Contacts of the helix formed by residues 48 - 60 (chain A) in PDB entry 3BS3
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 SER 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A GLN 3.9 0.8 + - - -
47A PRO* 1.3 75.9 - - - +
49A LEU* 1.3 66.4 + - - +
50A ASP* 2.6 27.2 + - - -
51A MSE 3.2 20.3 + - - +
52A LEU* 3.0 20.9 + - - +
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Residues in contact with LEU 49 (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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8A MSE 6.2 5.2 - - + -
47A PRO 5.7 0.9 - - - +
48A SER* 1.3 74.2 - - - +
50A ASP* 1.3 61.8 + - - +
52A LEU* 3.3 20.0 + - + +
53A VAL* 3.1 27.3 + - + +
67A ILE* 4.9 10.8 - - + -
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Residues in contact with ASP 50 (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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48A SER* 2.6 25.8 + - - -
49A LEU* 1.3 71.8 + - - +
51A MSE 1.3 83.4 + - - +
53A VAL* 3.3 10.2 + - - +
54A LYS* 3.1 20.6 + - - +
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Residues in contact with MSE 51 (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 MSE 3.6 23.1 - - + +
32A LYS* 3.3 40.4 - - - +
40A TRP* 4.1 4.5 - - + -
47A PRO* 4.1 13.7 - - + -
48A SER* 3.2 23.3 + - - +
50A ASP* 1.3 85.9 - - - +
52A LEU* 1.3 61.2 + - - +
54A LYS* 3.2 6.9 + - - +
55A VAL* 2.9 33.2 + - - +
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Residues in contact with LEU 52 (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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10A ASN* 4.7 3.6 - - + -
12A ILE* 4.1 10.8 - - + -
47A PRO* 3.6 25.7 - - + +
48A SER 3.0 12.1 + - - +
49A LEU* 3.5 19.5 - - + +
51A MSE 1.3 76.8 - - - +
53A VAL* 1.3 58.9 + - + +
55A VAL* 3.3 4.0 + - - -
56A ALA* 2.9 30.2 + - - +
63A PRO* 4.5 9.0 - - + +
66A LEU* 3.5 38.6 - - + +
67A ILE* 3.4 39.7 - - + -
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Residues in contact with VAL 53 (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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49A LEU* 3.1 16.9 + - + +
50A ASP* 3.5 10.5 - - - +
51A MSE 3.2 0.2 - - - -
52A LEU* 1.3 77.0 - - + +
54A LYS* 1.3 58.0 + - - +
56A ALA* 3.3 3.1 + - - +
57A GLU* 2.9 48.8 + - + +
63A PRO* 4.3 27.1 - - + -
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Residues in contact with LYS 54 (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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29A GLN 3.5 23.0 + - - -
30A MSE 3.7 20.2 + - + +
50A ASP 3.1 13.6 + - - +
51A MSE 3.2 11.6 + - - +
53A VAL* 1.3 72.9 - - - +
55A VAL* 1.3 66.7 + - - +
57A GLU* 3.2 21.3 + - + +
58A LEU* 3.0 43.7 + - + +
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Residues in contact with VAL 55 (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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12A ILE* 4.3 15.7 - - + -
26A LEU* 4.1 21.5 - - + -
30A MSE 3.7 22.2 - - + -
40A TRP* 4.0 17.3 - - + -
47A PRO* 5.7 0.2 - - + -
51A MSE 2.9 21.1 + - - +
52A LEU* 3.3 8.7 + - - +
54A LYS* 1.3 75.9 - - - +
56A ALA* 1.3 58.1 + - - +
58A LEU* 3.2 5.4 + - - +
59A LEU* 2.9 46.9 + - + +
66A LEU* 3.6 17.5 - - + -
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Residues in contact with ALA 56 (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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52A LEU 2.9 16.8 + - - +
53A VAL 3.5 4.9 - - - +
55A VAL* 1.3 74.5 - - - +
57A GLU* 1.3 61.1 + - + +
59A LEU 3.3 0.5 + - - -
60A ASN* 2.9 25.5 + - - -
61A VAL* 3.0 35.7 + - + +
63A PRO* 3.5 29.4 - - + -
66A LEU* 3.6 11.4 - - + +
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Residues in contact with GLU 57 (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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53A VAL* 2.9 36.0 + - + +
54A LYS* 3.2 28.1 + - + +
56A ALA* 1.3 75.6 - - + +
58A LEU* 1.3 64.1 + - + +
60A ASN* 3.2 22.4 + - - +
61A VAL 5.0 0.4 - - - -
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Residues in contact with LEU 58 (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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21A ARG* 4.7 5.4 + - - -
25A TRP* 3.6 29.4 - - + -
26A LEU* 3.8 11.4 - - + -
29A GLN* 3.6 44.4 - - + +
30A MSE 3.6 30.5 - - + -
54A LYS* 3.0 32.1 + - + +
55A VAL 3.6 6.5 - - - +
57A GLU* 1.3 79.2 - - + +
59A LEU* 1.3 59.0 + - - +
60A ASN* 3.3 8.1 + - - +
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Residues in contact with LEU 59 (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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12A ILE* 5.1 2.0 - - + +
15A VAL* 3.9 31.2 - - + -
16A LEU* 3.8 36.8 - - + +
19A LYS* 3.4 32.4 - - + +
21A ARG* 3.9 22.7 - - + +
25A TRP* 4.0 11.7 - - + -
26A LEU* 5.1 1.6 - - + -
55A VAL* 2.9 37.7 + - + +
56A ALA 4.1 2.5 - - - +
58A LEU* 1.3 77.0 - - + +
60A ASN* 1.3 71.5 + - - +
61A VAL* 3.3 5.5 + - + +
66A LEU* 4.6 5.2 - - + -
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Residues in contact with ASN 60 (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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19A LYS* 4.3 12.7 + - - +
21A ARG* 5.6 4.6 - - - +
56A ALA 2.9 6.4 + - - -
57A GLU* 3.2 14.8 + - - +
58A LEU 4.4 6.0 + - - +
59A LEU* 1.3 81.5 + - - +
61A VAL* 1.3 61.0 + - - +
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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