Contacts of the helix formed by residues 37 - 46 (chain A) in PDB entry 3BQY
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 37 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ASP 5.1 4.7 - - - +
35A THR 3.1 12.0 + - - +
36A LEU* 1.3 82.1 - - - +
38A MSE 1.3 59.4 + - - +
39A ARG* 3.5 9.6 + - - +
40A ARG* 2.7 33.3 + - - +
41A LEU* 2.9 29.9 + - - +
59A LYS* 4.4 9.6 - - - +
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Residues in contact with MSE 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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37A THR* 1.3 72.8 - - - +
39A ARG* 1.3 58.8 + - + +
41A LEU* 3.4 3.9 + - + -
42A ALA* 2.8 26.8 + - - +
49A ALA* 4.7 3.6 - - + -
52A LEU* 3.3 40.0 - - + +
53A TYR* 3.3 53.2 - - + +
56A PHE* 3.8 27.6 - - + +
58A ALA 4.7 2.9 - - - -
59A LYS* 4.1 28.2 - - + +
62A LEU* 4.0 27.1 - - - -
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Residues in contact with ARG 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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37A THR* 3.2 8.1 + - - +
38A MSE 1.3 78.8 - - + +
40A ARG* 1.3 56.8 + - - +
42A ALA* 3.2 8.5 + - - +
43A GLN* 2.8 46.2 + - - +
49A ALA* 4.5 20.3 - - + +
53A TYR* 6.1 2.4 - - + +
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Residues in contact with ARG 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.7 35.4 - - + +
30A GLU* 4.4 7.3 + - - +
31A SER* 4.8 9.7 + - - +
35A THR* 3.7 19.2 - - - +
36A LEU* 4.9 0.2 - - - -
37A THR* 2.7 32.5 + - - +
39A ARG* 1.3 72.4 - - - +
41A LEU* 1.3 56.6 + - - +
43A GLN* 3.3 25.1 + - - +
44A ALA* 3.0 36.7 + - - +
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Residues in contact with LEU 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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20A THR* 3.9 19.5 - - + +
23A THR* 3.7 19.1 - - + -
24A ALA* 3.7 32.5 - - + +
27A LEU* 3.7 12.7 - - + +
36A LEU* 4.8 2.2 - - + -
37A THR 2.9 17.0 + - - +
38A MSE 3.5 7.9 - - - +
40A ARG* 1.3 74.5 - - - +
42A ALA* 1.3 64.6 + - - +
44A ALA* 3.3 2.1 + - - +
45A MSE 3.1 36.2 + - - +
52A LEU* 3.8 14.8 - - + -
62A LEU* 3.4 33.4 - - + -
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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 MSE 2.8 20.9 + - - +
39A ARG* 3.4 6.7 - - - +
41A LEU* 1.3 69.3 - - - +
43A GLN* 1.3 67.1 + - + +
45A MSE 3.3 0.5 + - - -
46A ASP* 2.9 19.4 + - - -
47A VAL* 3.1 33.8 + - + +
48A GLN 4.0 1.6 - - - -
49A ALA* 3.7 27.1 - - + +
52A LEU* 3.6 8.0 - - + +
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Residues in contact with GLN 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 ARG* 2.8 34.1 + - - +
40A ARG* 3.6 30.2 + - - +
41A LEU 3.3 0.2 - - - -
42A ALA* 1.3 72.4 - - + +
44A ALA* 1.3 62.3 + - - +
46A ASP* 3.2 14.4 + - - +
47A VAL 5.1 0.7 - - - -
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Residues in contact with ALA 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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23A THR* 4.0 20.2 - - + +
27A LEU* 4.1 21.5 - - + -
40A ARG* 3.0 20.4 + - - +
41A LEU 3.5 9.9 - - - +
42A ALA 3.2 0.2 - - - -
43A GLN* 1.3 76.9 - - - +
45A MSE 1.3 58.7 + - - +
46A ASP* 3.8 0.5 + - - +
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Residues in contact with MSE 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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16A ASP* 5.1 2.2 - - - +
19A ARG* 4.0 8.5 - - + +
20A THR* 3.6 48.0 - - - +
23A THR* 3.6 28.0 - - + +
41A LEU* 3.1 22.1 + - - +
42A ALA 3.3 0.4 + - - -
44A ALA* 1.3 74.8 - - - +
46A ASP* 1.3 71.8 + - - +
47A VAL* 3.3 19.5 + - + +
52A LEU* 4.0 20.0 - - - -
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Residues in contact with ASP 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 2.9 6.5 + - - -
43A GLN* 3.2 11.5 + - - +
44A ALA 3.4 1.1 - - - +
45A MSE 1.3 80.2 - - - +
47A VAL* 1.3 62.9 + - - +
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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