Contacts of the helix formed by residues 46 - 59 (chain k) 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 k).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43k ILE* 3.6 29.0 - - + +
44k LYS 2.9 0.8 + - - -
45k ASP* 1.3 81.6 + - - +
47k VAL* 1.3 61.7 + - - +
49k PRO* 3.2 17.0 - - - +
50k MET* 3.0 26.0 + - + +
37l VAL* 5.9 1.8 - - + -
44l LYS* 3.5 37.7 + - + +
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Residues in contact with VAL 47 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33k LEU* 3.6 16.2 - - + -
37k VAL* 5.4 2.7 - - + -
43k ILE* 3.4 37.2 - - + +
44k LYS 3.4 3.4 + - - +
46k THR* 1.3 78.2 - - - +
48k PHE* 1.3 59.7 + - - +
49k PRO 3.4 0.4 - - - -
50k MET* 3.1 7.9 - - + +
51k ALA* 2.9 27.4 + - - +
34l ILE* 3.4 39.5 - - + +
37l VAL* 3.6 19.5 - - + -
38l SER* 4.0 11.2 - - - +
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Residues in contact with PHE 48 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50j MET* 4.8 25.4 - - + -
53j LEU* 4.9 15.3 - - + -
30k PHE* 6.3 2.5 - + - -
33k LEU* 4.1 24.8 - - + +
44k LYS* 3.1 35.2 + - + +
45k ASP* 4.8 2.5 - - - +
47k VAL* 1.3 78.3 - - - +
49k PRO* 1.3 66.0 - - + +
51k ALA* 3.3 7.6 + - - +
52k ILE* 3.3 44.8 + - + +
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Residues in contact with PRO 49 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45k ASP* 3.7 19.3 - - - +
46k THR* 3.2 22.0 - - - +
48k PHE* 1.3 98.8 - - + +
50k MET* 1.3 66.2 + - + +
52k ILE* 3.3 19.3 + - + +
53k LEU* 3.4 16.8 + - + +
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Residues in contact with MET 50 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46k THR* 3.0 33.7 - - + +
47k VAL* 3.1 25.8 - - + +
49k PRO* 1.3 78.6 - - + +
51k ALA* 1.3 65.6 + - - +
53k LEU* 3.0 24.4 + - + +
30l PHE* 3.0 31.6 - - + -
33l LEU* 4.2 26.2 - - + +
34l ILE* 4.7 6.1 - - + -
37l VAL* 4.3 25.1 - - + -
44l LYS* 4.9 7.4 - - + -
48l PHE* 4.6 22.4 - - + -
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Residues in contact with ALA 51 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29k VAL* 4.2 9.2 - - - +
30k PHE* 6.1 2.7 - - + -
33k LEU* 3.8 26.0 - - + -
47k VAL 2.9 18.8 + - - +
48k PHE 3.4 7.0 - - - +
49k PRO 3.2 0.4 - - - -
50k MET* 1.3 78.5 - - - +
52k ILE* 1.3 62.2 + - + +
54k GLY* 3.2 11.1 + - - -
55k PHE* 3.3 9.9 + - - +
30l PHE* 4.5 0.7 - - - -
34l ILE* 4.4 22.2 - - + -
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Residues in contact with ILE 52 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48k PHE* 3.3 41.5 + - + +
49k PRO* 3.6 10.8 - - + +
50k MET 3.2 0.4 - - - -
51k ALA* 1.3 74.1 - - + +
53k LEU* 1.3 67.3 + - + +
55k PHE* 3.0 32.7 + - + +
56k ALA* 3.5 6.6 + - - +
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Residues in contact with LEU 53 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49k PRO 3.5 11.9 - - - +
50k MET* 3.0 25.9 + - + +
52k ILE* 1.3 81.4 - - + +
54k GLY* 1.3 59.9 + - - +
55k PHE 3.3 0.7 + - - -
56k ALA* 3.5 7.6 + - - +
57k LEU* 3.1 26.7 + - + +
30l PHE* 4.1 9.2 - - + -
48l PHE* 4.7 16.4 - - + -
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Residues in contact with GLY 54 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29k VAL* 4.3 11.5 - - - +
50k MET 3.1 10.3 + - - -
51k ALA 3.2 5.1 + - - -
52k ILE 3.2 0.4 - - - -
53k LEU* 1.3 74.3 - - - +
55k PHE* 1.3 63.4 + - - +
56k ALA 3.5 0.2 - - - -
57k LEU* 3.4 4.7 + - - +
58k SER* 3.1 25.3 + - - -
26l ILE* 5.8 0.3 - - - +
30l PHE* 3.4 33.0 - - - +
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Residues in contact with PHE 55 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57j LEU* 3.6 42.8 - - + -
26k ILE* 3.5 34.1 - - + -
29k VAL* 4.7 2.2 - - - +
30k PHE* 6.4 0.7 - - + -
51k ALA 3.3 8.4 + - - +
52k ILE* 3.0 26.8 + - + +
54k GLY* 1.3 77.6 - - - +
56k ALA* 1.3 55.1 + - + +
58k SER* 3.1 4.8 + - - -
59k GLU* 2.7 68.8 + - + +
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Residues in contact with ALA 56 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52k ILE 3.5 6.2 + - - +
53k LEU* 4.0 8.1 - - - +
54k GLY 3.5 0.2 - - - -
55k PHE* 1.3 83.6 - - + +
57k LEU* 1.3 64.0 + - + +
59k GLU* 3.8 9.2 - - - +
60k ALA* 3.5 17.5 + - - +
63k LEU* 5.9 0.9 - - - +
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Residues in contact with LEU 57 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53k LEU* 3.1 13.5 - - + +
54k GLY 3.6 5.4 - - - +
55k PHE 3.1 0.4 - - - -
56k ALA* 1.3 81.2 - - + +
58k SER* 1.3 59.5 + - - +
60k ALA* 3.5 18.2 - - - +
61k THR* 4.8 1.7 + - - +
22l ALA 5.0 0.9 - - - +
26l ILE* 4.2 20.5 - - + +
30l PHE* 3.4 39.3 - - + -
55l PHE* 3.4 51.6 - - + -
59l GLU* 4.9 0.9 - - - +
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Residues in contact with SER 58 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21k GLY 3.7 2.8 + - - -
22k ALA* 3.9 7.8 - - - +
25k GLY 3.7 1.5 - - - -
26k ILE* 3.3 36.9 + - - +
29k VAL* 4.8 6.3 - - - -
54k GLY 3.1 16.6 + - - -
55k PHE* 4.9 0.2 - - - -
57k LEU* 1.3 73.0 - - - +
59k GLU* 1.3 57.3 + - - +
60k ALA 3.1 5.2 - - - -
61k THR* 3.1 23.9 + - - -
22l ALA 5.1 2.5 - - - -
23l GLY* 3.3 25.7 + - - -
26l ILE* 5.6 2.0 - - - -
27l ALA* 5.2 2.9 - - - -
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Residues in contact with GLU 59 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57j LEU 5.1 2.3 - - - +
60j ALA* 5.4 6.4 - - - +
64j PHE* 5.1 10.0 - - - -
22k ALA* 5.0 1.6 - - - +
26k ILE* 3.3 23.5 - - - +
55k PHE* 2.7 40.7 + - + +
56k ALA* 3.9 11.0 - - - +
57k LEU 3.3 0.4 - - - -
58k SER* 1.3 75.4 - - - +
60k ALA* 1.3 64.8 + - - +
61k THR 3.4 0.2 - - - -
62k GLY* 3.0 21.6 + - - +
63k 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
------------------------------------------------------------
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