Contacts of the strand formed by residues 89 - 93 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D GLU* 3.8 16.1 + - - +
39D LEU* 3.5 40.8 - - + +
40D ASN* 5.3 1.8 - - + -
43D ASN* 3.3 31.4 - - - -
54D ILE* 4.0 9.4 - - + -
55D HIS 3.2 8.5 - - - +
56D LYS* 3.5 38.1 - - + +
57D LYS* 5.5 0.4 - - - -
87D THR* 4.3 1.1 + - - -
88D ASN* 1.3 98.9 - - + +
90D ASN* 1.3 66.3 + - - +
99D ASP* 3.2 8.8 - - - +
100D PHE* 3.2 34.2 + - + -
101D GLU* 4.8 3.1 - - - -
102D ALA* 4.3 14.8 - - + +
189D TYR* 5.6 1.1 - - - -
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Residues in contact with ASN 90 (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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90B ASN* 2.9 35.5 + - - -
97B TYR* 5.3 0.2 + - - -
54D ILE* 3.7 7.6 - - - -
55D HIS* 3.0 26.8 + - - +
57D LYS* 4.5 24.3 - - - +
86D THR* 6.1 1.6 - - - -
87D THR* 5.6 1.8 + - - -
88D ASN 4.3 0.2 + - - -
89D TYR* 1.3 75.1 - - - +
91D GLY* 1.3 56.2 + - - +
97D TYR* 3.0 29.9 + - + +
98D ILE 3.0 19.1 - - - +
99D ASP* 4.1 3.8 + - + -
100D PHE 4.9 0.2 - - - +
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Residues in contact with GLY 91 (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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97B TYR* 2.9 30.6 - - - -
53D VAL 3.0 14.1 - - - -
54D ILE* 3.6 7.7 - - - +
90D ASN* 1.3 78.4 + - - +
92D ILE* 1.3 59.4 + - - -
97D TYR* 4.4 0.5 - - - -
98D ILE* 2.9 29.5 + - - -
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Residues in contact with ILE 92 (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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97B TYR* 3.6 29.2 - - + -
127B VAL* 4.0 10.5 - - + +
130B GLN* 3.1 40.8 - - + +
131B ASP 4.4 0.2 - - - -
132B GLY* 3.5 24.7 - - - +
52D ALA* 3.2 9.9 - - - +
53D VAL* 2.9 55.7 + - + +
54D ILE* 4.2 2.8 - - - +
91D GLY* 1.3 75.3 - - - -
93D TYR* 1.3 63.6 + - - +
95D GLY 4.2 7.4 - - - +
96D ARG 3.5 9.9 - - - +
98D ILE* 4.6 3.1 - - - -
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Residues in contact with TYR 93 (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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130B GLN* 5.2 0.2 - - - +
51D ILE* 3.9 22.3 - - + +
52D ALA* 4.0 11.0 - - + +
54D ILE* 6.4 0.4 - - + -
92D ILE* 1.3 74.5 - - - +
94D LYS* 1.3 91.1 - - + +
95D GLY 3.0 1.8 - - - -
96D ARG* 2.5 44.1 + - + +
98D ILE* 3.9 19.7 - - + +
190D ILE* 3.9 34.0 - - + +
193D ILE* 5.6 5.4 - - + -
194D GLU* 2.8 37.2 + - + +
198D PHE* 3.7 20.4 - + + -
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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