Contacts of the strand formed by residues 89 - 96 (chain B) in PDB entry 4B2Q
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 LEU 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B THR* 3.5 15.5 - - - +
31B GLY 4.2 1.3 - - - +
32B ARG* 3.6 24.8 - - - +
57B PHE* 3.6 1.6 - - - +
58B SER* 2.9 41.6 + - - +
88B GLU* 1.3 77.2 - - - +
90B VAL* 1.3 80.6 + - - +
91B LYS* 3.4 43.3 - - + -
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Residues in contact with VAL 90 (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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30B THR* 2.8 30.1 + - - -
31B GLY 3.1 18.4 + - - +
33B VAL* 3.6 22.7 - - + -
43B VAL* 3.9 21.1 - - + -
46B LEU* 4.3 14.7 - - + +
55B VAL* 4.9 3.4 - - + -
56B GLU 3.8 7.2 - - - +
57B PHE* 3.4 38.4 - - + -
75B ILE* 4.7 4.3 - - + -
89B LEU* 1.3 80.3 - - - +
91B LYS* 1.3 64.4 + - - +
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Residues in contact with LYS 91 (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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29B GLU 4.1 4.3 - - - +
30B THR* 4.5 4.7 - - - +
46B LEU* 5.0 0.4 - - - -
55B VAL* 3.8 3.8 - - - +
56B GLU* 2.9 44.3 + - + +
57B PHE 5.4 1.5 - - - -
89B LEU* 3.4 33.0 - - + -
90B VAL* 1.3 76.8 - - - +
92B ARG* 1.3 64.0 + - - +
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Residues in contact with ARG 92 (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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28B ASN 4.1 2.0 + - - -
29B GLU* 2.8 66.3 + - + +
46B LEU* 4.1 12.8 - - + -
48B ASN* 2.4 44.1 + - - +
49B ILE* 3.9 6.8 - - + +
53B GLU* 3.5 21.7 + - - +
55B VAL* 4.3 12.3 - - + -
56B GLU* 5.1 1.1 - - - -
91B LYS* 1.3 78.1 - - - +
93B THR* 1.3 63.4 + - - +
94B GLY* 4.3 9.6 - - - +
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Residues in contact with THR 93 (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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54B LEU* 3.4 46.6 + - + +
55B VAL* 4.0 6.8 + - - +
56B GLU* 4.7 4.0 + - - +
92B ARG* 1.3 75.3 - - - +
94B GLY* 1.3 59.6 + - - +
95B ASN* 3.5 31.3 + - + +
98B ASP* 6.1 0.7 - - - +
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Residues in contact with GLY 94 (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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50B GLN* 4.5 6.9 - - - +
53B GLU* 3.0 27.0 + - - +
92B ARG* 3.5 14.0 - - - -
93B THR* 1.3 77.0 - - - +
95B ASN* 1.3 69.7 + - - +
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Residues in contact with ASN 95 (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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50B GLN* 5.2 1.8 - - - -
53B GLU* 3.8 5.7 - - - +
54B LEU* 3.3 22.7 + - - +
93B THR* 3.2 20.2 + - + +
94B GLY* 1.3 87.4 - - - +
96B ILE* 1.3 70.9 + - - +
98B ASP* 5.0 7.2 - - - +
130B ARG* 4.5 12.1 + - - +
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Residues in contact with ILE 96 (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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50B GLN* 4.2 17.9 + - - +
51B ALA 4.6 4.5 - - - +
52B GLU* 3.2 27.4 - - + +
53B GLU* 4.2 3.8 - - - +
54B LEU 4.0 2.7 - - - +
64B MET* 6.2 0.4 - - - -
95B ASN* 1.3 78.4 - - - +
97B VAL* 1.3 78.0 + - + +
98B ASP* 3.1 15.8 + - - +
130B ARG* 3.4 42.7 + - + +
131B ALA* 5.1 3.8 - - + +
132B GLN* 5.6 8.7 - - + +
68F GLU* 4.1 27.8 - - + -
69F GLY* 4.8 3.4 - - - +
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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