Contacts of the strand formed by residues 20 - 26 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18E VAL* 3.3 4.8 - - - +
19E GLU* 1.3 94.0 - - + +
21E VAL* 1.3 63.2 + - - +
36E THR* 3.5 25.1 - - + -
37E ILE 3.4 4.5 - - - -
38E PRO* 3.7 15.5 - - + -
39E ALA 4.1 1.1 - - - +
84E ARG* 4.4 0.7 - - - +
86E ALA* 3.6 33.7 - - + -
87E LYS 3.2 3.2 + - - -
88E THR* 3.2 16.7 - - + +
89E LEU 2.9 24.6 + - - -
200F ASP* 3.9 13.9 - - - -
203F LEU* 3.3 24.0 - - + +
204F THR* 2.6 43.6 + - - -
207F ILE* 3.8 18.3 - - + +
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Residues in contact with VAL 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E VAL* 4.2 13.0 - - + -
20E TYR* 1.3 77.5 - - - +
22E ASP* 1.3 68.6 + - - +
23E VAL* 3.7 8.1 + - + -
36E THR* 3.5 4.3 - - - -
37E ILE* 2.8 51.0 + - + +
38E PRO 4.6 0.2 - - - -
39E ALA* 5.0 3.4 - - - -
42E PHE* 3.7 42.8 - - + -
88E THR* 4.5 0.2 - - - -
89E LEU* 3.3 17.0 - - + +
91E ILE* 3.8 23.1 - - + -
93E PHE* 5.5 0.9 - - + -
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Residues in contact with ASP 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E VAL* 1.3 73.4 - - - +
23E VAL* 1.3 62.5 + - - +
24E ARG* 2.8 32.6 + - - +
34E HIS* 2.8 34.1 + - - +
35E PHE 3.4 3.8 - - - +
36E THR* 2.8 21.5 + - - +
84E ARG* 2.9 18.3 + - - +
88E THR* 3.9 3.2 - - + +
89E LEU 2.8 8.9 + - - +
90E ASN* 3.2 20.0 - - - +
91E ILE* 3.0 30.1 + - - +
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Residues in contact with VAL 23 (chain E).
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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21E VAL* 4.3 11.2 - - + +
22E ASP* 1.3 71.8 - - - +
24E ARG* 1.3 61.2 + - - +
25E PHE* 4.9 1.6 - - + -
34E HIS* 3.1 6.2 - - - -
35E PHE* 2.8 69.5 + - + +
37E ILE* 4.4 11.0 - - + -
51E LEU* 3.8 22.9 - - + -
71E LEU* 4.0 10.1 - - + -
91E ILE 3.9 2.9 - - - -
93E PHE* 3.5 35.9 - - + -
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Residues in contact with ARG 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ASP* 2.8 33.2 + - - +
23E VAL* 1.3 77.4 - - - +
25E PHE* 1.3 61.4 + - - +
32E MET* 4.3 11.7 - - + +
33E GLN 3.2 6.7 - - - +
34E HIS* 4.0 7.6 + - + -
81E ASP* 3.8 1.8 + - - -
84E ARG* 5.3 2.0 - - - +
90E ASN* 3.5 29.2 + - - +
91E ILE 2.8 15.2 + - - +
92E ASN* 3.3 18.3 - - - +
93E PHE* 2.6 35.6 + - - +
244E LEU* 5.0 5.1 - - - +
247E TYR* 3.1 62.8 + - - +
189F VAL* 3.8 19.8 - - - +
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Residues in contact with PHE 25 (chain E).
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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23E VAL 4.9 2.5 - - - -
24E ARG* 1.3 79.1 - - - +
26E CYS* 1.3 67.6 + - - +
32E MET* 3.4 12.6 - - - -
33E GLN* 2.6 56.3 + - + +
35E PHE* 4.8 2.5 - + - -
53E PHE* 3.5 35.4 - + - -
58E ILE* 4.0 7.2 - - + -
61E PHE* 3.9 8.7 - + - -
71E LEU* 3.6 39.9 - - + -
93E PHE 3.8 17.0 - - - +
95E VAL* 4.1 15.0 - - + -
107E ASP* 5.8 0.4 - - - +
109E ARG* 5.2 1.3 - - - +
187F PHE* 3.7 32.1 - + - -
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Residues in contact with CYS 26 (chain E).
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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25E PHE* 1.3 80.8 - - - +
27E ASP* 1.3 75.4 + - - +
30E GLY* 4.0 6.1 - - - -
31E ILE 4.0 1.3 - - - -
32E MET* 3.5 14.3 - - + +
61E PHE* 3.4 11.3 - - - -
95E VAL* 5.2 0.2 - - - +
107E ASP* 4.6 3.0 + - - +
108E PRO* 3.4 22.1 - - + +
109E ARG* 4.5 8.6 - - + +
243E GLN* 3.6 25.1 - - - -
375E ASN* 3.4 18.4 - - - -
377E TYR* 3.8 18.2 - - + -
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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