Contacts of the strand formed by residues 21 - 27 (chain B) in PDB entry 3ZUT
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 21 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B MET* 3.0 20.2 - - + +
16B HIS* 5.1 1.3 - - - -
17B ASP* 3.1 13.7 + - + +
18B SER* 3.4 15.8 - - - +
20B ARG* 1.3 97.4 - - + +
22B GLU* 1.3 59.1 + - - +
38B MET* 3.5 31.0 - - + -
39B ARG 3.2 5.4 - - - +
40B ASP* 3.7 39.9 + - + -
41B LYS* 3.7 3.1 - - - -
42B GLN* 6.4 0.2 - - - -
47B VAL* 4.1 21.6 - - + +
81B LYS* 5.2 4.9 - - - +
82B GLU* 2.6 29.7 + - - -
84B ILE* 4.3 16.6 - - + -
93B VAL* 4.0 17.8 - - + +
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ARG* 3.0 25.0 + - - +
243A TYR* 3.6 12.4 - - + +
245A HIS* 3.8 20.2 + - + +
15B MET* 4.2 1.3 - - - -
21B TYR* 1.3 73.4 - - - +
23B LEU* 1.3 72.9 + - - +
24B VAL* 3.2 2.9 + - + +
38B MET* 3.3 2.3 - - - -
39B ARG* 2.3 79.0 + - - +
41B LYS* 3.8 13.6 - - + +
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ARG* 3.1 17.8 + - - -
243A TYR* 3.9 47.4 - - + +
15B MET* 3.6 37.9 - - + +
22B GLU* 1.3 77.2 - - - +
24B VAL* 1.3 62.1 + - - +
25B LYS* 4.0 9.0 - - - +
26B ASP* 3.4 17.9 - - - +
36B ARG* 3.4 41.1 - - + +
37B LEU 3.7 4.0 - - - +
38B MET* 4.3 1.8 - - - -
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Residues in contact with VAL 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ALA 3.7 23.6 - - - +
111A ARG* 2.7 53.5 + - + +
243A TYR* 3.8 6.1 - - - -
22B GLU* 3.2 4.5 + - + +
23B LEU* 1.3 75.2 - - - +
25B LYS* 1.3 67.6 + - + +
37B LEU* 2.8 20.3 + - + +
38B MET 3.8 0.2 - - - -
39B ARG* 3.5 34.8 - - + +
46B LEU* 3.7 17.5 - - + -
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Residues in contact with LYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLY* 3.8 36.7 + - - +
212A VAL 4.0 15.0 - - - +
213A GLY 3.5 21.5 + - - +
214A ALA* 4.9 8.0 - - - +
243A TYR* 4.1 19.3 - - - +
23B LEU* 3.8 5.4 - - - +
24B VAL* 1.3 85.6 - - + +
26B ASP* 1.3 80.9 + - - +
27B ILE* 3.7 9.0 + - + +
37B LEU* 2.8 34.7 + - + +
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Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A TYR* 5.4 2.0 + - - -
12B LEU* 3.7 24.4 - - + +
23B LEU* 3.4 12.0 - - - +
25B LYS* 1.3 92.4 + - - +
27B ILE* 1.3 60.2 + - - +
28B GLY 4.4 0.2 + - - -
35B ALA 3.6 2.7 - - - -
36B ARG* 2.7 54.5 + - - +
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Residues in contact with ILE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A CYS 5.2 7.2 - - - +
110A GLY* 5.3 0.9 - - - -
12B LEU* 4.9 2.2 - - - +
25B LYS* 3.7 13.9 + - + +
26B ASP* 1.3 77.7 - - - +
28B GLY* 1.3 58.9 + - - +
29B SER 5.0 8.3 - - - +
30B GLY* 6.5 0.4 - - - -
32B PHE* 4.5 15.0 - - + -
33B GLY 3.3 10.4 - - - +
34B VAL* 3.4 2.8 - - - +
35B ALA* 2.8 47.8 + - + +
37B LEU* 3.8 43.7 - - + -
96B TYR* 4.5 13.5 - - + +
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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