Contacts of the helix formed by residues 125 - 132 (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 HIS 125 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5271 C 2.7 51.7 + - - +
5281 A 5.1 1.3 - + - -
5591 G 4.2 16.4 - + - -
119J LEU 5.2 0.7 - - - -
120J ALA 3.6 8.7 - - - -
121J LYS* 3.1 32.3 - - + +
122J SER 2.4 21.5 + - - +
124J HIS* 1.3 66.2 - - - +
126J ALA* 1.3 57.4 + - - -
127J ARG 3.2 1.8 - - - -
128J VAL* 2.9 10.3 + - + +
129J LEU* 2.9 68.0 + - + +
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Residues in contact with ALA 126 (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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111J GLN* 4.4 20.0 - - + -
114J VAL* 5.5 3.6 - - + -
120J ALA* 3.9 23.8 + - + -
122J SER 3.8 0.4 + - - -
123J ILE* 2.6 27.7 + - + +
125J HIS* 1.3 75.7 - - - +
127J ARG* 1.3 54.5 + - - -
129J LEU* 4.0 12.3 - - + -
130J ILE* 2.9 39.2 + - + +
135J ILE* 5.9 0.7 - - + -
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Residues in contact with ARG 127 (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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5221 A 4.3 4.4 + - - -
5231 A 2.6 30.2 + - - -
36J GLY 3.9 11.8 + - - +
37J LEU* 5.1 0.6 - - - +
38J ARG* 3.9 28.7 - - - +
42J GLU* 5.0 3.4 + - - -
109J ARG* 4.2 10.5 - - - +
111J GLN* 3.1 25.7 + - - +
123J ILE* 2.9 16.8 + - + +
124J HIS* 3.7 5.8 - - - +
125J HIS 3.2 0.4 - - - -
126J ALA* 1.3 76.4 - - - +
128J VAL* 1.3 57.4 + - - +
130J ILE* 3.2 21.7 - - - +
131J ARG* 3.4 13.2 + - - +
145J PRO* 3.2 33.0 - - - +
31e ARG* 3.2 46.7 - - - +
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Residues in contact with VAL 128 (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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5261 A 3.4 37.0 - - + +
5271 C 4.3 7.9 - - - +
5591 G 4.2 15.7 - - - +
124J HIS 3.9 7.6 - - - +
125J HIS* 2.9 14.1 + - + +
127J ARG* 1.3 75.8 - - - +
129J LEU* 1.3 59.1 + - + +
130J ILE 3.2 0.4 - - - -
131J ARG* 4.6 3.4 - - - -
132J GLN* 3.0 60.9 + - + +
31e ARG* 3.6 7.9 - - - +
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Residues in contact with LEU 129 (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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114J VAL* 6.1 0.7 - - + -
119J LEU* 3.8 22.2 - - + +
120J ALA* 3.9 7.6 - - - +
125J HIS* 2.9 56.0 + - + +
126J ALA* 3.1 10.5 + - + +
128J VAL* 1.3 77.9 - - + +
130J ILE* 1.3 55.2 + - - +
132J GLN* 2.6 17.7 - - - +
134J HIS* 3.1 59.0 + - + +
135J ILE* 4.1 16.9 + - + +
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Residues in contact with ILE 130 (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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110J LEU* 3.8 27.8 - - + -
111J GLN* 5.0 12.1 - - + +
126J ALA* 2.9 26.8 + - + +
127J ARG* 3.2 25.8 - - - +
129J LEU* 1.3 75.2 - - - +
131J ARG* 1.3 69.1 + - - +
132J GLN 3.0 6.9 - - - +
133J ARG* 4.9 1.2 - - - +
135J ILE* 3.8 20.2 - - + -
142J VAL 4.0 5.3 - - - +
143J ASN* 3.1 31.1 - - - +
145J PRO* 3.5 41.5 - - + +
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Residues in contact with ARG 131 (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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5221 A 2.3 51.8 + - - -
5231 A 3.0 38.9 + - - +
5621 U 4.6 12.6 + - - +
5631 G 5.5 11.0 - - - +
127J ARG 3.4 15.1 + - - +
128J VAL* 4.0 4.0 - - - +
130J ILE* 1.3 78.7 - - + +
132J GLN* 1.3 67.1 + - + +
133J ARG* 3.8 2.6 + - - +
143J ASN* 3.0 42.3 + - - +
145J PRO* 4.4 10.7 - - + +
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Residues in contact with GLN 132 (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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5591 G 4.4 2.3 + - - +
5611 A 2.8 55.3 + - - +
5621 U 3.1 45.9 + - - +
128J VAL* 3.0 35.4 + - + +
129J LEU 2.6 20.4 - - - +
130J ILE 3.0 4.2 - - - +
131J ARG* 1.3 83.4 - - + +
133J ARG* 1.3 62.1 + - - +
134J HIS* 3.1 18.5 - - + +
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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