Contacts of the helix formed by residues 19 - 31 (chain B) 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 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B LEU 4.3 0.2 + - - -
16B GLY 3.8 6.4 + - - -
17B ALA 3.3 4.8 + - - -
18B ALA* 1.3 79.6 - - - +
20B GLN* 1.3 70.0 + - - -
21B ASP* 3.3 3.6 - - - -
22B LYS 3.7 0.6 + - - -
23B LEU* 3.2 24.9 + - - +
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Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLY* 5.2 4.6 + - - -
19B GLY* 1.3 72.0 - - - -
21B ASP* 1.3 69.4 + - - +
23B LEU* 3.4 21.6 + - - +
24B LEU* 2.9 33.7 + - + +
50B LYS 4.6 5.1 + - - +
51B LEU* 3.8 25.7 - - + +
76C GLN* 6.2 0.2 - - - +
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Residues in contact with ASP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLY* 3.3 1.0 - - - -
20B GLN* 1.3 79.0 - - - +
22B LYS* 1.3 58.8 + - - +
24B LEU* 3.0 7.4 + - - +
25B TYR* 2.9 25.6 + - - +
75C ARG* 3.9 42.3 - - + +
76C GLN* 2.9 39.0 + - + -
80C VAL 5.6 0.2 - - - +
81C ASP* 4.7 10.7 - - - +
82C SER* 5.1 6.4 + - - -
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Residues in contact with LYS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ALA* 3.4 38.3 + - + +
19B GLY 3.7 1.9 + - - +
20B GLN 3.4 0.2 - - - -
21B ASP* 1.3 79.7 - - - +
23B LEU* 1.3 57.2 + - - +
25B TYR* 3.1 27.1 - - + +
26B LEU* 2.8 32.4 + - + +
106B GLU* 4.6 7.6 + - + +
108B LEU* 3.9 29.6 - - + +
75C ARG 4.7 0.6 + - - -
79C GLY* 3.6 27.1 + - - -
81C ASP* 3.4 26.6 + - - +
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU* 3.4 50.5 - - + +
16B GLY* 5.2 1.8 - - - +
18B ALA* 4.8 4.0 - - + -
19B GLY 3.2 16.2 + - - +
20B GLN* 3.8 27.8 - - - +
21B ASP 3.3 0.4 - - - -
22B LYS* 1.3 75.1 - - - +
24B LEU* 1.3 53.6 + - - +
26B LEU* 3.1 4.8 + - + +
27B LYS* 2.7 33.4 + - - +
47B VAL* 3.4 18.6 - - + +
50B LYS* 4.0 28.3 - - + +
51B LEU* 3.8 22.4 - - + -
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLN* 2.9 24.7 + - + +
21B ASP 3.2 7.2 - - - +
23B LEU* 1.3 76.3 - - - +
25B TYR* 1.3 59.0 - - - +
27B LYS* 3.3 15.7 + - + +
28B HIS* 2.8 47.4 + - + +
51B LEU* 4.3 21.5 - - + -
53B GLN* 4.8 5.4 - - - +
76C GLN* 3.4 48.0 - - + +
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Residues in contact with TYR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ASP 2.9 12.0 + - - +
22B LYS* 3.1 31.9 - - + +
24B LEU* 1.3 74.3 - - - +
26B LEU* 1.3 63.2 + - + +
28B HIS* 3.3 2.2 + - - +
29B LYS* 2.7 70.6 + - + +
106B GLU* 3.4 22.0 + - - -
54C GLU* 2.9 25.8 + - - -
58C ARG* 3.7 5.8 + - - -
75C ARG 4.2 2.0 - - - +
76C GLN 3.1 11.9 + - - +
77C TRP 3.7 15.9 - - - -
78C ALA 3.5 16.4 - - - -
79C GLY* 3.2 28.9 - - - -
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU* 4.2 17.3 - - + -
22B LYS* 2.8 24.4 + - + +
23B LEU* 3.1 9.4 + - + +
25B TYR* 1.3 81.7 - - + +
27B LYS* 1.3 68.2 + - - +
29B LYS* 4.4 3.8 - - + -
30B LEU* 2.7 46.5 + - + +
43B LEU* 5.6 3.4 - - + -
47B VAL* 3.9 16.6 - - + -
103B LEU* 5.4 2.0 - - + -
106B GLU* 3.8 34.3 - - + +
108B LEU* 3.6 30.7 - - + -
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU 2.7 20.5 + - - +
24B LEU* 3.3 10.2 + - + +
26B LEU* 1.3 75.0 - - - +
28B HIS* 1.3 82.8 + - + +
31B LYS* 3.4 8.8 - - - +
44B HIS* 3.4 27.0 + - + -
47B VAL* 3.6 15.3 - - + +
48B LEU* 3.9 23.3 - - + -
51B LEU* 4.1 12.8 - - + -
53B GLN* 2.8 29.8 + - - +
56B GLU* 4.1 14.0 + - - -
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Residues in contact with HIS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU* 2.8 39.2 + - + +
25B TYR* 3.8 3.1 - - - +
27B LYS* 1.3 101.3 - - + +
29B LYS* 1.3 60.1 + - - +
31B LYS* 4.0 10.3 - - - +
32B THR* 5.0 5.7 + - - +
9C PRO* 5.3 8.4 - - + +
50C LYS* 5.4 4.0 + - - -
76C GLN* 2.8 22.7 + - - +
77C TRP* 3.3 58.9 + + + +
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Residues in contact with LYS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B TYR* 2.7 58.8 + - + +
26B LEU* 3.9 4.9 - - + +
28B HIS* 1.3 75.9 - - - +
30B LEU* 1.3 70.1 + - + +
31B LYS 3.2 3.0 + - - -
32B THR* 3.7 3.1 + - - +
34B ARG* 2.4 53.7 + - - +
106B GLU* 2.8 29.8 + - - +
54C GLU* 3.8 14.7 + - - +
58C ARG* 5.5 0.4 - - - +
77C TRP 6.0 0.2 - - - +
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 2.7 49.3 + - + +
29B LYS* 1.3 80.1 - - + +
31B LYS* 1.3 62.7 + - - +
32B THR 3.1 8.5 + - - +
40B GLN* 3.8 48.3 + - + +
41B ASP* 4.6 5.2 - - - +
43B LEU* 3.7 40.8 - - + +
44B HIS* 3.8 28.8 - - + +
47B VAL* 4.1 1.8 - - + -
102B LEU* 5.2 4.5 - - + -
106B GLU* 5.5 4.9 - - + +
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Residues in contact with LYS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LYS 3.4 18.2 + - - +
28B HIS* 4.0 8.1 - - - +
29B LYS 3.2 0.2 - - - -
30B LEU* 1.3 78.4 - - - +
32B THR* 1.3 66.2 + - + +
33B PRO* 4.3 3.3 - - - +
41B ASP* 5.0 6.6 - - - +
44B HIS* 3.6 29.7 + - + +
56B GLU* 4.2 15.7 + - - +
60B SER* 6.0 0.2 + - - -
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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