Contacts of the helix formed by residues 102 - 108 (chain J) 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 ILE 102 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27J GLN* 5.8 6.3 - - - +
31J LEU* 4.5 13.5 - - + -
43J VAL* 5.4 3.6 - - + +
46J VAL* 3.8 20.0 - - + +
47J LYS* 3.4 38.4 - - + +
50J LEU* 3.7 20.4 - - + -
54J ARG* 6.2 0.4 - - - +
101J LYS* 1.3 71.8 - - - +
103J GLU* 1.3 72.6 + - - +
104J ASP 3.1 3.7 + - - -
105J PHE* 3.4 6.4 + - - +
106J LEU* 3.4 35.6 + - + +
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Residues in contact with GLU 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J GLN* 5.4 6.2 + - - -
30J LYS* 5.6 3.3 + - - -
31J LEU* 4.0 16.9 - - + +
34J GLU* 4.4 8.9 - - - +
35J TYR* 3.1 38.1 + - + +
101J LYS* 3.3 43.4 - - + +
102J ILE* 1.3 79.4 + - - +
104J ASP* 1.3 55.2 + - - +
106J LEU* 3.8 7.4 - - - -
107J GLU* 2.9 27.5 + - - +
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Residues in contact with ASP 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86J VAL* 3.5 37.6 - - + +
100J LEU* 3.8 9.5 - - - +
101J LYS* 3.3 51.8 + - - +
102J ILE 3.1 0.2 + - - -
103J GLU* 1.3 75.7 - - - +
105J PHE* 1.3 61.7 + - + +
107J GLU* 2.9 32.1 + - - +
108J ARG* 3.3 10.4 + - - +
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Residues in contact with PHE 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J VAL* 4.4 13.7 - - + -
49J THR* 5.9 0.4 - - - +
50J LEU* 3.5 34.3 - - + -
53J ILE* 4.4 15.0 - - + -
81J LEU* 3.7 20.4 - - + -
84J ILE* 3.6 44.6 - - + -
86J VAL* 3.9 19.3 - - + -
100J LEU* 4.9 9.6 - - + -
101J LYS 4.3 6.1 - - - -
102J ILE 3.4 4.4 + - - +
104J ASP* 1.3 83.1 - - + +
106J LEU* 1.3 62.7 + - - +
108J ARG* 3.2 17.1 + - + +
109J ARG* 3.5 14.7 + - - +
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Residues in contact with LEU 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J LEU* 3.7 37.9 - - + -
35J TYR* 3.4 30.7 - - + +
37J LEU* 4.3 19.1 - - + -
43J VAL* 5.6 3.6 - - + -
46J VAL* 3.7 28.7 - - + -
102J ILE* 3.4 30.8 + - + +
103J GLU 3.7 7.9 - - - +
104J ASP 3.2 0.8 - - - -
105J PHE* 1.3 79.8 - - - +
107J GLU* 1.3 59.0 + - - +
109J ARG* 3.6 31.3 + - - +
112J THR* 3.5 7.4 + - - -
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Residues in contact with GLU 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35J TYR* 3.7 10.2 + - + +
101J LYS* 6.0 1.2 - - - -
103J GLU 2.9 13.7 + - - +
104J ASP* 2.9 17.6 + - - +
106J LEU* 1.3 76.6 - - - +
108J ARG* 1.3 51.5 + - + +
109J ARG 3.3 3.1 - - - -
112J THR* 3.2 33.8 - - + +
113J GLN* 2.7 29.2 + - - +
116J LYS* 4.0 21.1 + - + +
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Residues in contact with ARG 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J ILE* 2.5 39.1 + - + +
85J GLY* 4.5 11.5 + - - -
86J VAL* 4.6 7.4 - - + -
104J ASP 3.8 12.1 - - - +
105J PHE* 3.2 12.5 + - - +
107J GLU* 1.3 76.5 - - + +
109J ARG* 1.3 65.2 + - - +
113J GLN* 3.3 27.7 + - - +
147J PHE 3.5 8.7 - - - +
148J ILE* 4.3 4.0 - - + -
149J VAL 2.4 41.2 + - - +
150J ARG 3.4 1.6 + - - -
151J LEU* 3.2 26.4 - - - +
154J GLN* 3.1 34.2 + - - +
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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