Contacts of the helix formed by residues 46 - 59 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43R ILE* 3.2 30.6 - - + +
44R LYS 2.9 1.0 - - - -
45R ASP* 1.3 83.3 + - - +
47R VAL* 1.3 60.9 + - - +
49R PRO* 3.2 17.7 - - - +
50R MET* 3.0 25.8 - - + +
37S VAL* 4.9 5.4 - - + -
44S LYS* 3.4 37.9 + - + +
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Residues in contact with VAL 47 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R LEU* 3.6 14.4 - - + -
36R GLY* 6.4 0.2 - - - -
37R VAL* 6.0 0.9 - - + -
43R ILE* 3.4 34.3 - - + +
44R LYS 3.4 1.2 + - - -
46R THR* 1.3 77.2 - - - +
48R PHE* 1.3 60.9 + - - +
49R PRO 3.4 0.7 - - - -
50R MET* 3.1 11.1 - - + +
51R ALA* 2.9 27.4 + - - +
34S ILE* 3.3 43.1 - - + +
37S VAL* 4.7 14.6 - - + -
38S SER* 4.2 14.8 - - - +
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Residues in contact with PHE 48 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q MET* 4.5 31.9 - - + -
53Q LEU* 4.7 16.2 - - + -
30R PHE* 6.3 1.8 - + - -
33R LEU* 4.1 22.3 - - + +
44R LYS* 3.1 33.1 + - + +
45R ASP* 4.8 2.5 - - - +
47R VAL* 1.3 78.1 - - - +
49R PRO* 1.3 68.2 - - + +
51R ALA* 3.3 7.1 + - - +
52R ILE* 3.3 44.3 + - + +
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Residues in contact with PRO 49 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45R ASP* 3.7 19.7 - - - +
46R THR* 3.2 21.3 - - - +
48R PHE* 1.3 99.7 - - + +
50R MET* 1.3 66.0 + - + +
52R ILE* 3.3 19.6 + - + +
53R LEU* 3.4 17.3 + - + +
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Residues in contact with MET 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46R THR* 3.0 34.5 - - + +
47R VAL* 3.1 29.6 - - + +
49R PRO* 1.3 78.4 - - + +
51R ALA* 1.3 65.7 + - - +
53R LEU* 3.0 23.2 + - + +
30S PHE* 2.9 32.7 - - + -
33S LEU* 4.1 29.4 - - + +
34S ILE* 4.8 7.4 - - + -
37S VAL* 4.7 14.6 - - + -
44S LYS* 4.9 6.3 - - + -
48S PHE* 4.6 24.5 - - + -
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Residues in contact with ALA 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R VAL* 4.2 9.1 - - - +
30R PHE* 6.1 2.9 - - + -
33R LEU* 3.8 25.4 - - + -
47R VAL 2.9 19.8 + - - +
48R PHE 3.4 7.2 - - - +
49R PRO 3.2 0.4 - - - -
50R MET* 1.3 78.6 - - - +
52R ILE* 1.3 62.3 + - + +
54R GLY* 3.2 10.2 + - - -
55R PHE* 3.3 9.9 + - - +
30S PHE* 4.4 0.9 - - - -
34S ILE* 4.3 22.2 - - + -
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Residues in contact with ILE 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48R PHE* 3.3 41.7 + - + +
49R PRO* 3.6 11.9 - - + +
50R MET 3.2 0.6 - - - -
51R ALA* 1.3 73.5 - - + +
53R LEU* 1.3 67.3 + - + +
55R PHE* 3.0 33.1 + - + +
56R ALA* 3.5 6.1 + - - +
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Residues in contact with LEU 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49R PRO* 3.5 12.1 - - + +
50R MET* 3.0 24.5 + - + +
52R ILE* 1.3 79.5 - - + +
54R GLY* 1.3 59.6 + - - +
55R PHE 3.3 0.7 + - - -
56R ALA* 3.5 7.6 + - - +
57R LEU* 3.1 26.9 + - + +
30S PHE* 4.2 8.5 - - + -
48S PHE* 4.9 15.0 - - + -
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Residues in contact with GLY 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29R VAL* 4.3 12.2 - - - +
50R MET 3.1 10.3 + - - -
51R ALA 3.2 5.3 + - - -
52R ILE 3.2 0.4 - - - -
53R LEU* 1.3 74.3 - - - +
55R PHE* 1.3 64.7 + - - +
57R LEU* 3.4 5.1 + - - +
58R SER* 3.1 24.1 + - - -
26S ILE* 5.7 0.5 - - - +
30S PHE* 3.5 32.6 - - - -
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Residues in contact with PHE 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Q LEU* 3.3 48.7 - - + -
26R ILE* 3.5 31.2 - - + +
29R VAL* 4.7 2.2 - - - +
30R PHE* 6.1 0.7 - + + -
51R ALA 3.3 8.6 + - - +
52R ILE* 3.0 27.5 + - + +
54R GLY* 1.3 76.7 - - - +
56R ALA* 1.3 55.6 + - + +
58R SER* 3.1 4.7 + - - -
59R GLU* 2.7 69.8 + - + +
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Residues in contact with ALA 56 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52R ILE 3.5 6.4 + - - +
53R LEU* 3.5 8.5 + - - +
54R GLY 3.5 0.2 - - - -
55R PHE* 1.3 85.0 - - + +
57R LEU* 1.3 64.0 + - + +
59R GLU* 3.9 8.6 - - - +
60R ALA* 3.5 17.7 + - - +
63R LEU* 5.9 0.9 - - - +
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Residues in contact with LEU 57 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53R LEU* 3.1 13.7 - - + +
54R GLY 3.6 5.4 - - - +
55R PHE 3.1 0.6 - - - -
56R ALA* 1.3 81.6 - - + +
58R SER* 1.3 59.8 + - - +
60R ALA* 3.5 17.8 - - - +
61R THR* 4.7 1.7 + - - +
22S ALA 5.0 0.9 - - - +
26S ILE* 4.2 19.5 - - + +
30S PHE* 3.6 37.0 - - + -
55S PHE* 3.4 51.8 - - + -
59S GLU* 4.9 1.0 - - - +
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Residues in contact with SER 58 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21R GLY 3.7 2.9 + - - -
22R ALA* 3.9 7.6 - - - +
25R GLY 3.7 1.1 - - - -
26R ILE* 3.4 35.6 + - - +
29R VAL* 4.8 6.5 - - - -
54R GLY 3.1 16.8 + - - -
55R PHE 3.9 0.2 - - - -
57R LEU* 1.3 73.8 - - - +
59R GLU* 1.3 57.7 + - - +
60R ALA 3.1 5.4 - - - -
61R THR* 3.1 23.8 + - - -
22S ALA 5.1 2.0 - - - -
23S GLY* 3.2 27.2 + - - -
26S ILE* 5.6 2.5 - - - -
27S ALA* 5.2 3.1 - - - -
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Residues in contact with GLU 59 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Q LEU 4.8 2.9 - - - +
60Q ALA* 5.2 6.8 - - - +
64Q PHE* 5.0 9.7 - - - -
22R ALA* 5.0 2.1 - - - +
26R ILE* 3.3 22.8 - - - +
55R PHE* 2.7 39.7 + - + +
56R ALA* 3.9 11.7 - - - +
57R LEU 3.3 0.4 - - - -
58R SER* 1.3 75.1 - - - +
60R ALA* 1.3 65.1 + - - +
61R THR 3.4 0.2 - - - -
62R GLY* 3.0 21.4 + - - +
63R LEU* 3.1 40.5 + - + +
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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