - + +
42O ILE* 4.1 13.2 - - + -
45O HIS* 3.8 40.4 - - + -
48O GLN* 4.2 10.3 - - + -
49O LEU* 3.8 32.1 - - + -
52O VAL* 4.5 6.3 - - + -
59O ILE* 3.5 21.4 - - + +
68O THR* 5.1 7.9 - - - -
72O VAL* 3.9 29.2 - - + -
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Residues in contact with GLU 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30O ALA 3.0 14.1 + - - +
31O ALA* 3.5 18.0 - - - +
32O GLN 3.3 0.2 - - - -
33O TRP* 1.3 76.4 - - - +
35O SER* 1.3 56.6 + - - +
37O LEU* 3.8 10.2 - - - +
38O LYS* 3.0 60.3 + - + +
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Residues in contact with SER 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31O ALA 3.0 13.0 + - - -
32O GLN* 3.1 11.6 + - - -
34O GLU* 1.3 73.8 - - - +
36O VAL* 1.3 61.3 + - - +
38O LYS* 3.4 17.1 + - - +
39O SER* 2.8 37.9 + - - -
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Residues in contact with VAL 36 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32O GLN* 3.1 27.5 + - + +
33O TRP* 3.5 12.6 - - + +
35O SER* 1.3 73.9 - - - +
37O LEU* 1.3 63.0 - - - +
39O SER* 3.4 5.6 + - - -
40O GLY 3.2 2.9 + - - -
41O GLN* 2.9 56.9 + - - +
42O ILE* 3.8 20.6 - - + +
45O HIS* 3.6 38.6 - - + +
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Residues in contact with LEU 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O TRP* 2.8 24.1 + - + +
34O GLU* 3.8 8.7 - - - +
36O VAL* 1.3 76.0 - - - +
38O LYS* 1.3 63.3 + - + +
40O GLY* 3.1 14.7 + - - -
42O ILE* 4.2 15.5 - - + +
68O THR* 5.2 1.6 - - - +
71O HIS* 3.5 47.6 - - + +
72O VAL* 3.9 22.9 - - + -
75O VAL* 4.0 21.5 - - + -
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Residues in contact with LYS 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31O ALA 5.4 0.6 + - - -
34O GLU* 3.0 58.3 + - + +
35O SER* 3.7 16.9 + - - +
37O LEU* 1.3 78.6 - - + +
39O SER* 1.3 58.5 + - - +
40O GLY 3.2 1.0 + - - -
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Residues in contact with SER 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O SER* 2.8 24.4 + - - -
36O VAL* 3.7 3.8 - - - -
37O LEU 3.3 0.2 - - - -
38O LYS* 1.3 75.7 - - - +
40O GLY* 1.3 60.4 + - - +
41O GLN* 3.5 34.1 + - - +
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Residues in contact with GLY 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O VAL 3.2 0.2 + - - -
37O LEU* 3.1 16.2 + - - -
38O LYS 3.2 1.6 + - - -
39O SER* 1.3 79.8 - - - +
41O GLN* 1.3 59.6 + - - +
42O ILE* 3.5 5.4 + - - +
43O GLN 5.1 0.9 + - - -
44O PRO* 5.4 0.7 - - - +
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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