Contacts of the strand formed by residues 20 - 26 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A ASP* 3.5 15.2 + - + -
203A LEU* 3.4 23.6 - - + +
204A THR* 2.7 41.8 + - - -
207A ILE* 3.8 17.4 - - + +
18F VAL* 3.2 5.9 - - - +
19F GLU* 1.3 96.2 + - + +
21F VAL* 1.3 64.2 + - - +
36F THR* 3.5 25.1 - - + -
37F ILE 3.5 4.0 - - - -
38F PRO* 3.7 16.6 - - + -
39F ALA 4.1 1.1 - - - +
84F ARG* 4.4 0.7 - - - +
86F ALA* 3.6 33.0 - - + -
87F LYS 3.2 3.4 + - - -
88F THR* 3.2 16.8 - - + +
89F LEU 3.0 23.9 + - - -
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Residues in contact with VAL 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F VAL* 4.3 12.3 - - + -
20F TYR* 1.3 77.6 - - - +
22F ASP* 1.3 68.7 + - - +
23F VAL* 3.7 8.6 + - + -
36F THR* 3.4 3.5 - - - -
37F ILE* 2.8 51.7 + - + +
39F ALA* 4.9 3.8 - - - -
42F PHE* 3.7 42.8 - - + -
89F LEU* 3.3 15.9 - - + +
91F ILE* 3.8 23.8 - - + -
93F PHE* 5.6 0.7 - - + -
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Residues in contact with ASP 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F VAL* 1.3 72.7 - - - +
23F VAL* 1.3 62.8 + - - +
24F ARG* 2.8 33.3 + - - +
34F HIS* 2.7 35.3 + - - +
35F PHE 3.3 4.0 - - - +
36F THR* 2.9 21.1 + - - +
84F ARG* 3.0 18.4 + - - +
88F THR* 3.9 3.6 - - + +
89F LEU 2.9 8.3 + - - +
90F ASN* 3.3 19.5 - - - +
91F ILE* 3.0 27.4 + - - +
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Residues in contact with VAL 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F VAL* 4.3 11.2 - - + +
22F ASP* 1.3 70.1 - - - +
24F ARG* 1.3 61.1 + - - +
25F PHE* 4.8 1.6 - - + -
34F HIS* 3.1 22.9 - - - -
35F PHE* 2.8 49.9 + - + +
37F ILE* 4.5 11.4 - - + -
51F LEU* 3.7 22.9 - - + -
71F LEU* 4.0 10.8 - - + -
91F ILE 3.9 2.7 - - - -
93F PHE* 3.6 36.6 - - + -
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Residues in contact with ARG 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A VAL* 3.7 19.6 - - - +
22F ASP* 2.8 33.5 + - - +
23F VAL* 1.3 77.9 - - - +
25F PHE* 1.3 59.9 + - - +
32F MET* 4.3 12.4 - - + +
33F GLN 3.2 10.8 - - - +
34F HIS* 4.0 2.6 + - + -
81F ASP* 3.8 1.6 + - - -
84F ARG* 5.4 1.2 - - - +
90F ASN* 3.6 27.6 + - - +
91F ILE 2.8 16.3 + - - +
92F ASN* 3.3 19.3 - - - +
93F PHE* 2.6 35.4 + - - +
244F LEU* 4.9 5.3 - - - +
247F TYR* 3.0 63.4 + - - +
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Residues in contact with PHE 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A PHE* 3.7 31.4 - + - -
23F VAL 4.8 2.0 - - - -
24F ARG* 1.3 78.7 - - - +
26F CYS* 1.3 68.2 + - - +
32F MET* 3.4 12.3 - - - +
33F GLN* 2.7 50.5 + - + +
34F HIS 5.0 0.2 - - - -
35F PHE* 4.8 2.7 - + - -
53F PHE* 3.5 36.1 - + - -
58F ILE* 4.0 7.4 - - + -
61F PHE* 3.9 8.5 - + - -
71F LEU* 3.5 39.5 - - + -
93F PHE 3.9 17.5 - - - +
95F VAL* 4.1 15.5 - - + -
107F ASP* 5.9 0.2 - - - +
109F ARG* 5.3 1.1 - - - +
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Residues in contact with CYS 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F PHE* 1.3 78.9 - - - +
27F ASP* 1.3 78.3 + - - +
30F GLY* 4.0 6.5 - - - -
31F ILE 4.1 0.9 - - - -
32F MET* 3.5 15.7 - - + +
61F PHE* 3.4 10.6 - - - -
95F VAL* 5.2 0.2 - - - +
107F ASP* 4.6 2.6 + - - +
108F PRO* 3.4 21.9 - - + +
109F ARG* 4.5 10.1 - - + +
243F GLN* 3.5 26.2 - - - -
375F ASN* 3.7 16.6 - - - -
377F TYR* 3.8 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