Contacts of the strand formed by residues 19 - 25 (chain B) in PDB entry 3BRQ
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 THR 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A TYR* 2.5 32.5 + - + +
17B THR* 4.5 5.9 + - - +
18B GLN* 1.3 77.4 - - - +
20B LEU* 1.3 64.9 + - - +
50B ARG* 5.2 1.1 - - - -
51B GLN* 3.2 18.0 - - - +
53B LEU* 3.9 17.0 - - + -
75B ARG 4.5 3.3 + - - -
76B CYS* 3.7 28.8 - - - +
77B ASP* 2.7 39.2 + - - +
78B ALA 3.7 4.3 + - - -
268B LEU* 4.9 1.2 - - - +
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Residues in contact with LEU 20 (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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18B GLN 4.3 0.2 - - - -
19B THR* 1.3 74.0 - - - +
21B GLY* 1.3 62.3 + - - +
22B LEU* 4.5 3.4 - - + -
45B ALA* 4.2 13.9 - - + -
50B ARG* 4.7 8.8 - - + +
51B GLN 2.7 12.9 + - - +
52B LEU* 3.5 14.8 - - + +
53B LEU 2.9 26.6 + - - +
78B ALA* 3.7 16.4 - - + +
261B ILE* 3.8 26.5 - - + -
264B LEU* 3.6 41.1 - - + -
265B ILE* 3.7 32.3 - - + -
268B LEU* 5.1 3.4 - - + -
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Residues in contact with GLY 21 (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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20B LEU* 1.3 71.2 - - - +
22B LEU* 1.3 62.8 + - - +
53B LEU 3.4 5.8 - - - -
71B LEU* 3.7 17.5 - - - -
76B CYS* 3.8 13.6 - - - -
78B ALA 2.8 16.4 + - - -
79B ILE* 3.3 5.6 - - - +
80B MSE 2.7 32.1 + - - +
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Residues in contact with LEU 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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20B LEU* 4.3 5.8 - - + +
21B GLY* 1.3 85.3 - - - +
23B VAL* 1.3 58.1 - - - +
24B VAL* 6.0 0.2 - - + -
37B LEU* 5.4 2.2 - - + -
38B LEU* 3.9 26.5 - - + -
41B ALA* 3.9 13.7 - - + -
52B LEU* 3.5 34.3 - - + -
53B LEU 2.7 11.2 + - - +
54B LEU* 3.3 16.7 - - + +
55B ALA 2.8 31.9 + - - -
71B LEU* 3.6 3.0 - - - +
80B MSE 3.5 36.1 - - + -
261B ILE* 4.2 12.8 - - + -
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Residues in contact with VAL 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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22B LEU* 1.3 75.7 - - - +
24B VAL* 1.3 65.2 + - - +
55B ALA* 3.6 4.3 - - + +
57B GLY* 3.8 12.8 - - - -
64B GLU* 4.0 6.5 - - + +
67B ALA* 3.7 23.8 - - + -
68B ILE* 3.8 29.6 - - + +
71B LEU* 3.8 18.8 - - + -
79B ILE* 4.4 4.9 - - + -
80B MSE 3.0 9.2 + - - +
81B ILE* 3.3 26.7 - - + -
82B TYR 2.8 28.4 + - - +
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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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22B LEU* 4.2 0.4 - - + -
23B VAL* 1.3 81.1 - - - +
25B THR* 1.3 64.0 + - - +
26B ASN 3.8 0.7 + - - -
30B HIS* 3.4 29.2 - - + +
34B PHE* 3.8 33.8 - - + -
37B LEU* 4.8 3.8 - - + -
54B LEU* 3.8 18.5 - - + +
55B ALA 3.5 6.5 + - - +
56B ASP* 3.8 4.5 - - - +
57B GLY* 2.8 24.2 + - - -
80B MSE 4.2 18.8 - - + -
82B TYR* 3.8 19.3 - - + +
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Residues in contact with THR 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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23B VAL* 5.4 0.2 - - - +
24B VAL* 1.3 78.0 - - - +
26B ASN* 1.3 58.2 + - - +
27B THR* 3.0 19.4 + - + -
30B HIS* 2.8 31.7 + - - -
34B PHE* 4.8 2.1 - - - -
57B GLY* 4.3 1.3 - - - -
58B LYS 3.0 27.8 - - - +
59B HIS* 4.0 1.3 - - - -
64B GLU* 2.4 36.9 + - + +
82B TYR 3.7 6.7 + - - -
84B ARG* 3.4 12.2 + - + -
85B PHE* 3.7 24.0 - - + -
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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