Contacts of the strand formed by residues 38 - 45 (chain D) in PDB entry 3BRW
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 ASP 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312B ASN* 5.1 5.3 + - - -
17D SER* 5.4 0.5 - - - -
35D THR* 3.1 30.4 - - - +
36D ILE 5.8 0.2 + - - -
37D GLU* 1.3 84.2 + - - +
39D SER* 1.3 64.6 + - - +
40D TYR* 3.6 31.8 + - + +
56D LEU* 3.9 4.0 - - - +
57D ASP* 2.9 39.8 + - + +
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Residues in contact with SER 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D GLU* 4.9 5.7 + - - -
38D ASP* 1.3 78.7 - - - +
40D TYR* 1.3 70.8 + - - +
54D GLU* 4.0 18.8 + - - -
55D ILE 3.2 13.7 - - - -
56D LEU* 4.2 13.6 - - - +
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Residues in contact with TYR 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D SER* 5.7 1.0 - - - -
20D THR* 3.3 33.7 - - + -
21D VAL* 3.4 26.1 - - + +
24D VAL* 3.8 31.4 - - + -
25D GLN* 4.3 17.7 - - - -
38D ASP* 3.6 35.7 + - + +
39D SER* 1.3 80.8 - - - +
41D ARG* 1.3 61.1 + - - +
42D LYS 4.1 0.4 - - - -
53D LEU 3.8 0.3 - - - +
54D GLU* 3.5 5.9 - - - +
55D ILE* 2.8 34.5 + - + +
57D ASP* 4.6 8.8 + - + -
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Residues in contact with ARG 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLU* 4.4 21.6 + - - +
24D VAL* 5.5 1.1 - - - -
40D TYR* 1.3 75.9 - - - +
42D LYS* 1.3 61.1 + - - +
52D MET* 3.5 41.9 + - + +
53D LEU 3.1 10.3 - - - +
54D GLU* 3.8 33.9 + - + +
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Residues in contact with LYS 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PHE* 3.3 48.4 + - + +
24D VAL* 3.5 39.8 + - + +
40D TYR 4.1 1.2 + - - -
41D ARG* 1.3 74.2 - - - +
43D GLN* 1.3 76.4 + - - +
44D VAL* 4.1 15.9 - - + +
52D MET* 3.4 9.8 - - - +
53D LEU* 2.9 35.8 + - + +
55D ILE* 5.4 0.8 - - + +
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Residues in contact with GLN 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 3.3 22.8 - - + +
42D LYS* 1.3 84.2 + - - +
44D VAL* 1.3 63.8 - - - +
50D GLN* 3.0 31.8 + - - +
51D CYS 3.8 4.0 + - - +
52D MET* 3.7 28.9 - - + -
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Residues in contact with VAL 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PHE* 4.4 12.8 - - + -
42D LYS* 4.1 14.9 - - + -
43D GLN* 1.3 77.2 - - - +
45D GLU* 1.3 73.2 + - + +
46D VAL* 4.8 1.7 - - + +
50D GLN* 4.8 3.6 - - - +
51D CYS* 2.9 34.2 + - - +
53D LEU* 4.6 13.0 - - + +
159D TYR* 3.4 44.4 - - + +
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Residues in contact with GLU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D VAL* 1.3 86.8 - - + +
46D VAL* 1.3 67.6 + - - +
47D ASP* 4.2 2.8 + - - -
48D ALA* 4.2 19.9 + - - +
49D GLN 4.9 0.9 - - - +
50D GLN* 3.5 32.7 + - + +
159D TYR* 4.6 5.4 - - - -
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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