Contacts of the helix formed by residues 37 - 51 (chain H) in PDB entry 2ZP8
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 37 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G ILE 5.7 0.9 - - - -
24G THR* 3.4 17.0 - - - +
6H ASP 4.4 1.3 - - - +
7H ASP 2.6 30.0 + - - +
8H LEU 3.0 20.4 + - - +
9H GLU 4.4 0.4 - - - -
10H VAL* 3.8 26.9 - - + -
36H LEU* 1.3 75.9 - - - +
38H ALA* 1.3 65.2 + - - +
39H GLN* 3.4 3.1 + - - -
40H GLY 2.9 23.4 + - - -
41H TYR* 3.1 14.1 + - - -
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Residues in contact with ALA 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ILE 5.5 0.4 + - - +
22G GLU* 3.9 28.9 - - + +
24G THR* 3.7 7.6 + - - +
37H THR* 1.3 72.4 - - - +
39H GLN* 1.3 57.7 + - - +
40H GLY 3.3 0.2 + - - -
41H TYR* 3.3 7.9 + - - +
42H THR* 2.8 33.4 + - - -
1I MET* 4.1 15.9 - - + -
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Residues in contact with GLN 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ILE* 4.2 11.9 - - + -
7H ASP* 3.6 19.7 - - + +
8H LEU* 3.9 15.9 - - + +
37H THR* 3.2 2.0 + - - +
38H ALA* 1.3 78.2 - - - +
40H GLY* 1.3 62.5 + - - +
42H THR* 3.2 19.7 - - - +
43H LEU* 3.3 14.8 + - + +
1I MET* 3.2 27.1 - - + +
2I VAL* 3.3 14.5 + - - +
3I ILE* 2.4 66.0 + - - +
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Residues in contact with GLY 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H LEU* 3.8 8.5 - - - +
36H LEU* 4.9 2.2 - - - -
37H THR* 2.9 18.9 + - - -
39H GLN* 1.3 76.6 - - - +
41H TYR* 1.3 60.4 + - - -
43H LEU* 3.3 3.1 + - - +
44H LEU* 3.0 24.5 + - - +
46J PHE* 3.5 34.1 - - - -
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Residues in contact with TYR 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H ILE* 6.2 0.4 - - + -
36H LEU* 3.4 49.6 + - + +
37H THR 3.1 13.1 + - - -
38H ALA* 4.0 7.0 - - - +
40H GLY* 1.3 71.9 - - - +
42H THR* 1.3 61.1 + - - +
43H LEU 3.0 0.2 + - - -
44H LEU* 3.0 16.3 + - + -
45H ASP* 2.7 57.4 + - - +
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Residues in contact with THR 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H ALA 2.8 20.9 + - - -
39H GLN* 3.2 17.0 - - - +
41H TYR* 1.3 76.1 - - - +
43H LEU* 1.3 66.8 + - + +
45H ASP* 4.0 5.7 + - - +
46H PHE* 3.1 24.6 + - - +
1I MET* 3.5 17.8 - - - +
3I ILE* 3.8 18.8 - - + +
4I ALA 3.9 2.7 - - - +
5I THR* 3.7 36.9 + - - +
8I LEU* 4.4 4.9 - - + +
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Residues in contact with LEU 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ILE* 4.7 4.3 - - + -
8H LEU* 4.5 13.5 - - + -
39H GLN* 3.7 11.7 - - - +
40H GLY 3.3 5.8 + - - +
41H TYR 3.1 0.4 - - - -
42H THR* 1.3 81.6 - - + +
44H LEU* 1.3 58.1 + - - +
46H PHE* 3.1 5.3 + - + +
47H ILE* 2.7 41.3 + - + +
3I ILE* 3.7 30.1 - - + -
8I LEU* 3.9 15.3 - - + -
43I LEU* 4.0 21.8 - - + -
43J LEU* 4.2 26.7 - - + -
46J PHE* 5.1 2.7 - - + -
47J ILE* 4.1 17.5 - - + -
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Residues in contact with LEU 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H LEU* 4.2 14.6 - - + -
40H GLY 3.0 16.9 + - - +
41H TYR* 3.8 15.9 - - + +
43H LEU* 1.3 77.7 - - - +
45H ASP* 1.3 53.1 + - - +
47H ILE* 3.5 1.5 + - - -
48H GLN* 2.8 38.4 + - + +
46J PHE* 4.6 4.9 - - + -
47J ILE* 4.1 23.5 - - + +
50J HIS* 3.7 42.6 - - + +
51J LEU* 3.8 28.8 - - + +
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Residues in contact with ASP 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H TYR* 2.7 46.0 + - - +
42H THR* 4.0 4.7 + - - +
44H LEU* 1.3 70.1 - - - +
46H PHE* 1.3 66.8 + - - +
48H GLN* 3.9 5.1 - - - +
49H LYS* 3.0 26.8 + - - +
5I THR* 6.3 2.0 - - + -
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Residues in contact with PHE 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H THR 3.1 18.9 + - - +
43H LEU* 3.1 5.8 + - + +
45H ASP* 1.3 82.7 - - - +
47H ILE* 1.3 87.8 + - + +
49H LYS* 3.3 1.6 - - - +
50H HIS* 3.1 35.7 + + - -
5I THR* 5.5 4.9 - - + +
8I LEU* 3.5 38.6 - - + -
9I GLU* 3.4 23.1 - - + -
36I LEU* 3.7 26.9 - - + -
40I GLY* 3.3 36.3 - - - -
43I LEU* 4.3 5.8 - - + -
44I LEU* 4.0 13.9 - - + -
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Residues in contact with ILE 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H LEU* 2.7 23.9 + - + +
44H LEU* 4.0 2.7 - - - +
46H PHE* 1.3 96.9 - - + +
48H GLN* 1.3 63.7 + - - +
49H LYS 3.0 0.9 + - - -
50H HIS 3.0 1.2 + - - -
51H LEU* 2.9 39.1 + - + +
43I LEU* 4.6 4.7 - - + -
44I LEU* 4.0 17.9 - - + +
47I ILE* 3.8 39.7 - - + -
47J ILE* 4.0 23.8 - - + -
51J LEU* 3.9 24.0 - - + -
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Residues in contact with GLN 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H LEU* 2.8 23.2 + - + +
45H ASP* 3.9 4.9 - - - +
47H ILE* 1.3 73.9 - - - +
49H LYS* 1.3 62.6 + - - +
51H LEU* 4.2 10.3 + - - +
51J LEU* 3.7 15.2 - - + +
52J ASN* 3.1 35.5 + - - +
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Residues in contact with LYS 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H ASP 3.0 18.8 + - - +
46H PHE* 3.3 4.3 - - - +
48H GLN* 1.3 81.9 - - - +
50H HIS* 1.3 84.2 + - + +
51H LEU 3.8 2.9 + - - +
53H LYS* 5.0 2.9 - - - +
9I GLU* 2.9 30.8 + - - +
32I LYS* 3.3 36.0 + - - +
34I VAL* 3.8 17.5 - - - +
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Residues in contact with HIS 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H PHE* 3.1 37.6 + + - +
47H ILE 3.0 2.6 + - - -
49H LYS* 1.3 90.3 - - + +
51H LEU* 1.3 64.4 + - - +
52H ASN 3.5 1.4 + - - -
53H LYS* 3.0 54.0 + - - +
9I GLU* 2.6 28.7 + - + -
32I LYS* 3.8 14.9 - - + +
34I VAL* 5.2 5.2 - - + -
36I LEU* 3.5 24.3 - - + +
44I LEU* 3.8 27.4 - - + +
48I GLN* 4.7 2.4 + - - -
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Residues in contact with LEU 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H ILE* 2.9 28.7 + - + +
48H GLN* 4.2 7.5 + - - +
49H LYS 3.5 4.4 - - - +
50H HIS* 1.3 77.6 - - - +
52H ASN* 1.3 87.9 + - - +
53H LYS* 3.4 1.0 + - - +
44I LEU* 4.3 5.5 - - + +
47I ILE* 5.0 3.6 - - + -
48I GLN* 3.6 44.9 - - + +
51I LEU* 4.7 17.3 - - + -
51J LEU* 3.8 27.6 - - + -
52J ASN* 6.0 1.8 - - - +
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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