Contacts of the helix formed by residues 46 - 59 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43Q ILE* 3.4 28.0 - - + +
44Q LYS 2.9 0.8 + - - -
45Q ASP* 1.3 81.6 + - - +
47Q VAL* 1.3 62.2 - - + +
49Q PRO* 3.2 17.3 - - - +
50Q MET* 3.0 26.1 + - + +
37R VAL* 6.3 1.6 - - + -
44R LYS* 3.2 40.4 + - + +
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Residues in contact with VAL 47 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Q LEU* 3.6 16.8 - - + -
36Q GLY* 6.3 0.4 - - - -
37Q VAL* 5.9 0.7 - - + -
43Q ILE* 3.5 34.5 - - + +
44Q LYS* 3.4 2.1 + - - +
46Q THR* 1.3 77.8 - - + +
48Q PHE* 1.3 60.5 + - - +
49Q PRO 3.4 0.4 - - - -
50Q MET* 3.1 11.5 - - + +
51Q ALA* 2.9 27.2 + - - +
34R ILE* 3.6 37.5 - - + +
37R VAL* 3.6 24.7 - - + -
38R SER* 5.1 5.2 - - - +
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Residues in contact with PHE 48 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50P MET* 4.6 27.1 - - + -
53P LEU* 4.8 15.7 - - + -
30Q PHE* 6.3 2.2 - + - -
33Q LEU* 4.1 24.8 - - + +
44Q LYS* 3.1 33.5 + - + +
45Q ASP* 4.8 2.7 - - - +
47Q VAL* 1.3 78.2 - - - +
49Q PRO* 1.3 66.1 - - + +
51Q ALA* 3.3 7.7 + - - +
52Q ILE* 3.3 44.7 + - + +
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Residues in contact with PRO 49 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Q ASP* 3.7 20.0 - - - +
46Q THR* 3.2 21.8 - - - +
48Q PHE* 1.3 99.3 - - + +
50Q MET* 1.3 66.6 + - + +
52Q ILE* 3.3 19.7 + - + +
53Q LEU* 3.4 17.1 + - + +
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Residues in contact with MET 50 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46Q THR* 3.0 34.3 - - + +
47Q VAL* 3.1 31.4 - - + +
49Q PRO* 1.3 79.0 - - + +
51Q ALA* 1.3 65.9 + - - +
53Q LEU* 3.0 25.7 + - + +
30R PHE* 3.0 30.8 - - + -
33R LEU* 4.2 31.9 - - + +
34R ILE* 5.0 6.3 - - + -
37R VAL* 4.9 11.2 - - + -
44R LYS* 4.7 7.6 - - + -
48R PHE* 4.5 25.4 - - + -
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Residues in contact with ALA 51 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Q VAL* 4.2 9.1 - - - +
30Q PHE* 6.1 2.9 - - + -
33Q LEU* 3.8 29.8 - - + -
47Q VAL 2.9 20.5 + - - +
48Q PHE 3.4 7.2 - - - +
49Q PRO 3.2 0.4 - - - -
50Q MET* 1.3 78.6 - - - +
52Q ILE* 1.3 62.9 + - + +
54Q GLY* 3.2 11.1 + - - -
55Q PHE* 3.3 9.7 + - - +
30R PHE* 4.4 6.5 - - - -
34R ILE* 4.5 11.9 - - + -
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Residues in contact with ILE 52 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Q PHE* 3.3 41.2 + - + +
49Q PRO* 3.6 11.7 - - + +
50Q MET 3.2 0.4 - - - -
51Q ALA* 1.3 75.1 - - + +
53Q LEU* 1.3 66.7 + - + +
55Q PHE* 3.0 32.1 + - + +
56Q ALA* 3.5 6.6 + - - +
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Residues in contact with LEU 53 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Q PRO 3.5 11.2 - - - +
50Q MET* 3.0 25.2 + - + +
52Q ILE* 1.3 79.3 - - + +
54Q GLY* 1.3 60.5 + - - +
55Q PHE 3.3 0.7 + - - -
56Q ALA* 3.5 7.4 + - - +
57Q LEU* 3.1 26.5 + - + +
30R PHE* 4.2 7.9 - - + -
48R PHE* 4.7 15.5 - - + -
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Residues in contact with GLY 54 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Q VAL* 4.3 10.6 - - - +
50Q MET 3.1 9.7 + - - -
51Q ALA 3.2 5.1 + - - -
52Q ILE 3.2 0.2 - - - -
53Q LEU* 1.3 74.8 - - - +
55Q PHE* 1.3 64.9 + - - +
57Q LEU* 3.4 4.9 + - - +
58Q SER* 3.1 24.8 + - - -
26R ILE* 5.7 0.5 - - - +
30R PHE* 3.4 33.3 - - - -
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Residues in contact with PHE 55 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57P LEU* 3.4 49.1 - - + -
26Q ILE* 3.5 31.6 - - + -
29Q VAL* 5.4 1.6 - - - -
30Q PHE* 6.1 0.9 - + + -
51Q ALA 3.3 7.5 + - - +
52Q ILE* 3.0 26.5 + - + +
54Q GLY* 1.3 76.9 - - - +
56Q ALA* 1.3 55.2 + - + +
58Q SER* 3.1 4.8 + - - -
59Q GLU* 2.7 70.2 + - + +
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Residues in contact with ALA 56 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52Q ILE 3.5 6.1 + - - +
53Q LEU* 3.5 8.3 + - - +
54Q GLY 3.5 0.2 - - - -
55Q PHE* 1.3 83.6 - - + +
57Q LEU* 1.3 64.2 + - + +
59Q GLU* 3.9 8.8 - - - +
60Q ALA* 3.5 16.8 + - - +
63Q LEU* 5.9 0.9 - - - +
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Residues in contact with LEU 57 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53Q LEU* 3.1 13.9 - - + +
54Q GLY* 3.6 5.8 - - - +
55Q PHE 3.1 0.8 - - - -
56Q ALA* 1.3 82.7 - - + +
58Q SER* 1.3 58.9 + - - +
60Q ALA* 3.5 18.2 - - - +
61Q THR* 4.8 1.7 + - - +
22R ALA 5.1 0.3 - - - +
26R ILE* 4.3 20.1 - - + +
30R PHE* 3.6 37.0 - - + -
55R PHE* 3.3 53.5 - - + -
59R GLU* 4.8 1.0 - - - +
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Residues in contact with SER 58 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Q GLY 3.7 3.6 + - - -
22Q ALA* 3.9 8.3 - - - +
25Q GLY 3.7 1.2 - - - -
26Q ILE* 3.3 38.5 + - - +
29Q VAL* 4.8 6.7 - - - -
54Q GLY 3.1 16.2 + - - -
55Q PHE* 3.9 0.7 - - - -
57Q LEU* 1.3 73.6 - - - +
59Q GLU* 1.3 57.0 + - - +
60Q ALA 3.1 5.6 - - - -
61Q THR* 3.1 23.8 + - - -
22R ALA 5.2 5.2 - - - -
23R GLY* 3.4 19.9 + - - -
26R ILE* 5.3 3.1 - - - +
27R ALA* 5.4 2.5 - - - -
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Residues in contact with GLU 59 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57P LEU 4.9 2.8 - - - +
60P ALA* 5.2 6.5 - - - +
64P PHE* 5.0 10.4 - - - -
22Q ALA* 5.2 1.8 - - - +
26Q ILE* 3.3 23.2 - - - +
55Q PHE* 2.7 41.7 + - + +
56Q ALA* 3.9 11.7 - - - +
57Q LEU 3.3 0.2 - - - -
58Q SER* 1.3 74.6 - - - +
60Q ALA* 1.3 65.8 + - - +
61Q THR 3.4 0.2 - - - -
62Q GLY* 3.0 21.3 + - - +
63Q LEU* 3.1 41.0 + - + +
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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