Contacts of the helix formed by residues 42 - 59 (chain P) in PDB entry 2AIZ
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 42 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P VAL* 5.0 0.6 - - - +
33P TYR 4.2 17.0 - - - +
40P ASP* 4.9 7.6 - - - +
41P ILE* 1.3 83.3 - - - +
43P GLY* 1.3 55.4 + - - +
44P GLU* 3.7 10.5 + - - +
45P TYR* 2.8 49.5 + - + +
46P VAL* 3.1 12.9 + - - +
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Residues in contact with GLY 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41P ILE 4.3 0.6 + - - -
42P THR* 1.3 72.1 - - - +
44P GLU* 1.3 61.3 + - - +
46P VAL* 3.1 28.8 + - - +
47P GLN* 4.1 4.3 + - - +
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Residues in contact with GLU 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P THR* 2.9 11.3 + - - +
43P GLY* 1.3 76.0 - - - +
45P TYR* 1.3 70.5 + - + +
46P VAL 3.4 0.2 - - - -
47P GLN* 3.2 24.1 + - - +
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Residues in contact with TYR 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31P THR 2.8 31.4 - - - -
32P VAL* 3.5 23.3 - - + +
33P TYR* 3.0 53.5 - + + +
41P ILE* 4.3 2.5 - - + -
42P THR* 2.8 32.2 + - + +
44P GLU* 1.3 81.8 - - + +
46P VAL* 1.3 64.5 + - - +
47P GLN* 3.3 6.7 - - - +
48P ILE* 3.2 27.6 + - + +
49P LEU* 3.9 9.4 + - - +
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Residues in contact with VAL 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41P ILE* 4.6 9.4 - - + -
42P THR 3.3 17.9 - - - +
43P GLY* 3.1 21.4 + - - +
45P TYR* 1.3 76.6 - - - +
47P GLN* 1.3 70.0 + - - +
49P LEU* 2.7 28.7 + - + +
50P ASP* 3.2 9.6 + - + +
93P TYR* 3.8 26.0 - - + +
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Residues in contact with GLN 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20P TYR* 3.4 34.6 - - + +
29P TYR* 4.4 12.3 - - - +
43P GLY 4.1 3.8 + - - +
44P GLU 3.2 25.4 + - - +
45P TYR* 4.1 2.8 - - - +
46P VAL* 1.3 77.1 - - - +
48P ILE* 1.3 104.0 + - - +
50P ASP* 2.5 38.2 - - - +
51P ALA* 2.8 12.5 + - - +
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Residues in contact with ILE 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P LEU* 5.0 2.5 - - + -
29P TYR* 3.0 24.0 - - + +
30P ASN* 3.8 7.2 - - - +
31P THR 3.8 34.8 - - - +
32P VAL* 4.6 4.3 - - + -
45P TYR* 3.2 22.4 - - + +
47P GLN* 1.3 106.8 + - - +
49P LEU* 1.3 60.0 + - + +
51P ALA* 2.9 5.0 + - - -
52P HIS* 2.6 72.0 + - + +
132P LEU* 5.2 1.6 - - + -
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Residues in contact with LEU 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P VAL* 4.7 14.1 - - + -
41P ILE* 3.9 29.2 - - + -
45P TYR 4.0 11.9 - - - +
46P VAL* 2.7 20.0 + - + +
48P ILE* 1.3 79.0 - - + +
50P ASP* 1.3 56.5 + - - +
52P HIS* 4.8 2.2 - - - -
53P ALA* 3.0 30.2 + - - +
90P VAL* 3.8 26.0 - - + -
93P TYR* 3.6 46.9 - - + -
94P LEU* 3.3 12.3 - - + +
97P LYS* 4.7 2.0 - - - -
132P LEU* 5.2 9.2 - - + -
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Residues in contact with ASP 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18P GLY* 4.4 11.8 - - - +
46P VAL* 3.2 8.1 + - + +
47P GLN* 2.5 41.8 + - - +
49P LEU* 1.3 77.3 - - - +
51P ALA* 1.3 78.6 + - - +
53P ALA* 3.6 1.9 - - - +
54P ALA* 3.2 21.5 + - - +
93P TYR* 5.0 5.3 - - - +
97P LYS* 3.9 21.7 + - - +
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Residues in contact with ALA 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P PHE* 3.6 21.2 - - - +
18P GLY* 4.6 6.7 - - - +
20P TYR* 4.3 11.2 - - + -
25P LEU* 3.5 26.7 - - + -
47P GLN 2.8 13.5 + - - +
48P ILE* 3.6 2.7 - - - +
50P ASP* 1.3 83.5 + - - +
52P HIS* 1.3 66.6 + - - +
54P ALA* 3.1 13.4 + - - +
55P TYR* 3.1 13.0 + - - +
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Residues in contact with HIS 52 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P LEU* 3.0 41.2 + - + +
29P TYR 3.2 5.9 + - - -
30P ASN* 3.5 10.4 - - + +
48P ILE* 2.6 52.5 + - + +
49P LEU* 4.3 4.0 - - + +
51P ALA* 1.3 72.5 - - - +
53P ALA* 1.3 51.7 + - - +
55P TYR* 3.2 3.4 + - - +
56P LEU* 2.6 39.9 + - + +
64P VAL* 5.4 2.7 - - + -
94P LEU* 4.9 6.3 - - + -
132P LEU* 4.0 25.5 - - + +
134P TYR* 2.6 41.5 + + + +
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Residues in contact with ALA 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49P LEU 3.0 21.6 + - - +
50P ASP 3.6 1.3 - - - +
51P ALA 3.1 0.2 - - - -
52P HIS* 1.3 77.6 - - - +
54P ALA* 1.3 55.3 + - - +
56P LEU* 3.8 4.4 - - - +
57P ASN* 2.9 33.8 + - - +
94P LEU* 3.5 11.8 - - + +
97P LYS* 3.1 42.8 - - + +
99P VAL* 4.6 5.8 - - + +
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Residues in contact with ALA 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P PHE* 3.9 17.5 - - + -
18P GLY* 4.6 10.5 - - - +
50P ASP 3.2 10.5 + - - +
51P ALA 3.1 10.3 + - - +
53P ALA* 1.3 79.6 - - - +
55P TYR* 1.3 58.1 + - - +
57P ASN* 4.1 3.5 - - - +
58P ALA* 3.1 27.9 + - - +
97P LYS* 4.7 1.1 - - - +
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Residues in contact with TYR 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17P PHE* 3.7 31.8 - + + -
22P VAL* 4.0 36.9 - - + +
25P LEU* 4.6 9.0 - - + -
26P GLN* 4.5 10.7 + - - -
51P ALA 3.1 11.7 + - - +
52P HIS* 3.7 4.3 - - - +
54P ALA* 1.3 74.8 - - - +
56P LEU* 1.3 59.0 + - - +
58P ALA* 3.4 2.6 + - + +
59P THR* 2.7 51.9 + - + +
62P ALA* 4.8 8.3 - - + +
134P TYR* 3.1 50.3 - + - +
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Residues in contact with LEU 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52P HIS* 2.6 23.5 + - + +
53P ALA* 3.8 4.0 - - - +
55P TYR* 1.3 76.0 - - - +
57P ASN* 1.3 55.2 + - - +
59P THR* 2.7 32.4 + - - +
62P ALA* 3.5 17.9 - - + +
63P LYS 3.7 1.3 - - - -
64P VAL* 3.3 52.9 - - + +
94P LEU* 4.3 8.1 - - + -
99P VAL* 3.0 38.4 - - + -
103P LYS* 3.0 11.8 + - - +
104P LEU* 5.0 0.2 - - + -
134P TYR* 3.6 17.3 - - + +
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Residues in contact with ASN 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53P ALA 2.9 18.0 + - - +
54P ALA* 4.1 4.9 - - - +
56P LEU* 1.3 72.7 - - - +
58P ALA* 1.3 67.0 + - - +
59P THR 3.0 8.9 + - - -
60P PRO* 4.3 2.6 - - - +
97P LYS 4.5 8.5 + - - -
98P GLY* 4.3 23.0 + - - -
99P VAL* 4.7 10.0 - - + +
103P LYS* 4.9 5.0 + - - +
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Residues in contact with ALA 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P PHE* 3.7 23.6 - - + -
54P ALA 3.1 19.2 + - - +
55P TYR* 3.6 7.2 - - + +
57P ASN* 1.3 78.3 + - - +
59P THR* 1.3 61.4 + - + +
60P PRO* 3.6 7.8 - - - +
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Residues in contact with THR 59 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55P TYR* 2.7 33.2 + - + +
56P LEU 2.7 19.6 - - - +
57P ASN 3.0 2.4 - - - +
58P ALA* 1.3 80.0 - - + +
60P PRO* 1.3 58.5 - - + +
61P ALA 3.4 0.9 - - - -
62P ALA* 2.7 30.2 + - + +
103P LYS* 2.7 17.7 + - - -
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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
------------------------------------------------------------
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