Contacts of the helix formed by residues 23 - 40 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E SER 3.5 14.1 - - - +
22E PHE* 1.3 78.0 - - - +
24E LYS* 1.3 60.1 + - - +
25E GLU* 3.5 10.0 + - - +
26E GLN* 3.0 37.7 + - - +
27E SER* 3.0 26.7 + - - -
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Residues in contact with LYS 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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23E THR* 1.3 71.2 - - - +
25E GLU* 1.3 60.1 + - - +
27E SER* 3.3 7.9 + - - -
28E ALA* 2.9 29.5 + - - +
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Residues in contact with GLU 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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23E THR* 3.5 10.5 + - - +
24E LYS* 1.3 75.2 - - - +
26E GLN* 1.3 66.8 + - + +
28E ALA* 3.1 7.3 + - - +
29E GLN* 3.0 37.6 + - - +
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Residues in contact with GLN 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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21E SER* 3.8 4.8 + - - -
22E PHE* 3.4 32.6 - - + +
23E THR* 3.0 51.6 + - - +
25E GLU* 1.3 76.5 - - + +
27E SER* 1.3 62.6 + - - +
29E GLN* 3.4 8.3 + - - +
30E ALA* 3.1 24.1 + - - +
60E VAL* 2.8 31.3 - - - +
61E SER* 3.5 20.6 - - - +
62E THR* 3.6 10.2 - - - +
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Residues in contact with SER 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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22E PHE* 3.5 18.3 - - - -
23E THR 3.0 13.7 + - - -
24E LYS* 3.5 12.3 - - - -
25E GLU 3.1 0.2 - - - -
26E GLN* 1.3 77.7 - - - +
28E ALA* 1.3 60.6 + - - +
30E ALA* 3.4 4.7 + - - +
31E ALA* 3.1 23.6 + - - +
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Residues in contact with ALA 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 LYS 2.9 16.7 + - - +
25E GLU* 3.1 7.6 + - - +
27E SER* 1.3 76.7 - - - +
29E GLN* 1.3 58.3 + - + +
31E ALA* 3.6 6.4 + - - +
32E GLN* 3.1 44.0 + - - +
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Residues in contact with GLN 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 GLU* 3.0 24.3 + - - +
26E GLN* 3.8 6.7 - - - +
28E ALA* 1.3 76.5 - - + +
30E ALA* 1.3 60.0 + - - +
32E GLN* 3.2 17.6 + - - +
33E TRP* 3.0 42.1 + - + +
52E VAL* 5.6 4.5 - - - +
59E ILE 4.2 13.7 - - - +
60E VAL* 4.0 12.4 - - + +
61E SER* 5.0 5.1 + - - -
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Residues in contact with ALA 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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22E PHE* 4.7 9.6 - - + -
26E GLN 3.1 17.5 + - - +
27E SER* 3.6 7.0 - - - +
29E GLN* 1.3 74.1 - - - +
31E ALA* 1.3 59.6 + - - +
33E TRP* 3.4 3.6 + - - +
34E GLU* 2.9 34.3 + - - +
60E VAL* 3.8 12.2 - - + +
68E THR* 3.6 23.4 + - - +
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Residues in contact with ALA 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 SER 3.1 14.3 + - - +
28E ALA* 3.7 7.6 - - - +
30E ALA* 1.3 78.6 - - - +
32E GLN* 1.3 51.5 + - + +
34E GLU* 3.1 8.4 + - - +
35E SER* 2.8 36.2 + - - -
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Residues in contact with GLN 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 ALA* 3.1 33.1 + - - +
29E GLN* 3.2 20.7 + - - +
31E ALA* 1.3 73.6 - - + +
33E TRP* 1.3 61.2 + - + +
35E SER* 3.3 8.3 + - - -
36E VAL* 3.0 34.6 + - + +
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Residues in contact with TRP 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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29E GLN* 3.0 35.6 + - - +
30E ALA 3.9 1.1 - - - +
32E GLN* 1.3 77.1 - - + +
34E GLU* 1.3 58.5 + - - +
36E VAL* 3.4 16.8 + - + +
37E LEU* 3.0 34.8 + - + +
42E ILE* 5.9 3.4 - - + -
45E HIS* 4.0 27.6 - + + -
48E GLN* 4.2 21.3 - - + -
49E LEU* 3.7 47.1 - - + -
52E VAL* 4.4 12.9 - - + +
59E ILE* 3.2 32.5 + - + +
60E VAL* 4.6 2.7 - - + -
68E THR* 3.9 21.8 - - + -
72E VAL* 4.1 19.1 - - + -
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Residues in contact with GLU 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 ALA* 2.9 20.7 + - - +
31E ALA* 3.5 8.7 - - - +
33E TRP* 1.3 75.9 - - - +
35E SER* 1.3 53.1 + - - +
37E LEU* 3.4 24.1 - - - +
38E LYS* 2.8 34.2 + - - +
67E SER* 5.5 0.7 + - - -
68E THR* 4.1 14.6 + - - +
71E HIS* 3.2 33.9 + - - -
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Residues in contact with SER 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 ALA 2.8 13.7 + - - -
32E GLN* 3.4 13.0 - - - -
34E GLU* 1.3 75.1 - - - +
36E VAL* 1.3 58.8 + - - +
38E LYS* 3.3 8.5 - - - +
39E SER* 3.0 30.8 + - - -
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Residues in contact with VAL 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 GLN* 3.0 21.6 + - + +
33E TRP* 3.4 24.4 + - + +
35E SER* 1.3 72.7 - - - +
37E LEU* 1.3 67.3 + - + +
39E SER* 3.0 11.9 + - - -
40E GLY 3.1 0.2 + - - -
41E GLN* 2.9 53.3 + - - +
42E ILE* 3.8 11.2 - - + +
45E HIS* 3.7 37.7 - - + +
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Residues in contact with LEU 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 TRP* 3.0 18.9 + - + +
34E GLU* 3.4 29.2 - - - +
36E VAL* 1.3 77.8 - - + +
38E LYS* 1.3 65.2 + - - +
40E GLY* 3.0 14.9 + - - -
41E GLN 5.1 0.2 - - - +
42E ILE* 4.7 11.7 - - + +
68E THR* 6.2 0.2 - - + -
71E HIS* 3.5 31.9 - - + +
72E VAL* 3.8 18.8 - - + +
75E VAL* 4.0 36.1 - - + -
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Residues in contact with LYS 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 GLU 2.8 19.5 + - - +
35E SER* 3.3 12.1 - - - +
37E LEU* 1.3 77.4 - - - +
39E SER* 1.3 59.4 + - - +
40E GLY 3.4 0.7 + - - -
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Residues in contact with SER 39 (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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35E SER 3.0 18.0 + - - -
36E VAL* 3.0 10.2 + - - -
38E LYS* 1.3 74.8 - - - +
40E GLY* 1.3 59.3 + - - +
41E GLN* 3.5 25.7 + - - +
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Residues in contact with GLY 40 (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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37E LEU* 3.0 16.3 + - - -
38E LYS 3.2 2.0 + - - -
39E SER* 1.3 78.9 - - - +
41E GLN* 1.3 58.8 + - - +
42E ILE* 3.4 10.3 + - - +
43E GLN* 4.9 1.7 + - - +
44E PRO* 5.3 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