Contacts of the helix formed by residues 22 - 35 (chain U) in PDB entry 1P3Q
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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20U SER 4.5 2.9 - - - +
21U ASP* 1.3 78.0 - - - +
23U ILE* 1.3 67.8 + - - +
24U GLU* 3.7 7.7 + - - +
25U ASN* 3.0 35.0 + - - +
26U VAL* 3.0 22.2 + - - +
52U ASP 3.5 11.9 - - - +
53U GLY* 4.0 15.0 - - - +
54U ARG 3.1 11.4 - - - +
55U THR* 4.0 10.8 - - + +
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Residues in contact with ILE 23 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22U THR* 1.3 72.0 - - - +
24U GLU* 1.3 63.9 + - - +
26U VAL* 3.2 6.4 + - + +
27U LYS* 2.9 44.6 + - - +
43U LEU* 4.1 11.9 - - + -
50U LEU* 3.7 49.4 - - + +
51U GLU 3.2 24.5 - - - +
52U ASP* 3.4 4.2 + - - +
54U ARG 2.9 10.9 + - - +
55U THR 4.5 2.0 - - - +
56U LEU* 3.9 23.3 - - + -
59U TYR* 3.9 13.2 - - + -
67U LEU* 5.5 1.1 - - + -
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Residues in contact with GLU 24 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22U THR* 3.1 8.0 + - - +
23U ILE* 1.3 77.0 - - - +
25U ASN* 1.3 67.9 + - - +
27U LYS* 3.3 7.4 + - - +
28U ALA* 3.1 22.7 + - + +
38U PRO* 5.5 2.3 - - + +
52U ASP* 2.9 38.6 + - + +
53U GLY* 5.8 1.2 - - - -
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Residues in contact with ASN 25 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20U SER 5.0 0.5 - - - +
21U ASP* 3.7 23.4 - - + +
22U THR* 3.0 39.9 + - - +
24U GLU* 1.3 82.7 + - - +
26U VAL* 1.3 59.4 + - - +
28U ALA* 3.1 8.9 + - - +
29U LYS* 2.9 35.0 + - - +
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Residues in contact with VAL 26 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3U ILE* 5.8 1.8 - - + -
5U VAL* 5.1 2.0 - - + -
15U LEU* 3.9 20.9 - - + -
17U VAL* 4.3 11.7 - - + -
21U ASP* 4.4 5.4 - - + -
22U THR 3.0 13.9 + - - +
23U ILE* 3.2 9.8 + - + +
25U ASN* 1.3 74.3 - - - +
27U LYS* 1.3 65.7 + - - +
29U LYS* 3.1 9.7 + - + +
30U ILE* 3.1 22.0 + - + +
43U LEU* 3.8 19.1 - - + -
56U LEU* 4.0 34.8 - - + -
67U LEU* 4.7 12.3 - - + -
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Residues in contact with LYS 27 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23U ILE* 2.9 30.3 + - - +
24U GLU* 3.8 6.3 - - - +
26U VAL* 1.3 76.3 - - - +
28U ALA* 1.3 57.3 + - - +
30U ILE* 3.2 1.1 + - - -
31U GLN* 2.9 24.4 + - - +
38U PRO* 4.0 29.4 + - + +
41U GLN* 3.0 62.7 + - - +
42U ARG* 4.9 1.2 - - - +
43U LEU* 3.6 19.3 - - + +
49U GLN* 5.3 6.3 - - - +
50U LEU 4.9 5.2 + - - -
52U ASP* 2.9 32.0 + - - +
72U ARG* 5.6 2.6 - - - +
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Residues in contact with ALA 28 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24U GLU* 3.1 14.0 + - + +
25U ASN* 3.1 12.8 + - - +
27U LYS* 1.3 76.1 - - - +
29U LYS* 1.3 60.2 + - + +
31U GLN* 3.3 17.5 + - - +
32U ASP* 3.0 34.1 + - - +
38U PRO* 4.4 5.8 - - + +
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Residues in contact with LYS 29 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15U LEU* 4.3 16.2 - - + +
16U GLU 3.2 27.5 + - - +
17U VAL* 3.7 14.7 - - + +
21U ASP* 3.4 29.1 + - - -
25U ASN* 2.9 23.8 + - - +
26U VAL* 3.1 11.6 + - - +
28U ALA* 1.3 76.7 - - - +
30U ILE* 1.3 64.2 + - - +
32U ASP* 3.3 10.3 + - - +
33U LYS* 3.1 24.6 + - - +
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Residues in contact with ILE 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5U VAL* 4.1 12.8 - - + -
13U ILE* 3.5 40.4 - - + -
15U LEU* 3.4 26.7 - - + -
26U VAL* 3.1 16.1 + - + +
27U LYS* 3.2 7.6 + - - +
29U LYS* 1.3 73.0 - - - +
31U GLN* 1.3 59.0 + - - +
33U LYS* 3.2 2.2 + - + -
34U GLU* 2.7 46.5 + - + +
36U ILE* 4.6 5.8 - - + -
41U GLN* 3.6 25.1 - - - +
43U LEU* 5.4 3.1 - - + -
69U LEU* 4.5 10.1 - - + -
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Residues in contact with GLN 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27U LYS 2.9 12.4 + - - +
28U ALA* 3.4 15.6 - - - +
30U ILE* 1.3 77.5 - - - +
32U ASP* 1.3 64.1 + - - +
35U GLY* 2.8 29.0 + - - -
36U ILE 3.2 27.8 + - - +
37U PRO* 4.3 7.7 - - - +
38U PRO* 3.5 29.0 - - + +
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Residues in contact with ASP 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28U ALA* 3.0 19.4 + - - +
29U LYS* 3.6 11.4 - - - +
30U ILE 3.2 0.4 - - - -
31U GLN* 1.3 85.0 - - - +
33U LYS* 1.3 63.9 + - + +
35U GLY 4.6 0.7 + - - -
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Residues in contact with LYS 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13U ILE* 3.4 16.4 - - + +
14U THR* 3.0 31.1 + - - +
15U LEU* 3.8 10.1 - - + +
29U LYS 3.1 15.8 + - - +
30U ILE* 3.9 2.0 - - - +
32U ASP* 1.3 84.3 - - + +
34U GLU* 1.3 92.6 + - + +
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Residues in contact with GLU 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11U LYS* 6.1 1.2 - - - -
13U ILE* 3.5 38.4 - - + +
30U ILE* 2.7 19.1 + - + +
33U LYS* 1.3 104.8 - - + +
35U GLY* 1.3 58.2 + - - +
36U ILE* 3.4 22.3 + - + +
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Residues in contact with GLY 35 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31U GLN* 2.8 22.4 + - - +
32U ASP 4.5 0.8 + - - -
33U LYS 3.7 0.8 - - - -
34U GLU* 1.3 77.4 - - - +
36U ILE* 1.3 61.9 + - - +
37U PRO* 3.7 8.1 - - - +
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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