Contacts of the strand formed by residues 84 - 90 (chain D) in PDB entry 5FLX
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 VAL 84 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PHE* 6.2 0.7 - - + -
46D THR* 3.2 27.4 - - + +
48D ILE* 3.7 13.0 - - + -
70D THR* 4.2 3.1 - - - +
73D VAL* 3.6 33.9 - - + +
74D GLN* 3.5 32.0 + - + +
77D PHE* 6.1 0.2 - - + -
79D PHE* 3.6 36.1 + - + -
82D GLY 3.5 2.5 - - - +
83D SER* 1.3 74.8 - - - +
85D GLU* 1.3 65.2 + - - +
86D LEU* 3.7 15.3 - - + -
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Residues in contact with GLU 85 (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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45D ARG* 5.5 10.5 - - + +
46D THR 2.8 12.2 + - - +
48D ILE 3.3 20.0 + - - -
67D ARG* 4.8 11.8 + - - -
70D THR* 4.4 10.7 + - - +
74D GLN* 5.2 1.9 + - - -
82D GLY* 4.9 6.0 - - - +
83D SER 4.4 3.6 - - - +
84D VAL* 1.3 79.0 - - - +
86D LEU* 1.3 71.0 + - - +
87D TYR* 3.4 44.3 - - + +
98K ARG* 5.8 6.0 - - - +
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Residues in contact with LEU 86 (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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21D LEU* 6.3 0.2 - - + -
25D LEU* 5.8 0.7 - - + -
48D ILE* 3.3 18.4 - - + +
50D ILE* 3.7 29.2 - - + -
66D ILE* 4.5 15.7 - - + +
69D LEU* 3.9 12.6 - - + +
70D THR* 3.2 52.5 + - + +
73D VAL* 3.9 18.6 - - + -
84D VAL* 3.7 26.9 - - + -
85D GLU* 1.3 84.5 - - - +
87D TYR* 1.3 66.6 + - - +
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Residues in contact with TYR 87 (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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45D ARG* 4.3 18.2 + - - -
47D GLU* 3.9 32.1 - - + -
48D ILE 2.9 7.7 + - - -
49D ILE* 3.4 16.0 - - + +
50D ILE* 2.8 29.6 + - - +
66D ILE* 5.1 2.5 - - - -
85D GLU* 3.4 46.6 - - + +
86D LEU* 1.3 77.5 - - - +
88D ALA* 1.3 63.0 + - - +
89D GLU* 5.9 1.6 - - + -
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Residues in contact with ALA 88 (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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50D ILE* 3.6 8.3 - - + +
52D ALA* 6.4 1.3 - - + -
55D THR* 3.9 19.7 - - - +
58D VAL* 4.2 11.7 - - + -
59D LEU* 4.7 5.2 - - + -
66D ILE* 3.8 25.0 - - + +
87D TYR* 1.3 76.0 - - - +
89D GLU* 1.3 67.7 + - - +
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Residues in contact with GLU 89 (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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38D GLU* 5.4 0.9 - - - +
49D ILE* 3.5 33.3 - - + +
50D ILE 3.2 9.6 + - - +
51D LEU* 3.5 26.3 - - + +
52D ALA* 3.4 24.2 + - - +
55D THR* 4.3 12.2 - - - -
87D TYR* 5.4 1.6 - - + -
88D ALA* 1.3 79.6 - - - +
90D LYS* 1.3 64.0 + - - +
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Residues in contact with LYS 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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51D LEU* 6.3 0.7 - - - -
52D ALA 4.1 0.9 - - - +
53D THR* 2.4 35.5 + - - +
54D ARG* 4.0 11.5 - - - +
55D THR* 4.5 20.4 - - + +
89D GLU* 1.3 78.8 - - - +
91D VAL* 1.3 76.8 + - - +
92D ALA* 3.7 5.3 + - - +
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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