Contacts of the strand formed by residues 89 - 93 (chain B) in PDB entry 5FDK
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 TYR 89 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLU* 3.7 20.0 + - - +
39B LEU* 3.6 40.3 - - + +
40B ASN* 5.1 3.1 - - + -
43B ASN* 5.7 3.4 - - + -
54B ILE* 4.4 14.1 - - + -
55B HIS 3.6 3.8 - - - +
56B LYS* 3.4 42.3 - - + +
57B LYS* 5.4 0.2 - - - -
87B THR 3.5 1.7 - - - -
88B ASN* 1.3 95.5 - - + +
90B ASN* 1.3 62.4 + - - +
99B ASP* 3.1 9.5 - - - -
100B PHE* 2.8 47.4 + - + +
101B GLU 4.6 6.5 - - - -
102B ALA* 3.5 27.2 - - + +
189B TYR* 6.0 0.7 - - - -
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Residues in contact with ASN 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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54B ILE* 3.4 8.8 - - - +
55B HIS 2.9 37.6 + - - +
57B LYS* 4.3 15.6 - - + +
87B THR 5.6 0.4 - - - +
88B ASN 4.1 0.2 + - - -
89B TYR* 1.3 77.4 - - - +
91B GLY* 1.3 61.4 + - - +
97B TYR* 2.7 35.0 + - - +
98B ILE 3.1 16.2 - - - +
99B ASP* 3.8 4.9 - - - +
100B PHE 4.7 0.2 - - - +
57D LYS* 6.0 0.5 - - - +
90D ASN* 2.9 34.8 + - - +
97D TYR* 4.6 0.8 - - - -
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Residues in contact with GLY 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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53B VAL* 3.1 11.7 - - - -
54B ILE* 3.7 7.5 - - - +
90B ASN* 1.3 82.1 - - - +
92B ILE* 1.3 60.9 + - - -
97B TYR* 3.6 1.2 - - - -
98B ILE 2.9 26.4 + - - +
97D TYR* 3.3 28.5 - - - -
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Residues in contact with ILE 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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52B ALA* 3.8 2.3 - - - +
53B VAL* 2.9 50.0 + - + +
54B ILE* 4.1 1.6 - - - +
91B GLY* 1.3 75.0 - - - +
93B TYR* 1.3 67.3 + - - +
95B GLY 3.9 11.7 - - - +
96B ARG 3.6 9.0 - - - +
98B ILE* 4.4 1.8 - - - -
97D TYR* 3.6 32.7 - - + -
127D VAL* 4.5 6.5 - - - +
130D GLN* 3.1 42.2 - - + +
131D ASP 3.8 2.2 - - - -
132D GLY* 3.4 28.9 - - - +
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Residues in contact with TYR 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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51B ILE* 3.1 32.3 - - + -
52B ALA* 3.8 12.6 - - + -
54B ILE* 5.6 0.4 - - + -
92B ILE* 1.3 80.7 - - - +
94B LYS* 1.3 98.1 + - + +
96B ARG* 3.3 17.3 + - - +
98B ILE* 4.4 12.0 - - + +
133B ILE* 6.1 0.4 - - + -
190B ILE* 3.9 35.7 - - + +
193B ILE* 4.4 23.1 - - + -
194B GLU* 2.5 40.1 + - - +
197B TYR* 5.2 5.2 - - + -
130D GLN* 4.7 2.7 - - - -
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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