Contacts of the strand formed by residues 51 - 58 (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 GLN 51 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A LYS* 2.8 37.0 + - - +
66A GLN* 5.2 7.9 + - - +
67A ALA* 5.9 2.8 - - - -
70A TYR* 4.0 28.9 - - + +
17B THR* 3.8 29.2 + - + +
18B GLN 3.0 6.5 + - - -
19B THR* 3.2 16.6 - - - +
20B LEU* 2.7 34.5 + - - +
45B ALA* 4.9 0.7 - - - -
49B GLY 5.6 1.4 + - - -
50B ARG* 1.3 76.2 - - - +
52B LEU* 1.3 57.4 + - - +
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Residues in contact with LEU 52 (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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29A TYR* 5.0 3.1 - - + +
54A LEU* 4.6 5.8 - - + -
55A ALA* 3.9 16.3 - - - +
56A ASP* 4.1 19.9 + - + +
58A LYS* 5.0 2.9 + - - +
70A TYR* 5.0 1.2 - - - -
20B LEU* 3.5 14.1 - - + +
22B LEU* 3.5 36.6 - - + -
38B LEU* 4.3 11.0 - - + -
41B ALA* 4.3 8.5 - - + +
42B ALA* 3.7 30.7 - - + +
45B ALA* 4.2 22.2 - - + -
50B ARG 4.0 1.2 + - - +
51B GLN* 1.3 80.0 + - - +
53B LEU* 1.3 73.5 + - - +
54B LEU 4.4 0.4 - - - +
261B ILE* 5.8 0.2 - - + -
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 4.0 6.3 - - + -
54A LEU 3.5 8.1 - - - +
55A ALA* 4.5 2.0 - - + -
70A TYR* 4.0 16.6 - - + +
71A LEU* 3.8 28.7 - - + -
74A LEU* 3.4 24.0 - - + -
19B THR* 3.9 25.8 - - + +
20B LEU 2.9 8.1 + - - +
21B GLY* 3.4 1.2 - - - -
22B LEU* 2.7 27.5 + - - +
52B LEU* 1.3 82.5 - - - +
54B LEU* 1.3 60.3 + - - +
71B LEU* 4.1 12.9 - - + +
74B LEU* 4.4 16.4 - - + +
76B CYS* 3.9 13.5 - - - -
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Residues in contact with LEU 54 (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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38A LEU* 4.0 18.4 - - + -
52A LEU 4.0 0.2 - - - +
53A LEU* 3.4 6.4 - - - -
54A LEU* 2.9 51.1 + - + +
22B LEU* 3.3 33.4 - - + +
24B VAL* 3.8 28.5 - - + +
34B PHE* 3.9 22.9 - - + -
38B LEU* 4.0 24.7 - - + -
52B LEU* 5.1 0.9 - - + +
53B LEU* 1.3 73.5 - - - +
55B ALA* 1.3 66.1 + - - +
56B ASP* 4.1 1.2 + - - +
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Residues in contact with ALA 55 (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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51A GLN* 4.1 10.1 - - - +
52A LEU 3.7 4.3 - - - -
53A LEU* 4.1 5.6 - - + -
22B LEU 2.8 9.9 + - - +
23B VAL* 3.6 3.9 - - + +
24B VAL 3.5 17.3 + - - +
53B LEU 4.1 0.8 + - - -
54B LEU* 1.3 77.6 - - - +
56B ASP* 1.3 65.3 + - - +
57B GLY 3.1 3.8 + - - -
67B ALA* 4.4 12.8 - - + +
70B TYR* 4.4 9.0 - - + -
71B LEU* 3.7 33.0 - - + +
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Residues in contact with ASP 56 (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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38A LEU* 6.6 0.2 - - - -
42A ALA* 3.4 20.5 - - + +
45A ALA* 5.4 0.3 - - - +
46A GLU* 2.5 38.6 - - - +
51A GLN* 3.2 20.7 + - - +
52A LEU* 3.2 26.4 + - + +
24B VAL 4.0 5.3 - - - +
26B ASN* 3.5 10.6 - - - +
54B LEU* 4.1 2.3 + - - +
55B ALA* 1.3 71.0 - - - +
57B GLY* 1.3 61.2 + - - +
58B LYS* 2.8 29.1 + - + +
67B ALA* 3.7 9.3 - - - +
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Residues in contact with GLY 57 (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* 3.8 21.8 - - - -
24B VAL 2.8 21.3 + - - -
25B THR* 4.3 3.4 - - - -
55B ALA 3.1 3.4 + - - -
56B ASP* 1.3 71.4 - - - +
58B LYS* 1.3 70.8 + - - +
59B HIS 3.3 2.3 + - - -
63B GLU* 3.5 3.6 - - - +
64B GLU* 3.5 28.7 + - - +
67B ALA* 3.9 6.3 - - - -
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Residues in contact with LYS 58 (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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17A THR* 5.2 7.9 + - - +
46A GLU* 3.3 34.9 - - + +
49A GLY 5.5 2.8 + - - -
50A ARG 4.2 21.9 + - - +
51A GLN* 3.5 35.1 - - - +
25B THR* 3.0 6.2 - - - +
26B ASN* 2.8 28.6 + - - +
56B ASP* 2.8 23.0 + - - +
57B GLY* 1.3 79.7 - - - +
59B HIS* 1.3 67.1 + - - +
63B GLU* 3.5 37.3 + - + +
66B GLN* 5.3 4.9 + - - -
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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