Contacts of the helix formed by residues 33 - 45 (chain A) in PDB entry 4BIT
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 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ASN* 3.1 19.8 + - - -
32A PHE* 1.3 73.4 - - - +
34A LEU* 1.3 58.5 + - - +
35A ASP* 4.0 6.9 - - - +
36A THR* 2.8 36.2 + - - -
37A ILE* 2.8 33.1 + - - +
78A SER* 3.2 11.2 - - - -
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Residues in contact with LEU 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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33A SER* 1.3 71.5 - - - +
35A ASP* 1.3 62.1 + - - +
38A GLU* 3.1 27.8 + - - +
69A ILE 5.6 0.7 - - - +
70A LEU* 4.1 27.6 - - + +
74A THR* 3.6 15.3 - - + +
75A ARG* 3.4 45.5 - - + +
78A SER* 3.4 13.3 + - - +
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Residues in contact with ASP 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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33A SER* 4.0 7.6 - - - +
34A LEU* 1.3 81.6 - - - +
36A THR* 1.3 75.9 + - - +
38A GLU* 3.4 6.1 + - - +
39A LYS* 2.6 62.4 + - - +
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Residues in contact with THR 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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30A VAL* 3.6 18.6 - - + -
31A ASN* 3.3 27.7 + - + +
33A SER* 2.8 22.3 + - - -
35A ASP* 1.3 82.8 + - - +
37A ILE* 1.3 60.1 + - - +
39A LYS* 3.4 8.3 + - + +
40A GLU* 3.0 32.1 + - + +
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Residues in contact with ILE 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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21A PHE* 3.6 23.9 - - + -
22A TYR* 5.4 0.7 - - + -
25A LEU* 3.7 19.5 - - + -
32A PHE* 3.8 22.9 - - + -
33A SER 2.8 29.9 + - - +
34A LEU 4.5 0.7 - - - +
36A THR* 1.3 70.5 - - - +
38A GLU* 1.3 60.6 + - - +
40A GLU* 3.3 4.4 + - - +
41A LEU* 2.8 33.3 + - + +
74A THR* 4.5 13.0 - - + -
77A MET* 3.6 48.7 - - + +
78A SER* 3.9 3.8 - - - +
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Residues in contact with GLU 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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34A LEU 3.1 22.5 + - - +
35A ASP* 3.5 7.5 - - - +
37A ILE* 1.3 77.5 - - - +
39A LYS* 1.3 68.4 + - - +
41A LEU* 3.2 8.8 + - - +
42A ILE* 3.1 26.8 + - + +
59A LEU 5.8 2.9 - - - +
60A GLY 5.5 1.3 - - - +
61A ALA* 4.1 3.8 - - + +
67A THR* 2.8 25.4 + - + +
68A LYS* 2.6 54.2 + - - +
69A ILE* 3.5 10.6 + - + +
74A THR* 4.4 10.7 - - + +
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Residues in contact with LYS 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 ASP* 2.6 51.3 + - - +
36A THR* 3.7 9.0 - - + +
38A GLU* 1.3 82.1 - - + +
40A GLU* 1.3 68.8 + - - +
42A ILE* 3.0 26.3 + - + +
43A SER* 3.2 14.2 + - - -
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Residues in contact with GLU 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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21A PHE* 3.5 13.5 - - + -
25A LEU* 4.8 4.0 - - + -
28A ARG* 2.6 47.1 + - - +
30A VAL* 4.1 17.3 - - + -
36A THR* 3.0 23.2 + - + +
37A ILE* 4.0 3.6 - - - +
39A LYS* 1.3 77.7 - - + +
41A LEU* 1.3 60.2 + - - +
43A SER* 3.1 13.9 + - - -
44A PHE* 2.8 34.8 + - - +
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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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17A PHE* 3.9 28.7 - - + -
18A LEU* 4.4 7.9 - - + -
21A PHE* 3.3 27.3 - - + -
37A ILE* 2.8 21.9 + - + +
38A GLU* 3.4 8.5 - - - +
39A LYS 3.2 0.2 - - - -
40A GLU* 1.3 78.2 - - - +
42A ILE* 1.3 62.7 + - - +
44A PHE* 4.2 0.5 - - - +
45A CYS* 3.4 19.1 + - - +
56A CYS* 4.9 3.1 - - - -
59A LEU* 4.3 26.0 - - + +
61A ALA* 3.6 21.0 - - + +
73A VAL* 5.2 7.6 - - + -
74A THR* 4.7 13.5 - - - +
77A MET* 5.3 0.4 - - - -
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Residues in contact with ILE 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 GLU* 3.1 20.6 - - + +
39A LYS* 3.0 18.1 + - + +
41A LEU* 1.3 77.2 - - - +
43A SER* 1.3 61.1 - - - +
45A CYS* 3.3 17.3 + - - +
46A LEU* 3.8 10.8 + - + +
61A ALA* 3.7 22.3 - - - +
62A THR* 4.1 23.3 - - - +
63A LYS* 4.4 5.8 - - + +
67A THR* 3.7 25.8 - - + -
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Residues in contact with SER 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 LYS 3.2 9.8 + - - -
40A GLU* 3.1 30.4 + - - -
42A ILE* 1.3 75.3 - - - +
44A PHE* 1.3 55.8 + - - +
45A CYS 3.0 4.9 - - - -
46A LEU* 3.0 41.5 + - - +
47A ASP 4.6 0.5 + - - -
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Residues in contact with PHE 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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17A PHE* 3.9 15.3 - + + -
20A ARG* 3.3 49.1 - - + -
21A PHE* 3.3 46.0 - + + -
24A SER* 3.2 35.2 - - - -
28A ARG* 5.6 5.4 - - - +
40A GLU 2.8 20.3 + - - +
41A LEU 4.2 2.5 - - - +
43A SER* 1.3 77.7 + - - +
45A CYS* 1.3 59.0 + - - +
46A LEU 3.2 0.9 - - - -
47A ASP* 3.3 22.6 - - - +
48A THR* 4.1 4.0 + - - +
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Residues in contact with CYS 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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17A PHE* 4.2 2.2 - - + -
41A LEU 3.4 15.0 + - - +
42A ILE 3.4 9.0 - - - +
43A SER 3.0 1.0 - - - -
44A PHE* 1.3 78.8 - - - +
46A LEU* 1.3 61.2 + - - +
48A THR* 2.8 38.6 + - - +
53A ASN* 3.3 22.8 + - - -
56A CYS* 2.0 50.5 - - + -
61A ALA 4.3 2.7 - - - +
62A THR* 4.7 1.8 - - + -
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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