Contacts of the helix formed by residues 39 - 51 (chain C) in PDB entry 4BSX
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 GLY 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C GLN* 1.3 75.0 - - - +
40C GLN* 1.3 54.1 + - - +
41C ASP 3.2 3.7 - - - +
42C LEU* 3.1 11.4 + - - +
43C LEU* 2.8 34.8 + - - +
98C ARG* 4.7 8.3 - - - +
99C LEU* 3.6 11.5 - - - +
102C LEU* 3.7 7.2 - - - -
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Residues in contact with GLN 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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30C LEU* 3.9 33.3 + - + +
32C THR 3.7 7.5 + - - -
33C PRO* 3.6 11.9 - - - +
34C ARG* 3.1 44.6 + - - +
37C CYS* 3.0 45.2 + - + +
38C GLN 3.4 0.4 - - - -
39C GLY* 1.3 77.6 - - - +
41C ASP* 1.3 62.8 + - - +
43C LEU* 3.5 3.0 + - - +
44C HIS* 2.8 30.0 + - - +
102C LEU* 3.5 17.8 - - + +
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Residues in contact with ASP 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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30C LEU 4.6 8.5 - - - +
31C LYS* 5.0 5.5 - - - +
33C PRO* 5.6 8.6 - - - +
39C GLY* 3.2 1.7 - - - +
40C GLN* 1.3 83.1 + - - +
42C LEU* 1.3 63.5 + - - +
44C HIS* 3.2 11.7 + - - +
45C ALA* 3.2 17.8 + - - +
60C SER* 5.4 1.0 - - - -
64C LEU* 3.8 35.2 - - + +
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Residues in contact with LEU 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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8C LEU* 5.5 0.4 - - + -
39C GLY* 3.1 14.1 + - - +
41C ASP* 1.3 76.3 - - - +
43C LEU* 1.3 64.1 + - - +
45C ALA* 3.0 15.2 + - - +
46C MSE 3.0 24.8 + - - +
61C LEU* 4.2 12.8 - - + -
64C LEU* 3.9 9.8 - - + +
67C ASP* 5.2 3.4 - - - +
69C VAL* 4.0 25.8 - - + -
70C ALA* 4.0 21.5 - - + +
73C VAL* 4.0 24.9 - - + -
95C ALA* 4.6 7.9 - - + -
99C LEU* 4.2 22.7 - - + -
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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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15C LEU* 4.0 24.0 - - + -
26C LEU* 5.6 4.3 - - + -
30C LEU* 3.6 22.2 - - + -
39C GLY 2.8 16.9 + - - +
40C GLN 3.8 4.5 - - - +
42C LEU* 1.3 78.2 - - - +
44C HIS* 1.3 62.4 + - - +
46C MSE 4.4 12.1 - - + -
47C VAL* 2.9 31.1 - - + +
99C LEU* 3.8 21.2 - - + +
102C LEU* 3.7 33.2 - - + -
103C LEU* 4.3 25.4 - - + -
106C GLU* 6.2 2.0 - - + -
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Residues in contact with HIS 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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27C LYS* 3.5 36.2 + - + -
30C LEU* 3.8 18.3 - - + +
31C LYS* 3.6 40.8 + - + +
40C GLN 2.8 19.1 + - - +
41C ASP* 3.4 12.8 - - - +
42C LEU 3.2 0.2 - - - -
43C LEU* 1.3 76.4 - - - +
45C ALA* 1.3 63.6 + - - +
47C VAL* 3.3 4.8 - - - +
48C LEU* 3.1 54.1 + - + +
56C GLU* 4.4 5.2 + - - -
60C SER* 3.9 14.0 + - - -
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Residues in contact with ALA 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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41C ASP 3.2 8.7 + - - +
42C LEU* 3.0 10.4 + - + +
44C HIS* 1.3 81.0 - - - +
46C MSE 1.3 56.8 + - + +
48C LEU* 3.3 14.7 + - - +
49C LEU* 3.0 32.5 + - - +
57C ALA* 3.6 3.2 - - - +
60C SER* 4.1 13.2 - - - -
61C LEU* 3.7 36.6 - - + -
64C LEU* 5.0 1.1 - - + -
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Residues in contact with MSE 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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8C LEU* 3.8 20.2 - - + -
11C ALA* 4.0 20.0 - - + -
12C PHE* 3.4 42.1 - - + +
15C LEU* 4.1 9.9 - - + -
42C LEU* 3.0 29.6 + - + +
43C LEU* 3.8 12.1 - - + +
45C ALA* 1.3 72.8 - - - +
47C VAL* 1.3 61.2 + - - +
49C LEU* 3.1 6.0 + - - +
50C LYS* 2.9 31.2 + - - +
73C VAL* 4.4 13.7 - - + -
99C LEU* 3.5 37.9 - - + -
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Residues in contact with VAL 47 (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 LEU* 4.0 26.9 - - + +
23C LEU* 3.4 32.8 - - + +
26C LEU* 3.9 18.6 - - + -
27C LYS* 3.6 21.3 - - + +
30C LEU* 4.2 7.9 - - + -
43C LEU* 2.9 22.5 - - + +
44C HIS* 3.4 7.0 - - - +
45C ALA 3.3 0.2 - - - -
46C MSE 1.3 75.8 + - - +
48C LEU* 1.3 62.4 + - - +
50C LYS* 3.3 5.2 - - - +
51C LEU* 3.1 25.4 - - + -
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Residues in contact with LEU 48 (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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27C LYS* 4.0 23.8 - - + -
44C HIS* 3.1 38.5 + - + +
45C ALA* 3.4 8.5 - - - +
46C MSE 3.3 0.2 - - - -
47C VAL* 1.3 75.7 + - + +
49C LEU* 1.3 59.8 + - - +
51C LEU* 3.1 9.6 + - + +
53C GLN* 2.8 58.7 + - + +
56C GLU* 3.8 33.9 - - + +
57C ALA* 3.8 10.3 - - + +
60C SER* 3.7 16.4 - - - +
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Residues in contact with LEU 49 (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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12C PHE* 4.1 16.8 - - + -
45C ALA 3.0 19.8 + - - +
46C MSE 3.1 8.3 + - - +
48C LEU* 1.3 76.7 - - - +
50C LYS* 1.3 58.9 + - - +
52C GLY* 3.0 18.2 + - - -
53C GLN 4.7 2.0 - - - +
54C GLU* 4.3 21.7 - - + +
57C ALA* 3.4 20.0 - - + -
61C LEU* 4.5 3.6 - - + -
73C VAL* 4.2 13.7 - - + -
77C TRP* 3.8 36.8 - - + +
78C ALA* 3.9 21.5 - - + -
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Residues in contact with LYS 50 (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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28B HIS 5.4 4.8 + - - -
32B THR* 4.1 24.9 + - - +
12C PHE* 3.6 32.4 + - + +
13C ASP* 5.0 7.6 + - - +
15C LEU* 4.1 12.3 - - + -
16C GLY* 3.4 39.0 - - - +
20C GLN* 4.7 6.1 + - - +
23C LEU* 4.0 15.8 - - + +
46C MSE 2.9 14.8 + - - +
47C VAL* 3.8 5.4 - - - +
48C LEU 3.3 0.2 - - - -
49C LEU* 1.3 76.6 - - - +
51C LEU* 1.3 57.2 + - - +
52C GLY 3.2 2.0 + - - -
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Residues in contact with LEU 51 (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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20C GLN* 3.8 15.7 - - - +
23C LEU* 3.8 42.0 - - + +
24C LEU* 4.1 9.2 - - + +
27C LYS* 4.2 14.6 - - + -
47C VAL* 3.1 22.7 - - + -
48C LEU* 3.1 8.4 + - - +
50C LYS* 1.3 76.0 - - - +
52C GLY* 1.3 58.2 + - - +
53C GLN* 3.2 33.6 + - - +
131D HIS* 3.7 40.2 - - + +
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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