Contacts of the helix formed by residues 129 - 134 (chain D) in PDB entry 5FL6
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 ARG 129 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A GLN* 5.9 0.4 + - - -
130A VAL* 5.5 8.5 - - - +
131A ASP* 6.1 0.7 - - - -
268A Y0R 3.9 35.5 - - - +
123D LEU* 3.8 12.1 - - - +
127D PHE* 3.4 1.8 - - - +
128D ALA* 1.3 89.6 - - + +
130D VAL* 1.3 65.7 + - - +
131D ASP* 2.7 38.0 + - - +
132D GLU* 3.2 44.9 + - - +
133D ALA 3.4 6.9 + - - -
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Residues in contact with VAL 130 (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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129A ARG* 5.5 7.7 - - - +
91D LEU* 3.3 36.3 - - + -
123D LEU* 3.9 12.6 - - + +
129D ARG* 1.3 73.0 - - - +
131D ASP* 1.3 60.8 + - - +
133D ALA* 2.8 19.6 + - - +
134D LEU* 3.0 22.9 + - + +
140D LEU* 4.4 14.8 - - + -
266D Y0R 3.7 52.9 - - + +
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Residues in contact with ASP 131 (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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129A ARG* 5.9 1.9 - - - -
131A ASP* 5.4 1.4 - - - +
268A Y0R 4.8 10.0 - - - +
129D ARG* 2.7 50.1 + - - +
130D VAL* 1.3 80.8 + - - +
132D GLU* 1.3 59.6 + - - +
134D LEU* 3.8 28.0 + - + +
266D Y0R 3.9 25.1 - - + +
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Residues in contact with GLU 132 (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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73A THR* 5.8 0.2 + - - -
127D PHE* 3.5 15.7 - - + -
128D ALA* 3.2 33.3 + - - +
129D ARG* 3.2 50.0 + - + +
130D VAL 3.2 0.6 - - - -
131D ASP* 1.3 77.2 - - - +
133D ALA* 1.3 63.0 + - - +
134D LEU 3.3 1.0 - - - +
136D ARG* 2.9 35.8 + - - +
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Residues in contact with ALA 133 (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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123D LEU* 3.4 33.2 - - + -
127D PHE* 3.8 18.4 - - + -
129D ARG 3.4 1.2 + - - -
130D VAL 2.8 6.9 + - - +
132D GLU* 1.3 79.5 - - - +
134D LEU* 1.3 64.1 + - - +
135D GLY 3.2 0.9 + - - -
136D ARG* 3.0 21.0 + - - +
139D GLY* 3.6 21.2 - - - +
140D LEU* 4.1 7.7 + - + +
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Residues in contact with LEU 134 (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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130D VAL* 3.0 21.1 + - + +
131D ASP* 3.9 28.4 - - + +
132D GLU 3.3 1.9 - - - +
133D ALA* 1.3 76.0 - - - +
135D GLY* 1.3 60.0 + - - +
136D ARG* 3.3 11.3 + - - -
140D LEU* 4.0 15.3 - - + -
199D LEU* 3.6 30.7 - - + -
203D PRO* 4.3 14.1 - - + -
205D ALA* 3.9 15.3 - - + -
266D Y0R 4.1 18.6 - - + -
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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