Contacts of the helix formed by residues 33 - 48 (chain A) in PDB entry 3BRQ
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 TYR 33 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A HIS 5.0 6.3 + - - -
34A PHE* 1.3 68.0 + - + +
35A SER* 3.4 13.5 + - - -
36A GLU* 3.5 15.1 - - - +
37A LEU* 3.0 32.9 + - + +
82A TYR* 3.4 38.4 - + - -
105A LEU* 4.0 9.7 - - + +
106A ASN* 2.6 31.3 + - - -
121A HIS* 6.3 2.9 - + - -
234A ASP* 5.5 12.2 + - - +
251A ILE* 5.6 2.9 - - + -
253A VAL* 3.7 40.9 - - + +
256A MSE 5.5 3.5 - - - +
257A ILE* 5.6 0.3 - - - +
701A FRU 3.8 40.7 - - - +
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Residues in contact with PHE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 4.2 14.4 - - + -
28A LEU* 3.2 25.6 - - + +
29A TYR* 3.5 35.9 - + + -
30A HIS 4.1 14.8 - - - +
33A TYR* 1.3 81.1 - - + +
35A SER* 1.3 68.3 + - - +
37A LEU* 3.4 16.9 + - + +
38A LEU* 3.0 54.7 + - + +
54A LEU* 4.6 2.0 - - + -
82A TYR* 5.9 2.0 - + + -
701A FRU 5.2 0.6 + - - +
34B PHE* 5.9 0.9 - + - -
35B SER* 3.7 27.1 - - - -
38B LEU* 3.4 26.2 - - + -
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Residues in contact with SER 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A HIS 5.6 0.8 + - - -
33A TYR 3.9 11.8 + - - +
34A PHE* 1.3 83.3 - - - +
36A GLU* 1.4 66.2 + - - +
38A LEU* 4.0 3.3 - - - +
39A PHE* 3.1 28.9 + - - +
33B TYR* 4.6 23.8 - - - -
34B PHE* 6.2 0.2 - - - -
35B SER* 4.8 6.1 - - - +
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Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A TYR* 3.4 19.0 + - - +
35A SER* 1.4 81.8 + - - +
37A LEU* 1.3 57.1 + - - +
39A PHE* 3.1 5.1 + - - +
40A HIS* 2.8 55.7 + - + +
234A ASP 5.0 6.8 - - - +
251A ILE 5.4 0.2 - - - +
253A VAL* 3.8 32.9 - - + +
254A THR* 3.4 22.2 + - - -
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 4.3 13.0 - - + -
24A VAL* 4.2 18.4 - - + -
33A TYR* 3.0 20.2 + - + +
34A PHE* 3.8 17.5 - - + +
36A GLU* 1.3 80.6 - - - +
38A LEU* 1.3 59.1 + - - +
41A ALA* 2.8 42.6 + - + +
80A MSE 4.4 5.6 - - + -
82A TYR* 4.2 27.4 - - + -
105A LEU* 4.3 8.1 - - + -
253A VAL* 4.8 2.4 - - + +
257A ILE* 3.5 37.0 - - + -
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 5.0 7.0 - - + -
34A PHE* 3.0 54.5 + - + +
35A SER* 4.0 3.8 - - - +
37A LEU* 1.3 76.9 - - - +
39A PHE* 1.3 66.1 + - - +
41A ALA* 4.2 2.6 - - - +
42A ALA* 3.1 31.7 + - + +
52A LEU* 5.0 10.8 - - + -
54A LEU* 4.0 16.4 - - + -
34B PHE* 3.9 32.3 - - + -
38B LEU* 3.9 12.3 - - + -
54B LEU* 4.0 11.2 - - + -
56B ASP* 6.6 0.2 - - - -
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Residues in contact with PHE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A SER 3.1 18.5 + - - +
36A GLU* 3.6 4.7 - - - +
38A LEU* 1.3 77.2 - - - +
40A HIS* 1.3 88.3 + + - +
43A ARG* 2.9 72.0 + - + +
26B ASN* 3.1 23.1 - - - +
27B THR 3.7 17.9 - - - +
28B LEU* 3.7 43.1 - - + +
34B PHE* 6.0 1.1 - - - -
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Residues in contact with HIS 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLU* 2.8 51.6 + - - +
37A LEU 4.3 0.4 - - - +
39A PHE* 1.3 98.1 - + - +
41A ALA* 1.3 59.5 + - - +
43A ARG* 3.9 6.2 - - - +
44A MSE 2.9 33.3 + - - +
253A VAL* 5.6 1.1 - - + -
254A THR* 3.1 40.8 + - + +
257A ILE* 3.7 20.0 - - + -
258A GLN* 5.8 0.2 + - - -
28B LEU* 6.2 0.2 - - - +
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 4.5 6.5 - - + -
37A LEU* 2.8 37.9 + - + +
38A LEU 4.2 0.7 - - - +
40A HIS* 1.3 73.1 - - - +
42A ALA* 1.3 57.6 + - - +
44A MSE 3.8 0.3 - - - -
45A ALA* 2.9 31.2 + - - +
52A LEU* 3.6 18.1 - - + +
80A MSE 4.9 2.7 - - - -
257A ILE* 3.4 13.7 - - + +
261A ILE* 4.0 17.3 - - + +
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 3.1 24.0 + - + +
41A ALA* 1.3 77.8 - - - +
43A ARG* 1.3 63.0 + - - +
45A ALA* 3.2 3.7 + - - +
46A GLU* 3.0 30.0 + - - +
52A LEU* 3.5 14.6 - - + +
26B ASN* 3.4 15.7 - - + +
56B ASP* 3.4 27.4 - - + +
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Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A PHE* 2.9 55.6 + - + +
40A HIS* 3.9 9.2 - - - +
42A ALA* 1.3 76.8 - - - +
44A MSE 1.3 55.7 + - - +
46A GLU* 3.3 15.5 + - - +
47A GLU* 3.0 49.1 + - - +
26B ASN* 2.5 46.0 + - - +
27B THR* 4.9 1.0 - - - +
28B LEU* 5.1 1.4 - - - +
59B HIS* 3.4 25.6 + - - +
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Residues in contact with MSE 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A HIS 2.9 21.8 + - - +
41A ALA 4.1 1.8 - - - +
43A ARG* 1.3 70.9 - - - +
45A ALA* 1.3 68.5 + - - +
47A GLU* 3.4 20.0 + - - +
48A LYS* 3.2 55.6 + - - +
257A ILE* 5.0 1.1 - - + -
258A GLN* 3.0 58.3 - - + +
261A ILE* 3.5 23.6 - - + -
262A GLY* 3.6 14.6 - - - +
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 4.4 16.6 - - + -
41A ALA 2.9 19.3 + - - +
42A ALA 3.7 4.3 - - - +
44A MSE 1.3 78.1 - - - +
46A GLU* 1.3 59.1 + - + +
48A LYS* 3.2 5.9 + - - +
49A GLY 3.1 4.9 + - - -
50A ARG* 3.0 41.6 + - + +
52A LEU* 4.2 20.6 - - + +
261A ILE* 4.2 8.9 - - + +
56B ASP* 5.4 0.4 - - - +
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA 3.0 12.7 + - - +
43A ARG* 3.6 12.5 + - - +
45A ALA* 1.3 72.6 - - - +
47A GLU* 1.3 63.3 + - + +
48A LYS 3.0 5.3 + - - -
49A GLY* 3.1 13.0 + - - +
50A ARG 4.2 6.1 - - - +
26B ASN* 3.3 22.2 + - - +
56B ASP* 2.5 34.1 - - - +
58B LYS* 3.3 42.8 - - + +
59B HIS* 4.3 4.7 + - - +
63B GLU* 5.2 1.4 - - - +
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Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ARG* 3.0 39.7 + - + +
44A MSE 3.8 26.6 - - - +
45A ALA 3.4 0.4 - - - -
46A GLU* 1.3 75.4 - - + +
48A LYS* 1.3 65.1 + - + +
49A GLY 4.0 0.2 + - - -
258A GLN* 5.3 5.2 + - - -
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Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A MSE 3.2 46.1 - - + +
45A ALA 3.2 5.8 + - - +
46A GLU 3.0 0.4 - - - -
47A GLU* 1.3 85.8 - - + +
49A GLY* 1.3 55.3 + - - +
50A ARG* 3.0 26.7 + - - +
261A ILE* 4.8 0.2 - - + -
262A GLY* 5.0 5.4 - - - -
265A ILE* 3.4 38.8 - - + -
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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