Contacts of the helix formed by residues 23 - 39 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C PHE* 1.3 89.8 - - + +
24C LYS* 1.3 54.5 + - - +
25C GLU* 3.2 19.9 + - - +
26C GLN* 3.0 40.1 + - - +
27C SER* 2.7 31.4 + - - -
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Residues in contact with LYS 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C THR* 1.3 72.6 - - - +
25C GLU* 1.3 67.5 + - - +
27C SER* 3.7 6.6 + - - -
28C ALA* 3.1 27.4 + - - +
86F SER 5.2 1.6 - - - +
87F SER 4.1 20.8 - - - +
88F LYS* 4.2 34.0 - - + +
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Residues in contact with GLU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C THR* 3.1 18.4 + - - +
24C LYS* 1.3 84.2 + - + +
26C GLN* 1.3 60.3 + - + +
28C ALA* 3.6 7.0 + - - +
29C GLN* 3.1 26.7 + - - +
85F ALA 4.9 12.4 - - - +
86F SER* 5.7 2.3 - - - -
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Residues in contact with GLN 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C SER 2.9 23.1 - - - +
22C PHE* 3.7 12.3 - - - +
23C THR* 3.0 43.4 + - - +
25C GLU* 1.3 76.5 - - + +
27C SER* 1.3 58.2 + - - +
29C GLN* 3.1 5.0 + - - +
30C ALA* 2.8 26.9 + - - +
60C VAL* 2.9 39.1 - - + +
61C SER* 3.0 21.9 - - - +
62C THR* 3.8 10.9 - - - +
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Residues in contact with SER 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C SER* 3.1 9.4 + - - +
22C PHE 2.8 14.0 + - - -
23C THR 2.7 27.7 + - - -
24C LYS* 3.9 5.4 - - - -
26C GLN* 1.3 70.7 - - - +
28C ALA* 1.3 57.7 + - - +
30C ALA* 3.2 7.4 + - - +
31C ALA* 2.9 31.7 + - - +
88F LYS 5.4 7.2 - - - -
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Residues in contact with ALA 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LYS 3.1 17.0 + - - +
25C GLU* 3.7 8.5 - - - +
27C SER* 1.3 78.7 - - - +
29C GLN* 1.3 56.5 + - - +
31C ALA* 3.5 6.1 + - - +
32C GLN* 3.0 27.7 + - - +
87F SER 5.3 3.6 - - - +
88F LYS 6.4 0.7 - - - -
89F ASP* 6.3 1.6 - - - +
90F VAL* 4.2 27.6 - - + +
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Residues in contact with GLN 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C GLU 3.1 14.5 + - - +
26C GLN* 3.1 12.2 + - - +
28C ALA* 1.3 74.1 - - - +
30C ALA* 1.3 65.4 + - - +
32C GLN* 3.4 6.0 + - + +
33C TRP* 3.1 47.8 + - - -
52C VAL* 3.5 18.5 - - - +
59C ILE* 2.9 47.0 + - - +
60C VAL* 3.4 11.2 - - + +
61C SER* 5.8 2.2 - - - +
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Residues in contact with ALA 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C SER* 5.2 8.7 - - - +
26C GLN 2.8 18.0 + - - +
27C SER* 3.7 8.1 - - - +
29C GLN* 1.3 74.4 - - - +
31C ALA* 1.3 63.0 + - - +
33C TRP* 3.5 3.1 + - - +
34C GLU* 3.1 21.1 + - - +
60C VAL* 4.2 11.6 - - + +
68C THR* 4.0 23.1 + - - +
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Residues in contact with ALA 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C SER 2.9 16.8 + - - +
28C ALA* 3.5 8.3 - - - +
30C ALA* 1.3 73.8 - - - +
32C GLN* 1.3 67.2 + - - +
34C GLU* 2.9 19.6 + - - +
35C SER* 2.9 18.8 + - - +
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Residues in contact with GLN 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ALA 3.0 12.8 + - - +
29C GLN* 3.5 12.8 - - + +
31C ALA* 1.3 78.6 - - - +
33C TRP* 1.3 93.0 + - + +
35C SER* 3.2 6.6 + - - -
36C VAL* 3.0 34.6 + - + +
45C HIS* 4.2 5.0 + - - -
48C GLN* 2.7 40.4 + - - +
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Residues in contact with TRP 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLN* 3.1 45.5 + - - -
30C ALA 4.0 1.6 - - - +
31C ALA 3.2 0.4 - - - -
32C GLN* 1.3 112.2 + - - +
34C GLU* 1.3 56.5 + - - +
36C VAL* 3.7 5.4 - - + +
37C LEU* 2.9 35.8 + - - +
42C ILE* 3.9 29.8 - - + -
45C HIS* 4.0 18.4 - - + -
48C GLN* 4.2 4.5 - - - -
49C LEU* 3.7 47.3 - - + -
52C VAL* 4.4 13.0 - - + +
59C ILE* 3.4 26.4 - - + +
68C THR* 3.6 21.5 - - + -
72C VAL* 4.1 12.1 - - + -
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Residues in contact with GLU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ALA 3.1 13.2 + - - +
31C ALA* 2.9 13.8 + - - +
33C TRP* 1.3 74.4 - - - +
35C SER* 1.3 63.4 + - - +
37C LEU* 3.2 11.2 + - - +
38C LYS* 3.0 31.3 + - + +
68C THR* 5.5 0.2 - - - +
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Residues in contact with SER 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ALA* 2.9 11.6 + - - +
32C GLN* 3.6 9.4 - - - -
34C GLU* 1.3 77.0 - - - +
36C VAL* 1.3 64.1 + - - +
38C LYS* 3.5 16.0 + - - +
39C SER* 3.0 26.2 + - - -
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Residues in contact with VAL 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLN* 3.0 37.7 + - + +
33C TRP* 3.7 7.2 - - + +
35C SER* 1.3 75.2 - - - +
37C LEU* 1.3 63.6 + - - +
39C SER* 2.7 21.5 + - - -
41C GLN* 3.0 32.5 + - + +
42C ILE* 3.9 17.7 - - + -
45C HIS* 3.7 46.7 - - + +
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C TRP* 2.9 23.7 + - + +
34C GLU* 3.5 7.6 - - - +
36C VAL* 1.3 76.7 - - - +
38C LYS* 1.3 58.8 + - - +
40C GLY* 3.0 19.9 + - - -
42C ILE* 4.3 12.6 - - + +
68C THR* 5.1 2.5 - - + +
71C HIS* 3.5 35.9 - - + +
72C VAL* 3.9 17.3 - - + -
75C VAL* 3.4 38.6 - - + -
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Residues in contact with LYS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLU* 3.0 22.1 + - + +
35C SER* 3.8 17.5 - - - +
37C LEU* 1.3 73.7 - - - +
39C SER* 1.3 58.1 - - - +
40C GLY 3.3 0.6 + - - -
122G ASN 5.7 3.0 + - - -
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Residues in contact with SER 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C SER 3.0 14.0 + - - -
36C VAL* 2.7 20.6 + - - -
38C LYS* 1.3 77.8 - - - +
40C GLY* 1.3 60.8 + - - +
41C GLN* 3.2 34.9 + - - +
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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