Contacts of the helix formed by residues 33 - 46 (chain C) in PDB entry 3BID
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C TYR* 3.9 5.4 - - - -
31C TYR* 4.3 2.3 - - - +
32C THR* 1.3 87.3 + - - +
34C LYS* 1.3 66.4 + - - +
35C GLN* 2.9 13.8 + - - +
36C ASN* 3.0 37.5 + - - +
37C CYS* 3.3 10.2 + - - +
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Residues in contact with LYS 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 4.5 16.8 - - + -
13C TYR* 3.3 41.9 - - + -
33C SER* 1.3 74.1 - - - +
35C GLN* 1.3 62.1 + - - +
37C CYS* 3.4 3.4 + - - +
38C GLN* 3.2 34.3 + - - +
55D GLU* 3.6 32.3 + - - +
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Residues in contact with GLN 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C SER* 2.9 11.8 - - - +
34C LYS* 1.3 80.0 - - - +
36C ASN* 1.3 67.3 + - - +
38C GLN* 3.3 16.5 + - - +
39C HIS* 3.2 22.5 + - + +
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Residues in contact with ASN 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C TYR* 3.9 22.7 - - + -
32C THR* 3.1 31.7 + - + +
33C SER* 3.0 23.1 + - - +
35C GLN* 1.3 81.3 - - - +
37C CYS* 1.3 61.1 + - - +
39C HIS* 3.4 7.8 + - - +
40C ALA* 3.3 21.3 + - - +
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Residues in contact with CYS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 4.1 14.4 - - + -
13C TYR* 4.4 7.6 - - + -
14C ARG* 3.5 42.0 - - - -
15C TRP* 3.9 14.8 - - - -
31C TYR* 3.9 21.4 - - + +
33C SER 3.3 8.0 + - - +
34C LYS* 3.6 9.2 - - - +
35C GLN 3.2 0.4 - - - -
36C ASN* 1.3 77.8 - - - +
38C GLN* 1.3 63.6 + - - +
40C ALA* 3.3 4.9 + - - +
41C VAL* 3.2 21.5 + - - +
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Residues in contact with GLN 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 4.1 22.6 - - + +
34C LYS* 3.2 26.6 + - - +
35C GLN* 3.7 15.7 + - - +
37C CYS* 1.3 76.8 - - - +
39C HIS* 1.3 65.2 + - - +
41C VAL* 3.4 4.6 + - + +
42C ASP* 3.0 39.2 + - - +
53D VAL* 5.2 9.5 - - + +
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Residues in contact with HIS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLN* 3.2 14.9 + - + +
36C ASN* 3.7 11.9 - - - +
37C CYS 3.2 0.2 - - - -
38C GLN* 1.3 74.4 - - - +
40C ALA* 1.3 67.3 + - - +
42C ASP* 3.3 10.7 + - + +
43C LEU* 3.1 52.3 + - + +
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C TRP* 4.6 5.8 - - - +
31C TYR* 2.9 41.3 - - + +
36C ASN 3.3 5.9 + - - +
37C CYS 3.5 8.1 - - - +
38C GLN 3.3 0.4 - - - -
39C HIS* 1.3 79.2 - - - +
41C VAL* 1.3 61.1 + - - +
43C LEU* 3.2 12.6 + - - +
44C LEU* 3.0 27.3 + - - +
25D ILE* 4.4 9.2 - - - +
26D ALA* 5.2 2.9 - - + -
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C PHE* 3.5 40.6 - - + -
5C ILE* 4.6 10.5 - - + -
15C TRP* 3.6 37.5 - - + -
37C CYS 3.2 16.0 + - - +
38C GLN* 3.7 8.1 - - + +
39C HIS 3.3 0.2 - - - -
40C ALA* 1.3 77.4 - - - +
42C ASP* 1.3 63.5 + - - +
44C LEU* 3.3 8.9 + - - +
45C LYS* 3.1 30.4 + - + +
53D VAL* 4.3 11.2 - - + -
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Residues in contact with ASP 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C GLN* 3.0 32.3 + - - +
39C HIS* 3.3 14.5 + - + +
41C VAL* 1.3 75.6 - - - +
43C LEU* 1.3 63.1 + - + +
45C LYS* 3.2 24.6 + - - +
46C SER* 3.1 23.6 + - - -
53D VAL* 5.2 5.0 - - - +
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C HIS* 3.1 49.3 + - + +
40C ALA* 3.2 8.0 + - - +
42C ASP* 1.3 75.5 - - + +
44C LEU* 1.3 64.8 + - - +
46C SER* 2.8 27.8 + - - +
47C THR* 3.5 8.8 + - - -
1D MSE 4.4 11.2 - - - +
17D LEU* 5.3 2.2 - - + +
25D ILE* 3.8 40.2 - - + -
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Residues in contact with LEU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C PHE* 4.7 10.3 - - + -
15C TRP* 3.2 46.7 - - + +
40C ALA 3.0 16.5 + - - +
41C VAL* 3.3 11.0 + - - +
43C LEU* 1.3 77.6 - - - +
45C LYS* 1.3 57.5 + - - +
47C THR* 3.1 28.5 + - - +
3D PHE* 4.4 18.3 - - + -
15D TRP* 4.2 21.1 - - + -
17D LEU* 4.4 14.3 - - + +
25D ILE* 6.0 0.4 - - + -
26D ALA* 4.6 11.0 - - + -
44D LEU* 4.3 26.0 - - + +
47D THR* 5.4 0.2 - - - -
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Residues in contact with LYS 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C PHE* 4.2 5.8 - - + -
41C VAL* 3.1 29.5 + - + +
42C ASP* 3.2 31.5 + - - +
44C LEU* 1.3 72.4 - - - +
46C SER* 1.3 58.7 + - - +
47C THR 3.0 6.4 - - - +
47D THR* 3.2 43.1 - - + +
48D THR* 3.7 20.3 - - - +
49D ALA* 4.0 20.5 + - + +
50D ALA 4.8 0.2 - - - -
51D THR* 2.7 32.7 + - - +
53D VAL* 3.8 15.1 - - + +
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Residues in contact with SER 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ASP 3.1 14.3 + - - -
43C LEU* 2.8 25.4 + - - +
44C LEU 3.2 0.6 - - - -
45C LYS* 1.3 75.2 - - - +
47C THR* 1.3 62.9 + - - +
48C THR* 3.8 2.9 + - - +
1D MSE 4.0 13.0 - - - +
49D ALA* 5.6 5.8 - - - -
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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