Contacts of the helix formed by residues 17 - 29 (chain D) in PDB entry 4B8Z
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 17 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLY 3.7 4.0 + - - -
15D GLY 3.4 1.8 - - - -
16D SER* 1.3 80.3 - - - +
18D LEU* 1.4 59.8 + - - -
19D VAL 3.5 2.5 - - - -
20D GLY 3.8 1.1 - - - -
21D LYS* 2.9 30.1 + - - +
177D HIS 3.7 4.5 - - - -
320D ARG* 4.1 3.8 - - - -
900D NAP 2.9 35.4 + - - -
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Residues in contact with LEU 18 (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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17D GLY* 1.4 71.8 - - - +
19D VAL* 1.3 61.5 + - + +
22D ALA* 3.4 19.4 + - - +
173D VAL* 3.8 41.5 - - + +
174D PHE 3.8 2.2 - - - -
175D GLY* 3.5 29.2 - - - +
176D PRO 3.4 24.3 - - - +
177D HIS 3.4 13.0 + - - +
178D ASP* 3.8 23.1 - - + +
220D SER* 3.9 8.7 - - - -
900D NAP 2.8 36.1 + - - +
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Residues in contact with VAL 19 (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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18D LEU* 1.3 70.9 - - + +
20D GLY* 1.3 59.9 + - - +
22D ALA* 3.4 6.6 + - + +
23D ILE* 3.0 37.6 + - + +
69D LEU* 3.7 27.4 - - + -
112D CYS* 5.5 1.8 - - - -
170D PRO* 6.3 1.3 - - + -
173D VAL* 4.5 25.4 - - + -
220D SER* 5.2 2.2 - - - +
223D LEU* 5.4 9.0 - - + -
224D ALA 5.5 1.6 - - - +
227D PHE* 4.1 17.9 - - + -
900D NAP 2.9 44.2 + - + +
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Residues in contact with GLY 20 (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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14D GLY 3.9 3.2 + - - -
15D GLY* 3.2 32.8 - - - +
17D GLY 3.5 3.8 + - - -
18D LEU 3.4 0.6 - - - -
19D VAL* 1.3 77.5 - - - +
21D LYS* 1.4 55.9 + - - +
23D ILE* 3.4 2.9 + - - +
24D GLN* 2.9 26.3 + - - +
40D PHE* 3.8 8.2 - - - -
69D LEU* 3.8 15.3 - - - +
900D NAP 4.5 1.0 + - - -
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Residues in contact with LYS 21 (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 GLY 3.5 8.9 + - - +
16D SER* 4.2 10.8 - - - +
17D GLY 2.9 22.0 + - - +
18D LEU 4.5 0.9 - - - +
20D GLY* 1.4 69.4 - - - +
22D ALA* 1.3 54.8 + - - +
24D GLN* 3.4 8.7 - - + +
25D LYS* 2.8 35.5 + - - +
177D HIS* 3.5 46.4 - - + +
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Residues in contact with ALA 22 (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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18D LEU 3.4 14.5 + - - +
19D VAL* 3.4 11.4 + - + +
20D GLY 3.3 0.4 - - - -
21D LYS* 1.3 75.3 - - - +
23D ILE* 1.4 58.6 + - - +
25D LYS* 3.4 5.2 + - - +
26D VAL* 3.0 33.8 + - - +
176D PRO 5.6 0.6 + - - +
220D SER* 3.3 41.1 - - - +
221D LEU* 4.1 3.3 - - - +
224D ALA* 3.5 4.0 - - + -
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Residues in contact with ILE 23 (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 VAL* 4.9 2.2 - - + -
19D VAL* 3.0 25.4 + - + +
20D GLY 3.8 4.0 - - - +
22D ALA* 1.4 72.3 - - - +
24D GLN* 1.4 58.0 + - - +
26D VAL* 3.5 2.8 + - - +
27D VAL* 3.0 33.1 + - + +
40D PHE* 3.8 20.6 - - + -
67D ILE* 4.1 22.9 - - + -
69D LEU* 4.1 21.1 - - + -
224D ALA* 3.8 27.8 - - + +
227D PHE* 4.0 26.7 - - + -
228D ILE* 5.8 6.3 - - + +
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Residues in contact with GLN 24 (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 GLY 4.8 4.3 - - - +
20D GLY 2.9 15.7 + - - +
21D LYS* 3.4 13.7 - - + +
22D ALA 3.3 0.2 - - - -
23D ILE* 1.4 75.4 - - - +
25D LYS* 1.4 56.5 + - - +
27D VAL* 4.0 1.6 - - - +
28D ALA* 3.2 29.1 + - - +
40D PHE* 3.7 43.3 - - + -
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Residues in contact with LYS 25 (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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21D LYS 2.8 19.8 + - - +
22D ALA* 3.8 5.8 - - - +
24D GLN* 1.4 71.6 - - - +
26D VAL* 1.4 61.4 + - + +
28D ALA* 3.4 4.8 + - - -
29D ASP* 2.9 42.3 + - - +
177D HIS* 6.4 2.0 - - + -
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Residues in contact with VAL 26 (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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22D ALA 3.0 22.7 + - - +
23D ILE* 4.0 3.4 - - - +
25D LYS* 1.4 70.9 - - + +
27D VAL* 1.4 66.2 + - - +
29D ASP* 3.2 17.5 + - - +
30D GLY 3.5 4.0 + - - -
31D ALA* 3.4 26.2 - - + +
221D LEU* 3.8 21.5 - - + +
224D ALA* 3.8 19.1 - - + +
225D GLN* 3.8 31.2 - - + +
228D ILE* 5.7 4.0 - - + -
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Residues in contact with VAL 27 (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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23D ILE* 3.0 21.7 + - + +
24D GLN* 4.0 4.9 - - - +
26D VAL* 1.4 74.9 - - - +
28D ALA* 1.4 60.5 + - - +
30D GLY* 3.4 9.7 + - - -
31D ALA* 3.5 17.3 + - - -
32D GLY* 3.8 15.1 + - - +
38D TRP* 5.5 6.7 - - + -
40D PHE* 4.8 11.7 - - + -
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Residues in contact with ALA 28 (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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24D GLN 3.2 20.6 + - - +
25D LYS* 3.7 6.1 - - - +
26D VAL 3.3 0.2 - - - -
27D VAL* 1.4 71.0 - - - +
29D ASP* 1.4 61.8 + - - +
30D GLY* 3.2 8.8 + - - -
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Residues in contact with ASP 29 (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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25D LYS* 2.9 28.3 + - - +
26D VAL* 3.2 9.2 + - - +
28D ALA* 1.4 79.0 - - - +
30D GLY* 1.3 58.1 + - - +
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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