Contacts of the helix formed by residues 19 - 32 (chain O) in PDB entry 5GJQ
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 PRO 19 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O GLN 5.4 1.1 - - - +
11O SER* 1.9 44.9 - - - +
12O GLN* 4.5 1.1 - - + -
15O GLY 3.2 3.0 - - - +
16O PRO* 2.9 27.7 - - + +
18O GLN* 1.3 74.8 - - - +
20O ALA* 1.3 51.5 + - - +
21O VAL 2.7 5.9 + - - -
22O TRP* 2.5 44.1 + - + +
23O HIS* 3.9 5.0 + - + +
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Residues in contact with ALA 20 (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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16O PRO 4.1 3.4 + - - +
17O GLY 4.4 8.5 + - - +
18O GLN 3.5 0.8 - - - -
19O PRO* 1.3 75.3 - - - +
21O VAL* 1.3 62.7 + - + +
22O TRP 3.6 0.2 + - - -
23O HIS* 3.8 16.3 + - - +
24O ARG* 3.6 13.8 + - - +
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Residues in contact with VAL 21 (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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18O GLN 4.0 11.6 + - - +
19O PRO 2.7 4.8 + - - -
20O ALA* 1.3 75.2 - - + +
22O TRP* 1.3 52.3 + - + +
24O ARG* 2.8 18.6 - - + +
25O LEU* 2.8 37.0 + - + +
40O GLN* 4.7 22.9 - - + +
43O ASP* 5.0 8.5 - - - -
44O PHE* 4.7 17.3 - - + -
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Residues in contact with TRP 22 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O PHE 4.6 2.5 - - - -
10O GLN* 4.3 5.4 - - + -
11O SER* 1.5 73.6 - - - +
18O GLN 4.7 3.4 - - - -
19O PRO* 2.5 26.0 + - + +
21O VAL* 1.3 71.5 - - + +
23O HIS* 1.3 50.6 + - + +
25O LEU* 2.9 15.3 + - + +
26O GLU* 2.6 39.1 + - + +
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Residues in contact with HIS 23 (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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19O PRO* 3.9 4.9 + - + -
20O ALA* 3.8 14.0 + - - +
21O VAL 3.3 0.2 - - - -
22O TRP* 1.3 76.2 - - + +
24O ARG* 1.3 65.7 + - + +
26O GLU* 2.9 14.4 - - + +
27O GLU* 2.8 26.4 + - - +
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Residues in contact with ARG 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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20O ALA 3.6 13.9 - - - +
21O VAL* 2.8 22.8 + - + +
23O HIS* 1.3 78.9 - - + +
25O LEU* 1.3 50.3 + - - +
27O GLU* 3.0 10.3 + - - +
28O LEU* 2.5 43.8 + - + +
40O GLN* 4.1 19.3 - - + -
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Residues in contact with LEU 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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7O PHE* 6.3 3.4 - - + -
21O VAL* 2.8 24.1 + - + +
22O TRP* 2.9 16.1 + - + +
24O ARG* 1.3 70.0 - - - +
26O GLU* 1.3 53.8 + - - +
28O LEU* 4.0 6.3 - - - +
29O TYR* 2.3 44.1 + - + +
37O LEU* 6.0 2.9 - - - +
40O GLN* 4.5 17.9 - - + +
41O VAL* 5.1 11.2 - - + +
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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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4O VAL* 2.3 52.1 - - - +
7O PHE* 4.8 3.1 - - - +
8O LEU* 4.3 10.9 + - - +
11O SER* 5.6 1.0 + - - +
22O TRP* 2.6 21.0 + - + +
23O HIS* 2.9 16.8 + - + +
25O LEU* 1.3 72.1 - - - +
27O GLU* 1.3 53.1 + - - +
29O TYR* 3.0 6.4 + - - +
30O THR* 2.5 41.8 + - - -
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Residues in contact with GLU 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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23O HIS 2.8 17.2 + - - +
24O ARG* 3.1 26.9 - - - +
26O GLU* 1.3 73.1 - - - +
28O LEU* 1.3 54.4 - - + +
30O THR* 2.8 11.2 - - - -
31O LYS* 2.2 51.0 + - + +
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Residues in contact with LEU 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 ARG* 2.5 35.0 + - + +
25O LEU* 3.4 5.8 - - - +
27O GLU* 1.3 74.2 - - + +
29O TYR* 1.3 60.8 + - - +
31O LYS* 4.0 5.4 - - + +
32O LYS* 2.3 40.1 + - - +
33O LEU* 4.4 13.0 - - + +
36O GLN* 4.0 27.1 - - + -
37O LEU* 4.3 15.3 - - + +
40O GLN* 4.7 2.2 - - + -
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Residues in contact with TYR 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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4O VAL* 5.9 6.3 - - + -
25O LEU* 2.3 33.4 + - + +
26O GLU* 3.3 6.7 - - - +
28O LEU* 1.3 67.6 - - - +
30O THR* 1.3 63.0 + - - +
32O LYS* 4.1 6.4 + - - +
37O LEU* 5.9 0.6 - - - +
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Residues in contact with THR 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* 2.5 22.4 + - - -
27O GLU* 2.8 20.0 + - - -
29O TYR* 1.3 76.7 - - - +
31O LYS* 1.3 61.5 + - - -
32O LYS* 3.2 2.9 + - - +
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Residues in contact with LYS 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 GLU* 2.2 42.5 + - + +
28O LEU* 4.2 2.7 - - + +
30O THR* 1.3 71.1 - - - -
32O LYS* 1.3 67.7 + - - +
33O LEU* 4.2 12.3 - - + +
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Residues in contact with LYS 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28O LEU 2.3 28.5 + - - +
29O TYR* 4.6 4.9 - - - +
30O THR 3.2 5.5 - - - +
31O LYS 1.3 70.7 - - - +
33O LEU* 1.3 58.7 + - - +
34O TRP* 3.5 4.7 - - + +
18W ASN* 3.2 23.1 + - - +
19W GLY 5.2 2.6 - - - +
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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