Contacts of the helix formed by residues 17 - 29 (chain D) in PDB entry 4B2B
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 THR 17 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLY 3.9 0.9 + - - +
16D LYS* 1.3 76.3 - - - +
18D VAL* 1.3 59.3 - - - +
19D ASP* 3.5 7.4 + - - +
20D GLN* 3.0 37.3 + - - +
21D ALA* 2.8 28.3 + - - +
60D THR 4.9 5.2 - - - +
61D ASN* 3.2 15.5 - - + +
62D VAL* 4.1 15.9 - - + +
63D VAL* 4.9 0.7 - - - -
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Residues in contact with VAL 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D THR* 1.3 72.3 - - - +
19D ASP* 1.3 61.2 + - - +
21D ALA* 3.2 6.6 + - - +
22D ARG* 2.8 56.3 + - - +
36D PHE* 3.8 23.7 - - + -
56D TYR* 3.5 47.8 - - + -
61D ASN* 2.9 24.2 + - + +
63D VAL* 5.0 2.0 - - + +
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Residues in contact with ASP 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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17D THR* 3.2 7.7 + - - +
18D VAL* 1.3 79.8 - - - +
20D GLN* 1.3 64.6 + - + +
22D ARG* 3.0 27.4 + - - +
23D GLU* 3.2 30.7 + - - +
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Residues in contact with GLN 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D GLY 4.4 2.3 - - - +
16D LYS* 3.4 24.8 + - + +
17D THR* 3.0 42.4 + - - +
19D ASP* 1.3 78.8 - - + +
21D ALA* 1.3 61.5 + - - +
23D GLU* 3.3 10.2 + - - +
24D TYR* 3.0 22.0 + - - +
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Residues in contact with ALA 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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13D VAL* 3.8 26.2 - - + -
16D LYS* 4.0 11.6 - - + +
17D THR 2.8 20.8 + - - +
18D VAL* 3.6 1.8 - - - +
20D GLN* 1.3 69.3 - - - +
22D ARG* 1.3 66.8 + - - +
24D TYR* 3.2 2.3 + - - +
25D PHE* 3.0 31.2 + - + -
36D PHE* 3.6 22.2 - - + -
63D VAL* 4.4 4.5 - - + -
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Residues in contact with ARG 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D VAL* 2.8 37.2 + - - +
19D ASP* 3.0 32.3 + - - +
20D GLN 3.3 0.2 - - - -
21D ALA* 1.3 77.8 - - - +
23D GLU* 1.3 63.0 + - + +
25D PHE* 4.0 2.2 - - - +
26D THR* 3.0 35.7 + - - +
36D PHE* 3.6 31.9 - - + +
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Residues in contact with GLU 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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19D ASP* 3.2 16.5 + - - +
20D GLN* 3.6 11.2 - - - +
21D ALA 3.2 0.2 - - - -
22D ARG* 1.3 80.4 - - + +
24D TYR* 1.3 64.3 + - - +
26D THR* 3.3 5.8 + - - +
27D LEU* 3.0 27.0 + - - +
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Residues in contact with TYR 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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10D PHE* 4.9 2.2 - + - -
12D GLU* 2.3 46.7 + - + +
13D VAL* 3.8 25.8 - - + -
16D LYS* 4.0 25.1 - - - +
20D GLN 3.0 14.3 + - - +
21D ALA* 3.2 7.6 + - - +
23D GLU* 1.3 77.8 - - - +
25D PHE* 1.3 65.5 + + - +
27D LEU* 4.8 1.3 - - - -
28D HIS* 2.9 62.9 + + - +
29D TYR* 3.5 27.8 + + - -
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Residues in contact with PHE 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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10D PHE* 3.7 42.2 - + + -
13D VAL* 3.8 33.9 - - + -
21D ALA* 3.0 29.7 + - + +
22D ARG* 4.2 3.6 - - - +
24D TYR* 1.3 81.2 - + - +
26D THR* 1.3 58.3 + - - +
29D TYR* 2.8 56.8 + + + +
30D PRO* 3.9 0.3 - - - +
32D TYR* 5.2 0.7 - + - -
34D VAL* 3.7 35.2 - - + -
36D PHE* 4.5 0.7 - + - -
52D VAL* 4.1 9.9 - - + -
54D VAL* 3.8 26.7 - - + -
67D PRO* 4.5 1.8 - - + -
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Residues in contact with THR 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 ARG* 3.0 26.9 + - - +
23D GLU* 3.6 6.3 - - - +
25D PHE* 1.3 79.0 - - - +
27D LEU* 1.3 62.6 + - - +
30D PRO* 3.6 23.2 - - + +
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Residues in contact with LEU 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 GLU 3.0 17.8 + - - +
24D TYR* 3.9 2.7 - - - +
26D THR* 1.3 80.9 - - - +
28D HIS* 1.3 88.8 + - + +
30D PRO* 3.8 6.2 - - - +
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Residues in contact with HIS 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 TYR* 2.9 49.8 + + + +
27D LEU* 1.3 103.1 - - + +
29D TYR* 1.3 88.4 + - + +
30D PRO* 3.4 5.4 - - - +
31D GLN* 4.2 2.4 + - - +
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Residues in contact with TYR 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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8D LYS* 3.6 28.2 + - - -
10D PHE* 3.9 22.8 - + - -
12D GLU* 3.9 7.8 + - - -
24D TYR* 3.5 34.0 + + - -
25D PHE* 2.8 28.6 + + + +
28D HIS* 1.3 98.6 - - + +
30D PRO* 1.4 58.2 - - - +
31D GLN* 3.0 31.4 + - - -
32D TYR* 3.1 31.3 + + + +
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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