Contacts of the strand formed by residues 48 - 54 (chain B) in PDB entry 4EEJ
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 ASN 48 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B ASP* 3.7 1.4 - - - +
44B GLN* 3.5 3.1 - - - -
45B ASP* 2.9 48.1 + - + +
46B GLY 3.2 0.2 - - - -
47B ASP* 1.3 82.0 - - - +
49B PHE* 1.3 59.7 + - - +
50B LYS* 5.6 8.5 - - - +
64B PHE 3.6 3.1 - - - +
65B THR* 2.9 34.2 + - - +
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Residues in contact with PHE 49 (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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4B ARG* 4.2 5.8 - - + -
42B ILE* 3.8 24.7 - - + -
43B ASP 3.3 3.4 - - - -
44B GLN* 3.4 44.6 - - + -
46B GLY 4.3 5.4 - - - -
47B ASP 3.6 10.1 - - - -
48B ASN* 1.3 75.9 - - - +
50B LYS* 1.3 65.5 + - - +
51B VAL* 4.2 5.8 - - + -
62B VAL 4.7 0.2 - - - -
63B ASP* 3.3 5.2 - - - +
64B PHE* 2.9 70.7 + + + +
66B VAL* 3.6 21.1 - - + -
88B TRP* 4.1 9.6 - + - -
93B LEU* 3.8 25.1 - - + -
108B LYS* 5.8 0.4 - - - -
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Residues in contact with LYS 50 (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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41B VAL 3.7 1.6 - - - +
42B ILE* 3.6 2.6 - - - -
43B ASP* 2.8 60.4 + - + +
48B ASN* 5.6 8.7 - - - +
49B PHE* 1.3 77.2 - - - +
51B VAL* 1.3 61.0 + - - +
52B LYS* 3.6 23.5 + - - +
63B ASP* 3.4 29.4 + - - +
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 3.6 26.5 - - + -
41B VAL 3.5 3.4 - - - +
42B ILE* 4.4 15.5 - - + -
49B PHE* 4.4 6.5 - - + -
50B LYS* 1.3 75.6 - - - +
52B LYS* 1.3 67.0 + - - +
53B CYS 4.2 0.9 - - - +
60B TYR* 3.9 2.2 - - + +
61B ASP* 3.3 4.7 - - - +
62B VAL* 2.9 45.7 + - + +
63B ASP* 4.2 1.3 + - - +
64B PHE* 3.9 29.8 - - + -
108B LYS* 4.9 1.8 - - - +
201B RET 3.9 28.3 - - + -
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Residues in contact with LYS 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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39B THR 3.5 1.9 - - - +
40B LEU* 3.4 3.8 - - - -
41B VAL* 2.8 56.3 + - + +
43B ASP* 6.0 0.2 - - - +
50B LYS* 3.6 35.1 - - - +
51B VAL* 1.3 77.2 - - - +
53B CYS* 1.4 60.0 + - - +
54B THR* 4.1 12.7 + - + +
60B TYR 3.5 3.8 - - - -
61B ASP* 3.6 25.6 - - - +
63B ASP* 4.5 5.5 + - - -
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Residues in contact with CYS 53 (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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38B GLN* 3.4 31.6 - - - -
39B THR 3.4 10.3 - - - -
40B LEU* 4.3 15.3 - - + +
51B VAL* 4.2 0.6 - - + +
52B LYS* 1.4 73.5 - - - +
54B THR* 1.4 61.1 + - - +
59B ASN* 3.3 5.5 - - - +
60B TYR* 2.7 40.4 + - + +
61B ASP* 4.4 0.2 + - - -
130B PHE* 5.6 1.8 - - - -
201B RET 3.9 46.9 - - + +
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Residues in contact with THR 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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37B THR 3.7 0.3 - - - +
38B GLN* 3.4 7.5 - - - +
39B THR* 2.9 47.9 + - - +
41B VAL* 5.8 3.1 - - + +
52B LYS* 4.6 13.2 - - + +
53B CYS* 1.4 82.5 - - - +
55B SER* 1.3 64.1 + - - +
58B TRP 4.0 0.7 - - - -
59B ASN* 3.4 21.8 - - + +
61B ASP* 5.2 1.1 - - - +
201B RET 5.5 0.7 - - - -
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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