Contacts of the strand formed by residues 20 - 26 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C VAL* 3.2 5.7 - - - +
19C GLU* 1.3 98.0 - - + +
21C VAL* 1.3 63.9 + - - +
36C THR* 3.5 24.5 - - + -
37C ILE 3.5 4.0 - - - -
38C PRO* 3.7 17.3 - - + -
39C ALA 4.1 0.9 - - - +
84C ARG* 4.5 0.7 - - - +
86C ALA* 3.7 28.5 - - + -
87C LYS 3.2 3.6 + - - -
88C THR* 3.2 16.7 - - + +
89C LEU 2.9 24.3 + - - -
200D ASP* 3.4 15.4 + - - -
203D LEU* 3.2 25.7 - - + +
204D THR* 2.8 43.3 + - - -
207D ILE* 3.8 18.0 - - + +
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Residues in contact with VAL 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C VAL* 4.3 13.2 - - + -
20C TYR* 1.3 77.0 - - - +
22C ASP* 1.3 68.0 + - - +
23C VAL* 3.7 7.5 + - + -
36C THR* 3.5 4.0 - - - -
37C ILE* 2.8 52.7 + - + +
39C ALA* 4.9 3.4 - - - -
42C PHE* 3.7 43.7 - - + -
89C LEU* 3.3 16.8 - - + +
91C ILE* 3.9 22.2 - - + -
93C PHE* 5.6 0.9 - - + -
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Residues in contact with ASP 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL* 1.3 72.4 - - - +
23C VAL* 1.3 62.3 + - - +
24C ARG* 2.8 33.4 + - - +
34C HIS* 2.8 33.4 + - - +
35C PHE 3.4 4.4 - - - +
36C THR* 2.9 21.0 + - - +
84C ARG* 3.0 17.9 + - - +
88C THR* 3.8 3.8 - - + +
89C LEU 2.8 8.9 + - - +
90C ASN* 3.2 20.4 - - - +
91C ILE* 3.0 29.3 + - - +
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Residues in contact with VAL 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL* 4.4 10.8 - - + +
22C ASP* 1.3 71.6 - - - +
24C ARG* 1.3 61.5 + - - +
25C PHE* 4.9 1.6 - - + -
33C GLN 3.9 0.2 - - - +
34C HIS* 3.1 5.7 - - - -
35C PHE* 2.8 67.6 + - + +
37C ILE* 4.5 11.4 - - + -
51C LEU* 3.8 22.2 - - + -
71C LEU* 4.0 10.3 - - + -
91C ILE 3.8 2.9 - - - -
93C PHE* 3.7 36.6 - - + -
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Residues in contact with ARG 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ASP* 2.8 34.2 + - - +
23C VAL* 1.3 78.5 - - - +
25C PHE* 1.3 60.0 + - - +
32C MET* 4.3 13.5 - - + +
33C GLN 3.2 6.7 - - - +
34C HIS* 3.9 7.8 + - + -
81C ASP* 3.8 1.8 + - - -
84C ARG* 5.3 1.4 - - - +
90C ASN* 3.7 27.8 + - - +
91C ILE 2.9 13.4 + - - +
92C ASN* 3.2 19.4 - - - +
93C PHE* 2.6 35.0 + - - +
244C LEU* 4.9 5.9 - - - +
247C TYR* 3.0 63.9 + - - +
189D VAL* 3.7 18.9 - - - +
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Residues in contact with PHE 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C VAL 4.9 1.3 - - - -
24C ARG* 1.3 78.7 - - - +
26C CYS* 1.3 67.2 + - - +
32C MET* 3.4 12.7 - - - +
33C GLN* 2.7 50.9 + - + +
35C PHE* 4.8 2.9 - + - -
53C PHE* 3.5 36.6 - + - -
58C ILE* 4.0 7.2 - - + -
61C PHE* 3.9 9.6 - + - -
71C LEU* 3.5 43.5 - - + -
93C PHE 4.0 14.1 - - - +
95C VAL* 4.2 14.4 - - + -
107C ASP* 5.8 0.2 - - - +
109C ARG* 5.2 1.6 - - - +
187D PHE* 3.7 29.6 - + - -
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Residues in contact with CYS 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C PHE* 1.3 80.3 - - - +
27C ASP* 1.3 78.1 + - - +
30C GLY* 3.9 7.4 - - - -
31C ILE 4.0 1.1 - - - -
32C MET* 3.6 14.1 - - + -
61C PHE* 3.3 18.0 - - - -
95C VAL* 5.1 0.2 - - - +
107C ASP* 4.7 3.0 + - - +
108C PRO* 3.5 15.2 - - + +
109C ARG* 4.5 9.9 - - + +
243C GLN* 3.6 25.1 - - - -
375C ASN* 3.6 17.0 - - - -
377C TYR* 3.9 16.2 - - + -
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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