Contacts of the helix formed by residues 129 - 134 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LEU* 4.0 6.7 - - - -
127B PHE* 3.8 7.1 - - - +
128B ALA* 1.3 89.7 - - + +
130B VAL* 1.3 64.9 + - - +
131B ASP* 2.8 39.7 + - - +
132B GLU* 3.3 27.3 + - - +
133B ALA* 3.3 14.2 + - - +
269B Y0R 6.0 1.6 - - - +
169D GLU* 3.0 38.9 + - - -
170D GLU 4.9 2.6 + - - -
171D GLY* 3.5 17.9 + - - -
172D SER* 3.5 10.5 - - - -
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.5 33.7 - - + -
123B LEU* 4.0 18.3 - - + +
129B ARG* 1.3 73.2 - - - +
131B ASP* 1.3 57.9 + - - +
133B ALA* 2.9 17.8 + - - +
134B LEU* 3.0 20.2 + - + +
140B LEU* 4.5 10.7 - - + +
269B Y0R 3.6 51.4 - - + +
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Residues in contact with ASP 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ARG* 2.8 47.7 + - - +
130B VAL* 1.3 79.9 - - - +
132B GLU* 1.3 69.7 + - - +
134B LEU* 3.7 19.0 + - + +
269B Y0R 4.3 19.7 - - + +
62D ARG* 2.9 20.6 + - - -
171D GLY 4.6 0.5 - - - +
172D SER* 3.3 3.3 - - - -
173D GLU* 3.0 48.6 + - - +
174D THR* 5.8 0.7 - - - -
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ARG* 3.8 16.9 + - - +
127B PHE* 3.6 12.6 - - + -
128B ALA* 3.4 26.6 + - - +
129B ARG* 3.3 30.9 + - - +
130B VAL 3.2 0.4 - - - -
131B ASP* 1.3 89.8 + - - +
133B ALA* 1.3 61.7 + - - +
136B ARG* 2.8 31.5 + - - +
62D ARG* 3.5 2.4 + - - -
64D ARG* 4.9 11.2 + - - +
173D GLU* 3.9 20.6 - - - +
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LEU* 3.5 29.4 - - + -
127B PHE* 3.9 15.2 - - + -
129B ARG 3.3 2.1 + - - +
130B VAL 2.9 9.2 + - - +
132B GLU* 1.3 77.4 - - - +
134B LEU* 1.3 66.3 - - - +
135B GLY 3.2 0.9 + - - -
136B ARG* 3.0 22.2 + - - +
139B GLY* 3.7 24.8 - - - +
140B LEU* 4.1 7.3 + - + +
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B VAL* 3.0 22.0 + - + +
131B ASP* 4.0 15.0 - - + +
132B GLU 3.4 1.2 - - - -
133B ALA* 1.3 75.8 - - - +
135B GLY* 1.3 59.2 + - - +
136B ARG* 3.4 0.5 + - - -
140B LEU* 3.7 26.5 - - + -
199B LEU* 3.8 23.3 - - + -
203B PRO* 4.8 12.1 - - + -
205B ALA* 3.9 13.0 - - + -
208B VAL* 6.2 0.7 - - + -
269B Y0R 3.8 29.4 - - + -
62D ARG* 3.0 30.3 + - - +
173D GLU 6.0 0.4 - - - +
174D THR* 6.4 2.0 - - - -
175D GLN* 3.7 9.9 + - + +
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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