Contacts of the helix formed by residues 39 - 51 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D GLN* 1.3 73.4 - - - +
40D GLN* 1.3 52.6 + - - +
41D ASP* 3.1 4.4 - - - +
42D LEU* 3.0 14.1 + - - +
43D LEU* 2.8 34.5 + - - +
98D ARG* 4.7 10.5 - - - +
99D LEU* 3.7 6.6 - - - +
102D LEU* 3.8 7.2 - - - -
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Residues in contact with GLN 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 3.9 33.8 + - + +
32D THR 3.7 8.3 + - - -
33D PRO* 3.7 11.1 - - - +
34D ARG* 3.2 43.7 + - - +
37D CYS* 3.0 43.8 + - + +
38D GLN 3.3 0.4 - - - -
39D GLY* 1.3 76.3 - - - +
41D ASP* 1.3 60.9 + - - +
43D LEU* 3.7 2.8 - - - +
44D HIS* 2.8 30.9 + - - +
102D LEU* 3.5 18.1 - - + +
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Residues in contact with ASP 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU 4.6 8.0 - - - +
31D LYS* 5.1 5.4 - - - +
33D PRO* 5.6 9.2 - - - +
39D GLY* 3.1 1.6 - - - +
40D GLN* 1.3 83.9 + - - +
42D LEU* 1.3 62.0 + - - +
44D HIS* 3.3 11.3 + - - +
45D ALA* 3.3 17.3 + - - +
60D SER* 5.4 1.4 - - - -
64D LEU* 3.8 35.5 - - + +
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Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D GLY* 3.0 13.9 + - - +
41D ASP* 1.3 79.3 - - - +
43D LEU* 1.3 62.3 + - - +
45D ALA* 3.1 6.7 + - - +
46D MSE 3.0 28.9 + - - +
61D LEU* 4.2 13.5 - - + -
64D LEU* 3.9 9.3 - - + +
67D ASP* 5.2 2.9 - - - +
69D VAL* 4.0 25.4 - - + -
70D ALA* 4.1 27.1 - - + +
73D VAL* 4.1 19.3 - - + -
95D ALA* 4.6 8.3 - - + -
99D LEU* 4.1 23.6 - - + -
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU* 4.0 25.4 - - + -
26D LEU* 5.7 4.3 - - + -
30D LEU* 3.6 21.8 - - + -
39D GLY 2.8 15.0 + - - +
40D GLN* 3.7 6.1 - - - +
42D LEU* 1.3 78.6 - - - +
44D HIS* 1.3 61.2 + - - +
46D MSE 4.4 10.8 - - + -
47D VAL* 2.9 31.8 - - + +
99D LEU* 3.7 21.9 - - + +
102D LEU* 3.6 33.7 - - + -
103D LEU* 4.3 24.5 - - + -
106D GLU* 6.2 1.8 - - + -
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Residues in contact with HIS 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D LEU 5.6 0.2 - - - -
27D LYS* 3.4 35.8 + - + -
30D LEU* 3.9 19.4 - - + +
31D LYS* 3.6 40.4 + - + +
40D GLN 2.8 18.3 + - - +
41D ASP* 3.4 11.2 - - - +
43D LEU* 1.3 76.3 - - - +
45D ALA* 1.3 63.2 + - - +
47D VAL* 3.3 4.2 - - - +
48D LEU* 3.1 54.8 + - + +
56D GLU* 4.4 5.6 + - - -
60D SER* 3.9 15.4 + - - -
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Residues in contact with ALA 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ASP 3.3 8.3 + - - +
42D LEU* 3.1 10.0 + - + +
44D HIS* 1.3 81.8 - - - +
46D MSE 1.3 56.7 + - - +
48D LEU* 3.2 14.5 + - - +
49D LEU* 2.9 33.8 + - + +
57D ALA* 3.7 3.5 - - - +
60D SER* 4.2 13.9 - - - -
61D LEU* 3.6 36.3 - - + -
64D LEU* 5.0 0.9 - - + -
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Residues in contact with MSE 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 3.8 20.6 - - + -
11D ALA* 3.9 20.6 - - + -
12D PHE* 3.5 43.9 - - + +
15D LEU* 4.0 9.8 - - + +
42D LEU* 3.0 29.3 + - + +
43D LEU* 3.9 13.9 - - + +
44D HIS 3.4 0.2 - - - -
45D ALA* 1.3 73.4 - - - +
47D VAL* 1.3 60.1 + - - +
49D LEU* 3.3 6.2 + - - +
50D LYS* 2.9 30.0 + - - +
73D VAL* 4.4 13.7 - - + -
99D LEU* 3.5 37.9 - - + -
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU* 3.9 27.8 - - + +
23D LEU* 3.5 32.6 - - + +
26D LEU* 4.0 18.8 - - + -
27D LYS* 3.7 22.4 - - + +
30D LEU* 4.2 7.0 - - + -
43D LEU* 2.9 21.8 - - + +
44D HIS* 3.4 6.5 - - - +
46D MSE 1.3 76.9 + - - +
48D LEU* 1.3 62.6 + - - +
50D LYS* 3.2 6.0 - - - +
51D LEU* 3.0 25.9 - - + -
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Residues in contact with LEU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D LYS* 3.9 23.3 - - + -
44D HIS* 3.1 38.6 + - + +
45D ALA* 3.2 8.0 + - - +
47D VAL* 1.3 75.0 + - + +
49D LEU* 1.3 61.3 + - - +
51D LEU* 3.1 11.3 + - + +
53D GLN* 2.8 60.9 + - + +
56D GLU* 3.8 30.1 - - + +
57D ALA* 3.8 9.9 - - + -
60D SER* 3.8 16.8 - - - +
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Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PHE* 4.1 17.0 - - + -
45D ALA 2.9 18.8 + - - +
46D MSE 3.5 8.3 - - - +
48D LEU* 1.3 76.7 - - - +
50D LYS* 1.3 57.8 + - - +
52D GLY* 3.1 17.5 + - - -
53D GLN 4.8 2.0 - - - +
54D GLU* 4.2 22.6 - - + +
57D ALA* 3.3 21.5 - - + -
61D LEU* 4.5 3.1 - - + -
73D VAL* 4.1 13.9 - - + -
77D TRP* 3.9 37.9 - - + +
78D ALA* 4.0 21.8 - - + -
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Residues in contact with LYS 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PHE* 3.6 31.3 + - + +
13D ASP* 5.0 7.6 + - - +
15D LEU* 4.1 10.3 - - + -
16D GLY* 3.4 37.9 - - - +
20D GLN* 4.7 6.4 + - - +
23D LEU* 4.1 18.1 - - + +
46D MSE 2.9 15.4 + - - +
47D VAL* 3.2 6.0 - - - +
49D LEU* 1.3 74.7 - - - +
51D LEU* 1.3 58.3 + - - +
52D GLY 3.2 3.3 + - - -
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLN* 3.8 27.2 - - + +
23D LEU* 3.8 43.1 - - + +
24D LEU* 4.2 18.6 - - + +
27D LYS* 4.1 14.1 - - + -
47D VAL* 3.0 21.6 - - + -
48D LEU* 3.1 9.6 + - - +
50D LYS* 1.3 75.8 - - - +
52D GLY* 1.3 58.3 + - - +
53D GLN* 3.2 34.2 + - - +
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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