Contacts of the strand formed by residues 30 - 36 (chain E) in PDB entry 5BRR
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 GLN 30 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24E ILE* 3.5 24.4 - - + +
27E HIS 2.9 13.2 + - - +
28E PRO 4.6 1.7 - - - -
29E TRP* 1.3 84.9 + - - +
31E ALA* 1.3 95.7 + - - +
43E GLY* 4.3 4.5 - - - -
44E GLY 3.6 5.6 + - - +
67E ILE 4.6 0.2 - - - +
68E LEU* 4.3 5.9 - - - +
69E GLY 4.3 8.1 + - - -
139E SER* 2.6 55.9 + - - +
140E GLY* 3.7 6.3 - - - +
141E TYR* 3.9 7.6 + - - +
155E LEU* 4.0 12.3 - - + -
194E ASP 5.3 0.2 + - - -
197E GLY* 3.8 7.4 - - - -
198E PRO* 3.4 17.7 - - + +
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Residues in contact with ALA 31 (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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29E TRP 4.3 0.9 - - - +
30E GLN* 1.3 95.4 + - - +
32E ALA* 1.3 60.2 + - - +
43E GLY* 3.5 3.1 - - - -
44E GLY* 2.9 37.6 + - - +
45E ILE* 4.4 1.1 - - - +
52E ILE* 4.6 4.0 - - + -
66E VAL* 4.0 16.4 - - + -
67E ILE 3.6 6.3 - - - +
68E LEU* 3.6 23.6 - - + -
141E TYR* 4.2 4.6 - - - -
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Residues in contact with ALA 32 (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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31E ALA* 1.3 75.5 - - - +
33E ILE* 1.3 62.3 + - - +
34E PHE* 3.8 24.5 - - + -
40E PHE* 4.2 9.0 - - + -
42E CYS 3.9 3.4 - - - -
65E THR 3.8 0.3 - - - +
66E VAL* 3.3 5.9 - - - +
67E ILE* 2.9 41.2 + - + +
70E ARG* 5.4 4.3 - - - -
73E ARG* 5.6 2.0 - - + -
141E TYR* 3.9 22.1 + - + +
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Residues in contact with ILE 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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32E ALA* 1.3 79.8 - - - +
34E PHE* 1.3 67.6 + - - +
40E PHE* 3.8 3.5 - - - -
41E LEU* 2.9 45.1 + - + +
42E CYS* 2.7 26.8 + - + +
43E GLY 3.5 10.5 - - - +
44E GLY* 4.5 0.7 - - - +
52E ILE* 3.9 29.2 - - + -
54E SER* 3.3 30.1 - - - +
59E PHE* 4.5 12.3 - - + -
64E LEU* 4.4 11.0 - - + -
65E THR 3.5 8.1 - - - +
66E VAL* 4.6 7.2 - - + -
106E LEU* 4.5 5.6 - - + -
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Residues in contact with PHE 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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32E ALA* 3.8 16.4 - - + -
33E ILE* 1.3 77.0 - - - +
35E ALA* 1.3 60.4 + - - +
38E GLU* 3.6 19.3 - - + -
39E ARG* 3.6 19.3 - - - -
40E PHE* 3.6 20.6 - + + -
41E LEU* 4.6 1.1 - - - -
63E HIS 3.6 0.6 - - - +
64E LEU* 3.2 11.8 - - - +
65E THR* 2.7 49.7 + - - +
67E ILE* 3.7 32.5 - - + -
70E ARG* 4.0 7.4 - - - -
73E ARG* 3.4 37.7 - - + -
74E VAL* 5.4 1.8 - - + -
304E GOL 4.4 15.7 - - - -
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Residues in contact with ALA 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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34E PHE* 1.3 75.2 - - - +
36E LYS* 1.3 63.8 + - - +
38E GLU* 3.7 3.1 - - - -
39E ARG* 2.8 43.3 + - + +
41E LEU* 4.4 12.1 - - + +
60E PHE* 3.9 33.2 - - + +
63E HIS 3.6 3.8 - - - -
64E LEU* 4.3 9.4 - - + -
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Residues in contact with LYS 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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35E ALA* 1.3 76.1 - - - +
37E HIS* 1.3 88.0 + - + +
38E GLU* 3.7 16.4 - - + +
39E ARG* 5.4 0.4 - - - +
60E PHE* 5.4 4.3 - - - +
62E HIS* 2.5 30.9 + - - -
63E HIS* 2.8 55.7 + - + +
64E LEU 4.8 0.2 + - - -
65E THR* 4.2 14.0 - - + +
84E GLU* 5.3 5.1 - - - +
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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