Contacts of the strand formed by residues 83 - 89 (chain B) in PDB entry 4B3E
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 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B PHE 4.8 0.4 - - - -
46B HIS* 4.8 3.4 - - - -
63B HIS* 3.0 15.8 + - - -
71B HIS* 3.0 12.3 + - + -
72B GLY 3.1 34.5 + - - +
73B GLY 4.7 0.2 - - - -
74B PRO* 3.5 11.3 - - - +
79B ARG* 3.4 24.8 + - + -
80B HIS* 2.7 58.5 + - - +
81B VAL 3.3 1.2 - - - -
82B GLY* 1.3 73.7 - - - +
84B LEU* 1.3 60.6 + - - +
85B GLY 3.4 2.7 - - - +
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Residues in contact with LEU 84 (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 PHE* 5.1 2.5 - - + -
31B VAL* 5.0 9.4 - - + -
45B PHE* 3.1 47.0 + - + +
47B VAL* 4.0 22.9 - - + -
74B PRO* 4.0 12.9 - - + +
79B ARG* 4.2 3.6 - - - +
82B GLY 3.1 8.6 + - - +
83B ASP* 1.3 76.6 - - - +
85B GLY* 1.3 61.1 + - - +
86B ASN 3.6 2.9 + - - +
99B ILE* 4.0 25.9 - - + +
101B ASP* 3.9 33.4 - - + +
104B ILE* 4.1 20.9 - - + -
117B LEU* 4.4 7.2 - - + -
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Residues in contact with GLY 85 (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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44B GLY* 3.3 6.2 - - - -
45B PHE* 2.8 29.1 + - - -
73B GLY* 5.0 1.1 - - - -
74B PRO* 3.6 20.5 - - - +
83B ASP* 3.4 3.6 - - - +
84B LEU* 1.3 77.7 - - - +
86B ASN* 1.3 64.6 + - - +
124B ASP* 3.9 11.7 + - - +
126B LEU* 4.3 11.9 - - - -
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Residues in contact with ASN 86 (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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42B LEU* 4.2 28.9 - - + +
43B HIS 3.4 4.4 - - - +
44B GLY 3.5 8.7 + - - -
45B PHE* 4.7 1.1 - - - -
84B LEU 3.6 4.1 + - - +
85B GLY* 1.3 74.8 - - - -
87B VAL* 1.3 69.1 + - - +
88B THR* 5.1 1.0 + - - -
99B ILE* 5.5 3.3 - - - +
123B ALA* 3.6 1.9 - - - -
124B ASP* 2.7 50.8 + - - +
126B LEU* 3.5 19.6 - - - +
55D ALA* 5.5 5.5 - - + +
58D THR* 4.5 6.1 - - - +
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Residues in contact with VAL 87 (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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35B ILE* 4.5 4.3 - - + -
38B LEU* 5.1 1.3 - - + -
41B GLY 3.6 1.2 - - - +
42B LEU* 3.4 5.9 - - - +
43B HIS* 3.0 51.0 + - + +
45B PHE* 3.8 29.4 - - + -
86B ASN* 1.3 76.4 - - - +
88B THR* 1.3 61.5 + - - +
95B ALA* 4.3 13.0 - - + -
97B VAL* 3.3 36.8 - - + -
99B ILE* 5.2 1.8 - - + -
119B VAL* 4.1 14.8 - - + -
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Residues in contact with THR 88 (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 GLY* 3.5 8.1 - - - +
42B LEU* 3.1 23.3 - - + +
86B ASN 5.1 0.7 + - - -
87B VAL* 1.3 73.4 - - - +
89B ALA* 1.3 69.2 + - - +
90B ASP* 3.9 1.8 + - - -
94B VAL 3.9 0.7 - - - +
95B ALA* 3.1 20.9 - - - +
96B ASP 4.1 3.7 + - - +
54D THR 4.0 11.4 + - - +
55D ALA* 3.7 19.2 - - - +
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Residues in contact with ALA 89 (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 LEU* 3.7 26.0 - - + -
39B THR 3.5 23.1 - - - +
40B GLU* 3.5 3.9 - - - +
41B GLY* 2.8 37.1 + - - +
43B HIS* 4.2 2.2 - - + -
87B VAL 4.1 0.6 - - - -
88B THR* 1.3 77.7 - - - +
90B ASP* 1.3 64.1 + - - +
93B GLY 4.1 12.1 - - - -
94B VAL 3.7 6.5 - - - -
95B ALA* 3.9 1.2 - - - +
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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