Contacts of the helix formed by residues 23 - 35 (chain O) in PDB entry 5A0Q
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 TYR 23 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10O ASP 4.4 6.3 - - - +
11O ARG* 3.6 56.0 + - + -
14O THR* 6.4 0.2 - - - +
15O ILE 4.7 3.8 + - - -
17O SER* 3.4 34.7 + - - -
18O PRO* 5.4 2.0 - - + +
19O GLU* 4.8 6.1 + - - +
21O ARG* 3.5 28.2 + - - -
22O LEU* 1.3 71.4 - - - +
24O GLN* 1.3 65.9 + - + +
25O VAL 3.2 0.4 - - - -
26O GLU* 3.1 25.8 - - - +
27O TYR* 3.0 56.6 + + + +
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Residues in contact with GLN 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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11O ARG 3.2 24.7 + - - +
12O HIS 4.0 21.3 - - - +
13O ILE 4.8 0.7 - - - +
14O THR* 3.6 33.8 - - + +
22O LEU* 3.5 0.4 - - - +
23O TYR* 1.3 77.4 - - - +
25O VAL* 1.4 55.9 + - - +
27O TYR* 3.3 16.1 + - - +
28O ALA 3.1 19.9 + - - -
132O ARG* 4.9 0.3 - - - +
133O PRO* 3.7 19.7 - - + +
12U SER 3.8 7.3 - - - +
13U THR* 3.9 3.3 - - - +
14U PHE* 3.2 53.9 + - - +
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Residues in contact with VAL 25 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14O THR* 5.3 2.2 - - + -
22O LEU* 3.6 39.4 + - + +
23O TYR 3.2 1.0 - - - -
24O GLN* 1.4 76.0 - - + +
26O GLU* 1.3 59.4 + - - +
28O ALA* 3.0 21.6 + - - +
29O PHE* 3.1 38.9 + - + -
126O THR* 3.8 20.2 - - + +
133O PRO* 4.6 6.3 - - + -
156O PRO 4.6 4.3 - - - +
157O ALA* 3.9 19.7 - - + +
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Residues in contact with GLU 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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21O ARG* 3.5 31.1 + - + +
22O LEU 3.2 14.0 + - - +
23O TYR* 3.1 43.0 - - - +
25O VAL* 1.3 75.5 - - - +
27O TYR* 1.4 68.1 + - + +
29O PHE* 3.2 21.6 + - + +
30O LYS* 2.9 36.8 + - + +
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Residues in contact with TYR 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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11O ARG* 3.5 39.9 + - + +
23O TYR* 3.0 45.1 + + + +
24O GLN* 3.3 35.2 - - - +
25O VAL 3.2 0.2 - - - -
26O GLU* 1.4 79.0 - - + +
28O ALA* 1.3 56.9 + - - +
30O LYS* 3.3 34.1 + - - +
31O ALA* 2.9 26.9 + - - +
14U PHE* 3.5 29.0 - - + -
15U SER 4.3 3.4 - - - +
16U PRO* 3.9 28.2 - - + +
18U GLY* 4.2 4.9 - - - -
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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 GLN 3.1 11.3 + - - +
25O VAL 3.0 13.4 + - - +
27O TYR* 1.3 74.1 - - - +
29O PHE* 1.4 56.9 + - - +
31O ALA* 3.2 9.5 + - - +
32O ILE* 3.0 29.6 + - - +
133O PRO* 3.8 22.7 - - + +
135O GLY* 4.2 4.3 - - - -
156O PRO* 3.6 22.0 - - + -
14U PHE* 4.4 10.9 - - + -
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Residues in contact with PHE 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 VAL* 3.1 34.7 + - + -
26O GLU* 3.2 21.5 + - + +
28O ALA* 1.4 73.8 - - - +
30O LYS* 1.4 62.0 + - + +
32O ILE* 3.2 10.6 + - + +
33O ASN* 2.8 31.7 + - - +
155O ASP* 4.0 16.6 - - + -
156O PRO* 3.6 31.2 - - + -
157O ALA* 3.9 16.4 - - + -
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Residues in contact with LYS 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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26O GLU* 2.9 22.6 + - + +
27O TYR* 3.6 35.2 - - - +
29O PHE* 1.4 75.9 - - + +
31O ALA* 1.3 55.2 - - - +
33O ASN* 3.4 9.9 + - - +
34O GLN* 3.1 31.9 + - - +
16U PRO* 3.0 34.2 + - - +
17U ASP* 3.8 15.9 - - - +
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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 TYR 2.9 13.5 + - - +
28O ALA* 3.2 10.1 + - - +
30O LYS* 1.3 73.2 - - - +
32O ILE* 1.3 58.1 + - - +
34O GLN* 3.4 3.8 + - - +
35O GLY* 3.1 23.6 + - - -
82O GLY* 4.4 2.8 - - - -
83O MET* 4.5 16.1 + - + +
135O GLY* 5.0 2.2 - - - -
14U PHE* 3.8 18.2 - - + -
18U GLY* 3.0 31.4 - - - +
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Residues in contact with ILE 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 3.0 13.3 + - - +
29O PHE* 3.2 14.1 + - + +
31O ALA* 1.3 74.0 - - - +
33O ASN* 1.4 67.2 + - - +
35O GLY* 3.2 13.2 + - - -
36O GLY 4.2 1.7 + - - -
37O LEU 5.0 0.3 - - - +
81O THR* 3.5 17.3 - - - +
82O GLY* 3.9 10.3 + - - -
135O GLY 3.7 17.7 - - - -
136O CYS 3.7 2.7 - - - +
137O CYS* 3.4 31.0 - - + +
155O ASP* 5.1 3.4 - - - +
156O PRO* 3.5 34.1 - - + -
168O ALA* 5.3 0.7 - - + -
169O GLY* 4.7 20.1 - - - +
172O GLN* 6.1 1.1 - - - +
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Residues in contact with ASN 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 PHE* 2.8 24.4 + - - +
30O LYS* 3.5 12.6 - - - +
31O ALA 3.3 0.2 - - - -
32O ILE* 1.4 78.3 - - - +
34O GLN* 1.4 65.6 + - - +
35O GLY 3.3 1.1 + - - -
36O GLY* 3.7 0.7 + - - -
169O GLY 3.7 18.9 + - - +
170O VAL* 3.5 38.5 + - + +
172O GLN* 3.5 27.1 + - - +
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Residues in contact with GLN 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 LYS 3.1 19.7 + - - +
31O ALA* 3.4 9.4 + - - +
32O ILE 3.2 0.2 - - - -
33O ASN* 1.4 80.9 - - - +
35O GLY* 1.4 58.1 + - - +
36O GLY* 3.1 7.2 + - - +
17U ASP 3.9 17.7 - - - +
18U GLY* 4.7 5.6 - - - +
19U ARG* 4.2 26.0 + - - +
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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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31O ALA 3.1 11.9 + - - -
32O ILE 3.2 9.8 + - - -
34O GLN* 1.4 77.2 - - - +
36O GLY* 1.3 55.1 + - - +
37O LEU* 3.2 19.8 + - - +
82O GLY* 3.6 25.3 - - - +
83O MET* 4.6 1.3 - - - -
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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