Contacts of the strand formed by residues 136 - 144 (chain C) 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 136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C LEU* 5.3 0.7 - - + -
79C GLU* 2.6 31.1 + - - -
82C TYR* 3.3 29.9 - + - -
98C LEU* 4.1 20.2 - - + +
131C GLY* 3.1 2.4 - - - -
132C ASP* 2.9 33.4 + - + +
134C ASN* 4.0 24.2 + - - +
135C GLY* 1.3 78.8 - - - +
137C VAL* 1.3 60.8 + - - +
162C ILE* 4.0 19.8 - - + +
163C VAL 3.6 2.9 - - - -
164C PRO* 3.7 15.9 - - + +
11V LEU* 3.5 23.7 - - + +
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Residues in contact with VAL 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C ILE 3.3 9.6 - - - +
131C GLY* 3.7 9.9 - - - -
132C ASP 4.0 0.2 - - - +
136C HIS* 1.3 78.9 - - - +
138C GLY* 1.3 56.5 + - - +
162C ILE* 3.6 7.2 - - - +
163C VAL* 2.7 36.7 + - + +
165C VAL* 4.0 14.1 - - + -
213C LEU* 4.8 11.9 - - + +
216C MET* 3.1 39.9 - - + +
217C ALA* 3.6 8.5 - - + +
241C PHE* 5.2 2.2 - - + -
244C ILE* 3.8 28.7 - - + -
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Residues in contact with GLY 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ALA* 3.4 5.0 - - - +
130C ILE* 2.8 33.9 + - - +
137C VAL* 1.3 75.4 - - - +
139C LEU* 1.3 61.7 + - - +
158C ALA* 3.9 12.3 - - - -
161C SER 4.0 0.4 - - - -
162C ILE* 3.6 18.2 - - - +
213C LEU* 5.2 1.3 - - - +
241C PHE* 3.8 9.6 - - - -
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Residues in contact with LEU 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C LEU* 4.7 7.9 - - + -
127C PHE* 6.2 3.8 - - + -
128C VAL 3.9 8.7 - - - +
129C ALA* 4.1 18.8 - - + -
138C GLY* 1.3 75.1 - - - +
140C GLY* 1.3 82.8 + - - +
141C VAL* 5.2 4.9 - - + -
157C LEU* 3.6 1.0 - - - +
158C ALA* 4.1 6.2 - - - +
161C SER* 3.3 24.7 + - - -
213C LEU* 4.5 14.8 - - + -
237C ALA* 3.7 40.8 - - + +
238C LYS* 4.7 17.3 - - + -
241C PHE* 3.9 23.3 - - + -
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Residues in contact with GLY 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C PHE* 4.2 3.3 - - - -
128C VAL 3.2 30.3 + - - +
139C LEU* 1.3 85.8 - - - +
141C VAL* 1.3 63.5 + - - +
154C ALA* 4.1 10.3 - - - +
157C LEU* 3.6 22.2 - - - -
158C ALA 4.2 0.8 - - - +
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Residues in contact with VAL 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13521 G 5.2 3.4 + - - +
125C LYS* 3.3 31.0 - - + +
126C ALA 4.0 4.0 - - - +
127C PHE* 3.4 24.7 - - + -
139C LEU* 5.2 4.5 - - + -
140C GLY* 1.3 75.3 - - - +
142C LYS* 1.3 65.0 + - - +
154C ALA* 5.1 0.7 - - - -
157C LEU* 3.2 20.9 - - + +
238C LYS* 5.0 19.7 - - + +
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Residues in contact with LYS 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13501 U 3.2 49.7 + - - +
13511 G 3.2 58.8 + - - +
13521 G 5.7 1.4 + - - -
123C ARG* 5.4 3.4 - - - +
124C PHE 4.1 0.7 - - - +
125C LYS* 3.8 4.4 - - - -
126C ALA* 3.2 28.9 + - - +
141C VAL* 1.3 81.1 - - - +
143C CYS* 1.3 80.5 + - - +
144C SER* 4.4 0.8 + - - -
150C ALA* 4.4 9.0 - - - +
153C GLY* 4.5 2.5 - - - -
154C ALA* 4.3 18.2 - - - +
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Residues in contact with CYS 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13501 U 3.8 1.9 + - - -
13531 A 6.0 1.6 - - - -
13571 A 5.4 1.1 - - - -
13581 U 4.8 13.5 - - - -
13591 U 5.8 0.9 - - - -
112C VAL* 4.2 7.9 - - + -
123C ARG* 3.8 36.1 + - - -
124C PHE 3.2 9.4 - - - +
125C LYS* 4.0 21.3 - - + +
142C LYS* 1.3 98.4 - - - +
144C SER* 1.3 63.6 + - - +
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Residues in contact with SER 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13491 G 2.4 27.7 + - - -
13501 U 3.9 11.0 - - - -
123C ARG* 3.5 8.5 - - - +
124C PHE* 2.4 46.0 + - - +
143C CYS* 1.3 76.9 - - - +
145C LYS* 1.3 60.4 + - - +
146C GLU 3.3 3.9 + - - +
149C THR* 3.3 20.4 - - - +
150C ALA* 3.7 28.2 - - - +
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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