Contacts of the strand formed by residues 20 - 26 (chain D) in PDB entry 3ZXR
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 TYR 20 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D VAL* 3.2 6.9 - - - +
19D GLU* 1.3 93.8 - - + +
21D VAL* 1.3 64.6 + - - +
36D THR* 3.4 25.8 - - + -
37D ILE 3.5 1.8 - - - -
38D PRO* 3.7 17.5 - - + -
39D ALA 4.1 0.9 - - - +
84D ARG* 4.4 0.7 - - - +
86D ALA* 3.6 32.5 - - + -
87D LYS 3.2 4.0 + - - -
88D THR* 3.3 14.6 - - + +
89D LEU 2.9 23.4 + - - -
200E ASP* 4.1 15.0 - - - -
203E LEU* 3.3 25.0 - - + +
204E THR* 2.8 42.4 + - - -
207E ILE* 3.8 18.2 - - + +
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Residues in contact with VAL 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 ALA* 5.5 0.4 - - + -
18D VAL* 4.2 12.3 - - + -
20D TYR* 1.3 77.0 - - - +
22D ASP* 1.3 68.5 + - - +
23D VAL* 3.7 8.2 + - + -
36D THR* 3.5 4.1 - - - -
37D ILE* 2.8 50.7 + - + +
38D PRO 4.6 0.2 - - - -
39D ALA* 4.9 3.6 - - - -
42D PHE* 3.8 41.3 - - + -
89D LEU* 3.3 17.7 - - + +
91D ILE* 3.8 22.7 - - + -
93D PHE* 5.6 0.9 - - + -
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Residues in contact with ASP 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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21D VAL* 1.3 72.8 - - - +
23D VAL* 1.3 61.0 - - - +
24D ARG* 2.9 32.4 + - - +
34D HIS* 2.8 34.4 + - - +
35D PHE 3.5 3.8 - - - +
36D THR* 2.9 13.1 + - - +
84D ARG* 2.9 27.4 + - - +
88D THR* 3.9 3.4 - - + +
89D LEU 2.9 8.1 + - - -
90D ASN* 3.2 20.8 - - - +
91D ILE* 3.0 28.9 + - - +
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Residues in contact with VAL 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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21D VAL* 4.4 10.5 - - + +
22D ASP* 1.3 70.6 - - - +
24D ARG* 1.3 60.5 + - - +
25D PHE* 4.8 1.5 - - + -
33D GLN 4.4 0.2 - - - -
34D HIS* 3.1 5.9 - - - -
35D PHE* 2.8 70.0 + - + +
37D ILE* 4.5 10.5 - - + -
51D LEU* 3.7 23.6 - - + -
71D LEU* 3.9 13.7 - - + -
91D ILE 3.9 3.6 - - - -
93D PHE* 3.7 30.7 - - + -
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Residues in contact with ARG 24 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D ASP* 2.9 32.7 + - - +
23D VAL* 1.3 79.6 - - - +
25D PHE* 1.3 60.1 + - - +
32D MET* 4.3 12.0 - - + +
33D GLN 3.1 6.5 - - - +
34D HIS* 3.9 7.8 + - + -
81D ASP* 3.7 1.2 + - - -
84D ARG* 5.3 1.8 - - - +
90D ASN* 3.6 28.7 + - - +
91D ILE 2.9 15.8 + - - +
92D ASN* 3.3 18.5 - - - +
93D PHE* 2.7 35.0 + - - +
244D LEU* 5.0 4.9 - - - +
247D TYR* 3.1 63.9 + - - +
189E VAL* 3.7 19.6 - - - +
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Residues in contact with PHE 25 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D VAL 4.8 1.8 - - - -
24D ARG* 1.3 79.6 - - - +
26D CYS* 1.3 67.8 + - - +
32D MET* 3.3 13.4 - - - +
33D GLN* 2.6 60.9 + - + +
34D HIS 5.0 0.2 - - - -
35D PHE* 4.8 2.7 - + - -
53D PHE* 3.5 37.2 - + - -
58D ILE* 4.0 7.6 - - + -
61D PHE* 3.9 7.9 - + - -
71D LEU* 3.5 42.0 - - + -
93D PHE 3.9 13.9 - - - +
95D VAL* 4.2 15.3 - - + -
107D ASP* 5.8 0.4 - - - +
109D ARG* 5.3 1.8 - - - +
187E PHE* 3.7 23.6 - + - -
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Residues in contact with CYS 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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25D PHE* 1.3 80.3 - - - +
27D ASP* 1.3 75.7 + - - +
30D GLY* 4.0 5.8 - - - -
31D ILE 4.0 0.7 - - - -
32D MET* 3.5 13.4 - - + +
61D PHE* 3.4 17.8 - - - -
95D VAL* 5.1 0.2 - - - +
107D ASP* 4.6 2.4 + - - +
108D PRO* 3.4 16.8 - - + +
109D ARG* 4.5 9.5 - - + +
243D GLN* 3.6 25.6 - - - -
375D ASN* 3.6 17.3 - - - -
377D TYR* 3.7 18.6 - - + -
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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