Contacts of the helix formed by residues 23 - 39 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21Q SER 3.7 11.9 - - - +
22Q PHE* 1.3 77.4 - - - +
24Q LYS* 1.3 60.3 + - - +
25Q GLU* 3.5 10.2 + - - +
26Q GLN* 2.8 41.2 + - - +
27Q SER* 3.0 28.3 + - - -
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Residues in contact with LYS 24 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Q THR* 1.3 75.4 - - - +
25Q GLU* 1.3 57.2 + - - +
27Q SER* 3.4 7.3 + - - -
28Q ALA* 2.9 30.5 + - - +
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Residues in contact with GLU 25 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Q THR* 3.6 10.5 - - - +
24Q LYS* 1.3 78.0 - - - +
26Q GLN* 1.3 58.0 + - + +
28Q ALA* 3.3 7.2 + - - +
29Q GLN* 2.9 54.4 + - - +
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Residues in contact with GLN 26 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Q SER* 3.8 2.6 + - - +
22Q PHE* 3.3 21.4 - - + -
23Q THR* 2.8 45.1 + - - +
25Q GLU* 1.3 77.8 - - + +
27Q SER* 1.3 60.8 + - - +
29Q GLN* 3.2 5.0 + - - +
30Q ALA* 2.9 27.5 + - - +
60Q VAL* 2.9 45.9 + - + +
61Q SER* 3.4 21.3 + - - +
62Q THR* 3.6 15.2 - - - +
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Residues in contact with SER 27 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Q PHE* 3.6 18.1 - - - -
23Q THR 3.0 13.7 + - - -
24Q LYS* 3.5 11.9 - - - -
26Q GLN* 1.3 76.7 - - - +
28Q ALA* 1.3 61.8 + - - +
30Q ALA* 3.3 5.9 + - - +
31Q ALA* 3.0 23.6 + - - +
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Residues in contact with ALA 28 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G SER* 5.4 4.5 - - - +
22G PHE* 4.3 15.8 - - + +
27G SER* 4.3 8.1 - - - +
24Q LYS 2.9 17.8 + - - +
25Q GLU* 3.5 8.1 - - - +
26Q GLN 3.3 0.2 - - - -
27Q SER* 1.3 76.6 - - - +
29Q GLN* 1.3 57.0 + - + +
31Q ALA* 3.3 7.5 + - - +
32Q GLN* 2.9 47.8 + - - +
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Residues in contact with GLN 29 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Q GLU* 2.9 44.5 + - + +
26Q GLN* 3.7 6.4 - - - +
28Q ALA* 1.3 76.0 - - + +
30Q ALA* 1.3 63.0 + - - +
32Q GLN* 3.3 18.0 + - - +
33Q TRP* 3.0 38.1 + - + +
52Q VAL* 6.0 0.9 - - - +
59Q ILE 4.5 11.3 - - - +
60Q VAL* 4.4 14.8 - - + +
61Q SER* 4.7 6.9 + - - -
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Residues in contact with ALA 30 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22Q PHE* 4.8 8.5 - - + -
26Q GLN 2.9 14.6 + - - +
27Q SER* 3.6 10.1 - - - +
29Q GLN* 1.3 75.9 - - - +
31Q ALA* 1.3 57.7 + - - +
33Q TRP* 3.3 2.6 + - - +
34Q GLU* 2.9 29.7 + - - +
60Q VAL* 3.9 10.6 - - + +
68Q THR* 3.5 27.1 + - - +
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Residues in contact with ALA 31 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G SER* 5.0 19.1 - - - -
22G PHE 5.5 1.3 - - - +
27Q SER 3.0 13.8 + - - +
28Q ALA* 3.6 10.5 - - - +
30Q ALA* 1.3 76.3 - - - +
32Q GLN* 1.3 57.9 + - + +
34Q GLU* 3.4 8.5 + - - +
35Q SER* 2.9 28.8 + - - -
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Residues in contact with GLN 32 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G PHE 2.8 27.1 + - - +
23G THR* 3.1 8.7 - - - -
24G LYS* 3.4 34.9 - - + +
27G SER* 2.9 25.0 + - - -
28Q ALA* 2.9 23.1 + - - +
29Q GLN* 3.5 19.4 - - - +
30Q ALA 3.2 0.2 - - - -
31Q ALA* 1.3 74.6 - - + +
33Q TRP* 1.3 67.2 + - + +
35Q SER* 3.2 9.4 + - - -
36Q VAL* 3.1 26.8 + - + +
48Q GLN* 5.7 1.9 + - - -
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Residues in contact with TRP 33 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Q GLN* 3.0 36.4 + - + +
30Q ALA 3.9 0.4 - - - +
32Q GLN* 1.3 77.3 - - + +
34Q GLU* 1.3 63.3 + - - +
36Q VAL* 3.4 20.4 + - + +
37Q LEU* 3.1 29.5 + - + +
42Q ILE* 4.7 9.0 - - + -
45Q HIS* 3.8 27.6 - - + -
48Q GLN* 4.0 30.1 - - + +
49Q LEU* 3.7 42.6 - - + -
52Q VAL* 4.5 10.4 - - + +
59Q ILE* 3.4 32.5 + - + +
60Q VAL* 4.9 0.2 - - + -
68Q THR* 3.9 19.7 - - + -
72Q VAL* 4.1 17.3 - - + -
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Residues in contact with GLU 34 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Q ALA 2.9 18.0 + - - +
31Q ALA* 3.5 10.3 - - - +
33Q TRP* 1.3 76.5 - - - +
35Q SER* 1.3 56.3 + - - +
37Q LEU* 3.3 12.1 + - - +
38Q LYS* 2.8 48.4 + - - +
68Q THR* 5.6 0.4 - - - +
71Q HIS* 6.6 0.2 - - + -
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Residues in contact with SER 35 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Q ALA 2.9 14.1 + - - -
32Q GLN* 3.2 12.5 + - - -
34Q GLU* 1.3 75.1 - - - +
36Q VAL* 1.3 54.2 + - - +
38Q LYS* 3.3 8.8 + - - +
39Q SER* 2.8 40.7 + - - -
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Residues in contact with VAL 36 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Q GLN* 3.1 19.6 + - + +
33Q TRP* 3.6 26.7 - - + +
35Q SER* 1.3 74.4 - - - +
37Q LEU* 1.3 62.4 + - + +
39Q SER* 2.9 11.8 + - - -
40Q GLY 3.1 0.2 + - - -
41Q GLN* 2.9 56.6 + - - +
42Q ILE* 3.6 12.8 - - + +
45Q HIS* 3.6 37.9 - - + +
48Q GLN* 5.6 0.4 - - - +
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Residues in contact with LEU 37 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Q TRP 3.1 16.9 + - - +
34Q GLU* 3.5 11.0 - - - +
36Q VAL* 1.3 76.6 - - + +
38Q LYS* 1.3 65.9 + - + +
40Q GLY* 3.0 14.7 + - - -
42Q ILE* 4.8 13.9 - - + +
68Q THR* 6.2 0.4 - - + -
71Q HIS* 3.5 42.2 - - + +
72Q VAL* 3.8 20.2 - - + +
75Q VAL* 3.9 32.3 - - + -
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Residues in contact with LYS 38 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Q GLU* 2.8 39.8 + - - +
35Q SER* 3.8 8.4 - - - +
37Q LEU* 1.3 75.2 - - + +
39Q SER* 1.3 59.4 + - - +
40Q GLY 3.2 0.8 + - - -
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Residues in contact with SER 39 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Q SER* 2.8 22.8 + - - -
36Q VAL* 2.9 10.9 + - - -
38Q LYS* 1.3 75.7 - - - +
40Q GLY* 1.3 61.2 + - - +
41Q GLN* 3.3 31.7 + - - +
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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