Contacts of the strand formed by residues 32 - 39 (chain E) in PDB entry 5BRZ
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 SER 32 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E PRO* 4.8 0.2 - - - +
30E HIS* 3.6 0.5 - - - +
31E ARG* 1.3 79.2 - - - +
33E VAL* 1.3 62.1 + - - +
34E SER* 4.4 0.9 + - - -
49E GLU* 3.0 26.3 + - - +
50E TYR 3.2 10.1 + - - -
51E PHE* 4.0 6.3 - - - -
93E ALA 4.2 0.4 - - - -
94E SER* 3.3 7.6 + - - -
95E SER* 2.9 49.5 + - - -
97E ASN 4.5 1.1 - - - -
98E MET* 3.6 19.2 - - - +
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Residues in contact with VAL 33 (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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24E CYS* 4.5 1.6 - - - +
26E PRO* 4.1 22.9 - - + -
31E ARG 4.0 0.6 + - - -
32E SER* 1.3 79.7 - - - +
34E SER* 1.3 63.3 + - - +
35E TRP* 3.7 15.2 - - + +
48E PHE 4.1 0.9 - - - +
49E GLU* 3.2 1.4 - - - -
50E TYR* 2.8 39.4 + - + +
69E GLN* 4.0 5.4 - - - +
73E SER 3.7 23.1 - - - +
75E SER* 3.7 27.1 - - - -
92E CYS* 3.7 24.5 - - - -
93E ALA 3.3 4.5 - - - +
94E SER* 5.1 0.4 - - - -
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Residues in contact with SER 34 (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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103D VAL* 5.8 0.3 - - - +
32E SER* 4.4 0.5 + - - -
33E VAL* 1.3 73.0 - - - +
35E TRP* 1.3 63.2 + - - +
36E TYR* 4.0 17.2 - - - -
46E PHE* 4.4 5.5 - - - -
48E PHE 3.5 5.8 - - - -
49E GLU* 3.0 37.2 + - - -
91E LEU 3.8 0.2 - - - +
92E CYS* 3.4 4.0 - - - -
93E ALA* 2.8 30.8 + - - -
102E GLN* 3.6 22.6 + - - -
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Residues in contact with TRP 35 (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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7E GLN* 4.2 17.0 - - - -
22E LEU* 3.7 35.4 - - + -
23E SER 4.1 2.7 - - - -
24E CYS* 3.6 29.4 - - + -
33E VAL* 3.7 13.6 - - + +
34E SER* 1.3 78.5 - - - +
36E TYR* 1.3 64.8 + - - +
46E PHE* 3.9 3.3 - - - -
47E LEU* 3.0 38.6 + - + +
48E PHE* 2.9 35.1 + + + +
50E TYR* 5.0 2.9 - + - -
75E SER* 3.2 34.5 + - - -
76E GLU 4.4 0.4 + - - -
77E MET* 3.4 36.9 - - + +
90E TYR* 4.8 3.4 - - + -
91E LEU 3.4 20.0 - - - -
92E CYS* 4.4 2.5 - - + -
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Residues in contact with TYR 36 (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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103D VAL* 3.8 10.3 + - - +
105D PHE* 3.6 23.6 - + - -
202D SO4 4.0 14.6 - - - -
34E SER* 4.0 24.0 + - - -
35E TRP* 1.3 74.2 - - - +
37E GLN* 1.3 58.6 + - - +
44E LEU* 4.0 21.5 - - + -
45E GLN 3.2 20.2 - - - +
46E PHE* 3.7 27.3 - + - -
47E LEU* 3.4 10.6 - - - +
90E TYR* 3.3 7.1 - - - +
91E LEU* 2.8 37.3 + - + +
93E ALA* 4.5 1.1 - - + -
102E GLN* 3.1 24.7 + - - -
104E PHE* 3.5 32.1 - + - -
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Residues in contact with GLN 37 (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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36E TYR* 1.3 76.0 - - - +
38E GLN* 1.3 61.7 + - - +
39E THR* 3.8 21.6 + - + +
43E GLY 3.4 2.4 - - - +
44E LEU* 4.7 0.2 - - - -
45E GLN* 2.9 35.5 + - - +
47E LEU* 3.4 15.8 - - + +
61E PHE* 3.3 33.5 - - + -
65E PHE* 4.7 1.8 - - - -
85E GLY 4.5 1.8 + - - -
86E ASP* 4.5 15.2 + - - +
88E ALA* 3.6 18.1 - - + +
89E LEU 3.6 4.0 - - - -
90E TYR* 3.6 26.7 + - + -
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Residues in contact with GLN 38 (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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39D GLN* 2.8 40.9 + - - -
42D GLY* 6.0 1.6 - - - -
45D LEU* 4.6 0.8 - - - +
90D LEU* 5.3 2.6 - - - +
36E TYR 4.2 0.2 - - - -
37E GLN* 1.3 72.6 - - - +
39E THR* 1.3 67.1 + - - +
40E PRO* 4.7 0.5 - - - +
43E GLY* 3.4 14.4 - - - +
44E LEU* 4.0 22.2 + - + +
88E ALA* 3.2 4.9 - - - +
89E LEU* 2.8 55.5 + - + +
91E LEU* 3.8 10.9 - - + +
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Residues in contact with THR 39 (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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37E GLN* 3.8 23.1 + - - +
38E GLN* 1.3 80.0 - - - +
40E PRO* 1.3 76.9 - - + +
41E GLY 2.7 23.7 + - - -
42E GLN* 3.5 8.7 - - - +
43E GLY* 3.0 33.8 + - - -
45E GLN* 5.5 0.3 - - - +
85E GLY 4.4 7.4 - - - +
87E SER 3.8 9.0 - - - +
88E ALA* 3.7 18.4 - - + -
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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