Contacts of the helix formed by residues 22 - 35 (chain O) in PDB entry 6T9L
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 22 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20O SER 4.5 2.5 - - - +
21O ASP* 1.3 78.9 - - - +
23O ILE* 1.3 65.5 + - - +
24O GLU* 3.0 27.1 + - - +
25O ASN* 3.4 19.3 + - - +
26O VAL* 3.9 7.3 + - - +
53O GLY* 5.1 4.3 - - - +
54O ARG 3.9 15.7 - - - +
55O THR* 3.7 22.0 - - + -
56O LEU* 4.8 4.8 - - - +
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Residues in contact with ILE 23 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22O THR* 1.3 71.3 - - - +
24O GLU* 1.3 71.5 + - - +
25O ASN 3.1 2.2 - - - -
26O VAL* 3.2 14.1 - - + +
27O LYS* 3.0 47.7 + - + +
43O LEU* 5.6 2.0 - - + -
50O LEU* 4.1 30.7 - - + +
51O GLU 3.2 31.0 - - - +
52O ASP* 3.2 27.6 - - - +
54O ARG 3.4 16.1 + - - +
55O THR 5.1 0.9 - - - +
56O LEU* 3.8 20.2 - - + -
59O TYR* 5.3 2.7 - - + -
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Residues in contact with GLU 24 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22O THR* 3.0 25.9 + - - +
23O ILE* 1.3 81.7 + - - +
25O ASN* 1.3 61.1 + - - +
27O LYS* 3.7 11.1 + - + +
28O ALA* 3.6 16.3 + - - +
52O ASP* 3.0 30.2 - - - +
53O GLY* 3.2 22.3 + - - -
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Residues in contact with ASN 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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21O ASP* 3.3 36.7 + - + -
22O THR* 3.4 17.4 + - - +
23O ILE 3.1 0.6 - - - -
24O GLU* 1.3 77.1 - - - +
26O VAL* 1.3 64.5 + - + +
28O ALA* 3.2 16.0 + - - +
29O LYS* 3.2 35.4 + - - +
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Residues in contact with VAL 26 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3O ILE* 4.8 5.8 - - + -
5O VAL* 6.5 0.4 - - + -
15O LEU* 4.6 8.7 - - + +
17O VAL* 3.6 40.8 - - + -
22O THR 4.1 2.5 - - - +
23O ILE* 3.2 29.2 - - + +
25O ASN* 1.3 76.0 - - + +
27O LYS* 1.3 59.2 + - - +
29O LYS* 3.7 12.0 - - + +
30O ILE* 3.0 30.7 + - - +
43O LEU* 4.3 22.2 - - + -
56O LEU* 4.7 12.1 - - + -
67O LEU* 5.6 4.9 - - + -
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Residues in contact with LYS 27 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O ILE* 3.0 39.6 + - + +
24O GLU* 3.9 10.5 - - + +
25O ASN 3.2 0.2 - - - -
26O VAL* 1.3 78.2 - - + +
28O ALA* 1.3 57.0 + - - +
30O ILE* 3.2 20.5 - - - +
31O GLN* 3.6 10.4 + - - +
38O PRO* 3.8 44.9 + - + +
39O ASP* 5.7 0.4 - - - +
41O GLN* 3.8 17.6 + - - +
43O LEU* 4.5 22.7 - - + -
50O LEU 5.6 2.1 + - - -
52O ASP* 3.9 20.7 + - - +
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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 GLU 3.6 9.4 + - - +
25O ASN* 3.2 12.0 + - - +
26O VAL 3.1 0.6 - - - -
27O LYS* 1.3 78.6 - - - +
29O LYS* 1.3 65.7 + - + +
30O ILE 3.3 0.4 - - - -
31O GLN* 3.1 20.3 + - - +
32O ASP* 3.1 18.3 + - - +
38O PRO* 5.9 0.2 - - - -
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Residues in contact with LYS 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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15O LEU* 3.7 31.5 - - + +
16O GLU 2.4 35.9 + - - +
17O VAL* 3.5 16.8 - - - +
21O ASP* 4.0 2.0 + - - -
25O ASN* 3.2 44.7 + - - +
26O VAL* 3.2 14.3 + - + +
28O ALA* 1.3 78.2 - - + +
30O ILE* 1.3 58.7 + - - +
32O ASP* 2.7 30.5 - - - +
33O LYS* 3.8 12.0 + - - +
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Residues in contact with ILE 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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5O VAL* 5.1 7.0 - - + -
7O THR* 5.2 2.5 - - + -
13O ILE* 3.7 28.3 - - + -
15O LEU* 4.3 8.2 - - + +
26O VAL 3.0 13.9 + - - +
27O LYS* 3.2 22.2 - - - +
29O LYS* 1.3 76.1 - - - +
31O GLN* 1.3 56.7 + - - +
33O LYS* 3.5 2.6 + - + -
34O GLU* 3.0 45.8 + - + +
36O ILE* 5.0 0.8 + - + -
41O GLN* 3.3 26.9 - - - +
43O LEU* 5.9 3.4 - - + -
69O LEU* 3.9 29.8 - - + -
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Residues in contact with GLN 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 LYS 3.6 10.1 - - - +
28O ALA* 3.1 14.5 + - - +
30O ILE* 1.3 77.4 - - - +
32O ASP* 1.3 62.3 + - - +
33O LYS 3.1 1.8 - - - -
35O GLY* 2.6 41.2 + - - +
36O ILE 3.5 22.8 + - - +
37O PRO* 4.4 5.3 - - - +
38O PRO* 3.8 27.7 - - - +
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Residues in contact with ASP 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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15O LEU* 5.6 0.2 - - - +
28O ALA 3.1 15.5 + - - +
29O LYS* 2.7 30.0 - - - +
31O GLN* 1.3 76.2 - - - +
33O LYS* 1.3 69.3 + - - +
35O GLY 4.9 0.2 - - - -
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Residues in contact with LYS 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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331K ASP* 4.1 23.1 + - - +
13O ILE* 4.4 25.1 - - + -
14O THR 5.1 1.3 - - - +
15O LEU* 3.9 26.7 - - + -
29O LYS 3.8 4.7 - - - +
30O ILE* 3.5 4.6 + - - +
31O GLN 3.1 0.6 - - - -
32O ASP* 1.3 95.0 + - - +
34O GLU* 1.3 73.7 + - + +
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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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367K HIS* 3.7 24.4 + - - -
7O THR* 4.5 18.2 - - + +
11O LYS* 5.5 4.5 + - - -
13O ILE* 5.2 5.7 - - + +
30O ILE* 3.0 32.6 + - + +
31O GLN 3.3 0.2 + - - -
33O LYS* 1.3 91.0 - - + +
35O GLY* 1.3 62.3 + - - +
36O ILE* 3.5 23.5 + - + +
69O LEU* 5.7 0.4 - - + -
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Residues in contact with GLY 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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367K HIS* 4.7 4.6 + - - -
371K GLY* 5.4 3.5 - - - -
31O GLN* 2.6 35.0 + - - +
34O GLU* 1.3 71.3 - - - +
36O ILE* 1.3 62.9 + - - +
37O PRO* 3.6 8.0 - - - +
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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