Contacts of the helix formed by residues 26 - 36 (chain D) in PDB entry 5A63
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 LEU 26 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203B TRP* 3.4 19.3 - - + +
204B ASN* 3.2 9.2 - - - +
207B VAL* 3.3 38.1 - - + -
208B VAL* 4.1 9.9 - - + -
211B ILE* 5.8 0.2 - - + -
21D GLY* 4.1 7.8 + - - +
22D GLY* 3.6 12.8 + - - -
24D ALA* 3.1 42.9 - - + +
25D PHE* 1.3 80.5 - - - +
27D PRO* 1.3 61.6 - - - +
28D PHE 3.1 1.8 - - - -
29D LEU* 3.0 47.6 + - + +
30D TRP* 3.1 9.4 + - - +
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Residues in contact with PRO 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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200B LEU* 5.0 6.3 - - + -
204B ASN* 3.4 14.6 - - - +
22D GLY 5.3 0.9 - - - +
25D PHE* 3.3 9.9 - - - -
26D LEU* 1.3 90.0 - - - +
28D PHE* 1.3 55.7 - - - +
30D TRP* 3.2 13.2 + - + +
31D LEU 2.9 24.1 + - - -
64D PHE* 3.3 31.8 - - + -
67D TRP* 3.5 45.8 - - + +
68D VAL* 6.1 0.4 - - + -
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Residues in contact with PHE 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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201B LEU* 5.9 6.5 - - + -
204B ASN* 2.7 34.6 + - + +
205B PHE* 5.0 7.2 - + - -
208B VAL* 3.5 31.6 - - + -
221B LEU* 4.2 14.6 - - + -
225B TYR* 4.2 11.4 - + - -
27D PRO* 1.3 72.5 - - - +
29D LEU* 1.3 55.5 + - - +
31D LEU* 3.2 21.6 + - + +
32D VAL* 2.9 43.7 + - + +
64D PHE* 5.2 2.0 - - - -
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Residues in contact with LEU 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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208B VAL* 3.4 16.9 - - + +
211B ILE* 3.6 38.4 - - + -
17D LYS 4.9 0.2 - - - +
18D TYR* 3.3 45.7 - - + +
21D GLY* 3.5 23.3 - - - -
22D GLY 3.6 1.3 - - - +
26D LEU* 3.0 30.3 + - + +
28D PHE* 1.3 78.3 - - - +
30D TRP* 1.3 58.3 + - - +
32D VAL* 3.2 7.2 + - + +
33D ASN* 2.9 28.6 + - - +
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Residues in contact with TRP 30 (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 TYR 4.2 1.3 - - - -
19D TYR* 3.2 32.9 + + - -
22D GLY* 3.0 35.2 - - - -
23D PHE* 3.4 38.1 - + - -
26D LEU 3.1 3.7 + - - +
27D PRO* 3.2 16.6 + - + +
29D LEU* 1.3 80.7 - - - +
31D LEU* 1.3 57.2 + - - +
33D ASN* 3.2 6.1 + - - +
34D ILE* 2.9 34.6 + - - +
59D ARG 5.7 0.4 - - - -
60D SER* 3.4 37.0 + - - +
63D GLY* 3.3 31.0 - - - -
64D PHE* 3.4 20.4 - - + -
66D PHE* 6.1 0.2 - + - -
67D TRP* 4.0 15.3 - + - -
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Residues in contact with LEU 31 (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 PRO 2.9 12.4 + - - +
28D PHE* 3.3 28.9 - - + +
30D TRP* 1.3 76.1 - - - +
32D VAL* 1.3 59.9 + - + +
34D ILE* 3.2 14.6 + - + +
35D PHE* 2.9 62.4 + - + -
64D PHE* 3.3 44.4 - - + -
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Residues in contact with VAL 32 (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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208B VAL* 5.2 2.7 - - + -
218B PRO* 3.6 27.5 - - + +
221B LEU* 3.5 27.6 - - + -
18D TYR* 3.6 21.8 - - + -
28D PHE* 2.9 38.5 + - + +
29D LEU* 3.2 11.2 + - + +
31D LEU* 1.3 77.1 - - + +
33D ASN* 1.3 58.8 + - - +
35D PHE* 3.2 8.5 + - - +
36D TRP* 2.9 32.9 + - + +
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Residues in contact with ASN 33 (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 CYS* 3.2 35.7 + - - +
18D TYR* 3.2 35.3 - - + +
19D TYR* 4.6 2.9 - - - +
29D LEU 2.9 12.6 + - - +
30D TRP* 3.2 11.2 - - - +
32D VAL* 1.3 77.4 - - - +
34D ILE* 1.3 63.6 + - - +
36D TRP* 3.2 1.6 + - - -
37D PHE* 3.0 41.5 + - - +
56D TYR 4.8 0.8 + - - -
57D VAL* 4.8 5.9 - - - +
60D SER* 3.3 27.1 + - - -
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Residues in contact with ILE 34 (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 TRP 2.9 29.5 + - - +
31D LEU* 3.3 15.7 - - + +
33D ASN* 1.3 76.6 - - - +
35D PHE* 1.3 64.8 + - + +
37D PHE 3.7 0.3 - - - -
38D PHE* 2.8 43.3 + - + +
57D VAL* 3.7 26.1 - - + +
60D SER* 3.6 9.6 - - - +
61D ALA* 3.2 47.1 - - + +
64D PHE* 4.3 8.1 - - + -
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Residues in contact with PHE 35 (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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218B PRO* 6.2 1.3 - - + -
31D LEU* 2.9 50.4 + - + +
32D VAL* 3.2 11.9 + - - +
34D ILE* 1.3 86.0 - - + +
36D TRP* 1.3 56.9 + - + +
37D PHE 3.3 3.9 + - - -
38D PHE* 3.5 14.0 + - - +
39D ARG* 4.0 14.0 + - - +
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Residues in contact with TRP 36 (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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216B LYS* 4.4 11.7 - - + -
217B GLY* 3.0 38.1 - - - -
218B PRO* 3.4 42.0 - - + +
3D LEU* 3.5 49.7 - - + +
14D LEU* 3.6 36.3 - - + -
18D TYR* 4.1 12.8 - + - -
32D VAL 2.9 16.5 + - - +
33D ASN 3.2 2.0 + - - +
35D PHE* 1.3 75.3 - - + +
37D PHE* 1.3 90.0 + + - +
39D ARG* 5.2 1.8 - - - -
40D GLU* 4.3 2.7 - - - +
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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