Contacts of the helix formed by residues 46 - 59 (chain O) in PDB entry 4B2Q
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 46 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43O ILE* 3.4 28.3 - - + +
44O LYS 2.9 1.0 + - - -
45O ASP* 1.3 81.2 + - - +
47O VAL* 1.3 62.1 + - + +
49O PRO* 3.2 16.9 - - - +
50O MET* 3.0 26.1 - - + +
37P VAL* 6.3 1.6 - - + -
44P LYS* 3.3 38.4 + - + +
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Residues in contact with VAL 47 (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 LEU* 3.6 16.6 - - + -
36O GLY* 6.3 1.8 - - - -
37O VAL* 5.8 1.3 - - + -
40O ASN* 6.0 0.2 - - - +
43O ILE* 3.5 31.0 - - + +
44O LYS* 3.4 4.0 + - - +
46O THR* 1.3 75.8 - - + +
48O PHE* 1.3 61.4 + - - +
49O PRO 3.4 0.4 - - - -
50O MET* 3.1 9.3 - - + +
51O ALA* 2.9 27.9 + - - +
34P ILE* 3.5 37.2 - - + +
37P VAL* 3.5 30.7 - - + +
38P SER* 5.9 2.0 - - - -
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Residues in contact with PHE 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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50N MET* 4.4 32.8 - - + -
53N LEU* 4.7 17.3 - - + -
30O PHE* 6.3 1.8 - + - -
33O LEU* 4.1 21.9 - - + +
44O LYS* 3.1 33.3 + - + +
45O ASP* 4.8 2.2 - - - +
47O VAL* 1.3 79.1 - - - +
49O PRO* 1.3 65.9 - - + +
51O ALA* 3.3 7.7 + - - +
52O ILE* 3.3 44.5 + - + +
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Residues in contact with PRO 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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45O ASP* 3.7 19.1 - - - +
46O THR* 3.2 22.2 - - - +
48O PHE* 1.3 99.0 - - + +
50O MET* 1.3 65.9 + - + +
52O ILE* 3.3 20.4 + - + +
53O LEU* 3.4 17.4 + - + +
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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 THR* 3.0 34.3 - - + +
47O VAL* 3.1 28.7 - - + +
49O PRO* 1.3 78.0 - - - +
51O ALA* 1.3 65.6 + - - +
53O LEU* 3.0 24.8 + - + +
30P PHE* 3.0 31.8 - - + -
33P LEU* 4.2 26.2 - - - -
34P ILE* 5.0 6.3 - - + -
37P VAL* 4.6 18.8 - - + -
44P LYS* 4.8 7.6 - - + -
48P PHE* 4.5 25.6 - - + -
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Residues in contact with ALA 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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29O VAL* 4.2 9.3 - - - +
30O PHE* 6.1 3.4 - - + -
33O LEU* 3.9 29.6 - - + -
47O VAL 2.9 19.7 + - - +
48O PHE 3.4 7.9 - - - +
49O PRO 3.2 0.4 - - - -
50O MET* 1.3 78.5 - - - +
52O ILE* 1.3 61.1 + - + +
54O GLY* 3.2 11.3 + - - -
55O PHE* 3.3 9.7 + - - +
30P PHE* 4.5 6.7 - - - -
34P ILE* 4.5 11.0 - - + -
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Residues in contact with ILE 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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48O PHE* 3.3 41.0 + - + +
49O PRO* 3.6 10.8 - - + +
50O MET 3.2 0.4 - - - -
51O ALA* 1.3 74.2 - - + +
53O LEU* 1.3 67.2 + - + +
55O PHE* 3.0 32.2 + - + +
56O ALA* 3.5 6.2 + - - +
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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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49O PRO 3.5 11.0 - - - +
50O MET* 3.0 25.0 + - + +
52O ILE* 1.3 80.2 - - + +
54O GLY* 1.3 61.6 + - - +
55O PHE 3.3 0.5 + - - -
56O ALA* 3.5 7.0 + - - +
57O LEU* 3.1 26.4 + - + +
30P PHE* 4.3 7.4 - - + -
48P PHE* 4.9 14.4 - - + -
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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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29O VAL* 4.3 12.2 - - - +
50O MET 3.1 9.5 + - - -
51O ALA 3.2 5.1 + - - -
52O ILE 3.2 0.6 - - - -
53O LEU* 1.3 74.0 - - - +
55O PHE* 1.3 64.3 + - - +
57O LEU* 3.4 5.3 + - - +
58O SER* 3.1 24.8 + - - -
26P ILE* 5.7 0.5 - - - +
30P PHE* 3.5 33.1 - - - -
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Residues in contact with PHE 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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57N LEU* 3.3 50.0 - - + -
26O ILE* 3.5 31.4 - - + -
29O VAL* 4.7 2.4 - - - +
30O PHE* 6.4 0.4 - - + -
51O ALA 3.3 7.8 + - - +
52O ILE* 3.0 27.0 + - + +
54O GLY* 1.3 77.8 - - - +
56O ALA* 1.3 55.1 + - + +
58O SER* 3.1 4.4 + - - -
59O GLU* 2.7 70.1 + - + +
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Residues in contact with ALA 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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52O ILE 3.5 5.9 + - - +
53O LEU* 3.5 8.7 + - - +
54O GLY 3.5 0.2 - - - -
55O PHE* 1.3 83.1 - - + +
57O LEU* 1.3 65.0 + - + +
59O GLU* 3.9 9.2 - - - +
60O ALA* 3.5 17.5 + - - +
63O LEU* 5.9 0.9 - - - +
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Residues in contact with LEU 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* 3.1 15.0 - - + +
54O GLY 3.6 5.8 - - - +
55O PHE 3.1 0.4 - - - -
56O ALA* 1.3 80.8 - - + +
58O SER* 1.3 59.6 + - - +
60O ALA* 3.5 18.2 - - - +
61O THR* 4.8 1.7 + - - +
22P ALA 5.0 0.3 - - - +
26P ILE* 4.3 19.8 - - + +
30P PHE* 3.6 36.3 - - + -
55P PHE* 3.3 53.4 - - + -
59P GLU* 4.8 0.7 - - - +
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Residues in contact with SER 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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21O GLY 3.7 3.3 + - - -
22O ALA* 3.9 7.6 - - - +
25O GLY 3.7 1.5 - - - -
26O ILE* 3.3 35.5 + - - +
29O VAL* 4.8 6.3 - - - -
54O GLY 3.1 16.2 + - - -
57O LEU* 1.3 73.4 - - - +
59O GLU* 1.3 57.1 + - - +
60O ALA 3.1 6.1 - - - -
61O THR* 3.1 24.3 + - - -
22P ALA 5.1 2.2 - - - -
23P GLY* 3.3 25.5 + - - -
26P ILE* 5.6 2.7 - - - -
27P ALA* 5.3 2.9 - - - -
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Residues in contact with GLU 59 (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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57N LEU 4.8 3.3 - - - +
60N ALA* 5.1 6.5 - - - +
64N PHE* 4.9 10.2 - - - -
22O ALA* 5.2 1.9 - - - +
26O ILE* 3.3 23.7 - - - +
55O PHE* 2.7 40.1 + - + +
56O ALA* 3.9 11.9 - - - +
57O LEU 3.3 0.4 - - - -
58O SER* 1.3 76.7 - - - +
60O ALA* 1.3 65.5 + - - +
61O THR 3.4 0.2 - - - -
62O GLY* 3.0 21.0 + - - +
63O LEU* 3.1 40.7 + - + +
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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
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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