Contacts of the helix formed by residues 46 - 61 (chain O) in PDB entry 2Z5S
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 LEU 46 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22O THR 4.3 5.4 + - - +
24O VAL* 4.6 6.4 - - + +
45O THR* 1.3 74.3 - - - +
47O LYS* 1.3 57.8 + - + +
49O VAL* 3.4 8.1 + - + +
50O MET* 3.1 41.2 + - + +
96O TYR* 5.7 4.0 - - + -
99O LEU* 4.6 14.4 - - + -
103O LEU* 4.8 13.9 - - + -
27R PRO 5.3 6.3 - - - +
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Residues in contact with LYS 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41M GLU* 6.3 1.0 - - - +
45O THR* 3.2 13.5 - - - +
46O LEU* 1.3 78.9 - - + +
48O GLU* 1.3 61.6 + - + +
50O MET* 4.0 7.7 - - - +
51O HIS* 3.2 22.7 + - - +
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Residues in contact with GLU 48 (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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43O VAL 4.1 4.0 - - - +
44O PHE* 3.4 23.4 - - + -
45O THR* 3.1 45.4 + - - +
47O LYS* 1.3 76.7 - - + +
49O VAL* 1.3 65.0 + - - +
50O MET 3.3 0.2 - - - -
51O HIS* 3.4 7.0 - - + +
52O TYR* 3.0 40.0 + - + -
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Residues in contact with VAL 49 (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 VAL* 4.2 2.5 - - + -
26O PRO* 4.7 0.2 - - + -
30O LEU* 4.4 4.9 - - + -
34O LEU* 3.8 27.2 - - + +
44O PHE* 3.5 22.2 - - + -
45O THR 3.1 18.6 + - - +
46O LEU* 3.6 10.1 - - + +
48O GLU* 1.3 77.0 - - - +
50O MET* 1.3 55.5 + - - +
52O TYR 3.4 0.2 + - - -
53O LEU* 3.1 29.2 + - + +
99O LEU* 3.8 31.4 - - + -
103O LEU* 4.2 25.6 - - + -
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Residues in contact with MET 50 (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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46O LEU* 3.1 29.5 + - + +
47O LYS* 4.1 8.3 - - - +
48O GLU 3.3 0.2 - - - -
49O VAL* 1.3 72.8 - - - +
51O HIS* 1.3 62.3 + - - +
53O LEU* 4.4 4.7 - - - -
54O GLY 3.1 8.1 + - - -
95O VAL* 4.2 11.4 - - + -
96O TYR* 4.3 13.9 - - + +
99O LEU* 3.5 28.9 - - + -
23R TRP* 2.6 54.1 + - + +
26R LEU* 3.9 34.3 - - + +
27R PRO 4.6 7.0 - - - +
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Residues in contact with HIS 51 (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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41N GLU* 3.0 33.3 + - - -
48N GLU* 5.8 4.5 - - - -
47O LYS 3.2 13.7 + - - +
48O GLU* 3.4 12.1 - - + +
50O MET* 1.3 79.1 - - - +
52O TYR* 1.3 78.8 + + - +
54O GLY* 3.2 4.0 + - - -
55O GLN* 2.9 57.0 + - + +
23R TRP* 4.7 3.9 + - - +
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Residues in contact with TYR 52 (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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40N GLN* 3.4 35.3 + - - +
41N GLU* 3.8 23.9 + - - -
34O LEU* 3.8 25.4 - - + +
37O ALA* 3.4 26.4 - - + +
38O GLY 3.9 1.8 - - - -
39O ALA* 3.4 39.7 - - + -
44O PHE* 3.9 16.4 - + - -
48O GLU* 3.0 32.9 + - + +
51O HIS* 1.3 86.8 - + - +
53O LEU* 1.3 52.8 + - - +
55O GLN* 3.4 4.4 - - + +
56O TYR* 2.8 34.8 + - - +
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Residues in contact with LEU 53 (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 LEU* 4.9 5.2 - - + -
33O ILE* 5.2 5.8 - - + -
34O LEU* 4.0 8.6 - - + +
49O VAL 3.1 18.0 + - - +
50O MET* 3.8 8.3 - - - +
51O HIS 3.3 0.2 - - - -
52O TYR* 1.3 73.5 - - - +
54O GLY* 1.3 63.4 + - - +
56O TYR* 3.2 8.5 + - + +
57O ILE* 3.0 45.4 + - + +
78O LEU* 3.8 25.6 - - + -
87O PHE* 5.8 0.4 - - + -
95O VAL* 4.2 17.3 - - + -
98O MET* 3.8 25.8 - - + -
99O LEU* 4.4 10.8 - - + -
23R TRP* 3.4 21.8 - - + -
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Residues in contact with GLY 54 (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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50O MET 3.1 8.7 + - - -
51O HIS 3.6 2.0 - - - -
53O LEU* 1.3 78.2 - - - +
55O GLN* 1.3 62.1 + - - +
57O ILE 3.3 1.4 + - - -
58O MET* 2.9 33.1 + - - +
19R PHE* 3.5 8.9 - - - -
23R TRP* 3.5 34.6 - - - -
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Residues in contact with GLN 55 (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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23N GLN* 4.5 6.9 + - - +
41N GLU* 3.3 18.4 - - - +
43N VAL* 3.4 33.1 - - + +
48N GLU* 5.0 3.6 - - - +
37O ALA* 4.1 12.8 - - + +
51O HIS* 2.9 54.6 + - + +
52O TYR* 3.3 10.5 + - + +
54O GLY* 1.3 74.9 - - - +
56O TYR* 1.3 52.9 + - - +
58O MET* 3.4 18.8 + - - +
59O MET* 2.8 36.1 + - - +
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Residues in contact with TYR 56 (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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33O ILE* 3.3 53.6 - - + +
36O VAL* 3.8 24.2 - - + -
37O ALA* 3.8 9.8 - - + +
52O TYR 2.8 17.3 + - - +
53O LEU* 3.2 9.2 + - + +
55O GLN* 1.3 70.6 - - - +
57O ILE* 1.3 69.1 + - + +
59O MET* 3.2 5.7 + - - +
60O LYS* 2.8 55.7 + - + +
62O LEU* 4.0 13.5 - - + -
76O ASP* 2.7 30.2 + - - -
77O PRO* 4.1 9.5 - - - +
78O LEU* 4.1 13.0 - - + -
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Residues in contact with ILE 57 (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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53O LEU* 3.0 33.9 + - + +
54O GLY 3.3 1.5 + - - +
56O TYR* 1.3 78.1 - - + +
58O MET* 1.3 58.0 + - - +
60O LYS 3.7 0.2 - - - -
61O GLN* 2.9 24.3 + - - -
62O LEU* 3.0 32.0 + - + -
63O TYR* 4.0 10.6 - - + +
71O VAL* 3.9 10.5 - - + -
78O LEU* 3.9 24.0 - - + -
87O PHE* 4.4 9.9 - - + -
19R PHE* 3.5 36.6 - - + -
23R TRP* 3.8 14.8 - - + -
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Residues in contact with MET 58 (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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23N GLN* 3.9 29.2 - - + +
43N VAL* 4.3 11.7 - - + -
106N LEU* 3.6 6.0 - - + +
107N ASN* 4.1 16.2 - - - -
54O GLY 2.9 23.3 + - - +
55O GLN* 3.6 19.7 - - - +
57O ILE* 1.3 76.1 - - - +
59O MET* 1.3 61.4 + - - +
61O GLN* 2.5 33.3 + - - +
63O TYR* 4.3 9.4 - - + -
19R PHE* 3.5 25.8 - - + +
20R SER* 3.2 40.6 - - - +
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Residues in contact with MET 59 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25N HIS* 4.7 15.0 - - + +
42N GLU* 4.0 27.6 - - + +
43N VAL* 3.6 15.2 - - + +
106N LEU* 4.2 12.7 - - + +
36O VAL* 3.3 41.3 - - + +
37O ALA* 4.0 12.3 - - - -
55O GLN 2.8 21.7 + - - +
56O TYR* 3.2 6.5 + - - +
58O MET* 1.3 75.8 - - - +
60O LYS* 1.3 64.5 + - + +
61O GLN* 3.4 6.2 + - - +
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Residues in contact with LYS 60 (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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36O VAL* 5.1 7.6 - - + -
56O TYR* 2.8 56.7 + - + +
59O MET* 1.3 80.3 - - + +
61O GLN* 1.3 71.3 + - - +
62O LEU* 3.4 23.6 + - + +
76O ASP* 3.5 12.8 - - - +
77O PRO* 5.8 0.2 - - + -
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Residues in contact with GLN 61 (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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106N LEU* 3.4 46.6 - - + +
107N ASN* 5.6 0.6 - - - -
57O ILE 2.9 7.7 + - - -
58O MET* 2.5 26.7 + - - +
59O MET 3.2 6.8 - - - +
60O LYS* 1.3 80.4 - - - +
62O LEU* 1.3 62.4 + - - +
63O TYR* 3.4 34.8 + - - +
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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
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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