Contacts of the strand formed by residues 133 - 139 (chain A) in PDB entry 5FDK
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 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ARG* 4.5 8.5 - - + -
97A TYR 3.1 11.2 + - - +
98A ILE* 3.6 23.9 - - + -
99A ASP* 3.0 25.6 + - - +
128A LYS* 4.1 2.7 - - - +
131A ASP* 5.8 0.4 - - - +
132A GLY* 1.3 68.8 - - - -
134A CYS* 1.3 57.4 + - - +
135A PHE* 3.5 17.8 - - + -
146A PHE* 5.3 1.8 - - + -
148A GLU* 5.7 0.2 - - - +
193A ILE* 3.5 37.0 - - + -
197A TYR* 4.0 33.0 - - + -
198A PHE* 3.7 26.5 - - + -
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Residues in contact with CYS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASP* 3.1 14.1 - - + +
124A MET* 3.2 52.5 - - - -
127A VAL* 3.9 19.7 - - + -
128A LYS* 2.8 43.6 + - + +
132A GLY 4.4 0.7 - - - +
133A ILE* 1.3 71.8 - - - +
135A PHE* 1.3 67.1 + - - +
148A GLU* 3.6 0.7 - - - +
149A ALA* 3.1 16.9 + - - +
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Residues in contact with PHE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ILE* 4.0 4.0 - - + -
99A ASP 3.0 13.2 + - - -
100A PHE* 3.0 54.1 - + + -
101A GLU 3.0 4.5 + - - -
124A MET* 4.3 3.7 - - - +
133A ILE* 3.5 18.4 - - + -
134A CYS* 1.3 76.5 - - - +
136A VAL* 1.3 78.7 + - - +
137A ILE* 3.4 20.4 - - + -
146A PHE* 2.5 52.5 - + + -
147A LEU 3.8 10.5 - - - +
148A GLU* 4.2 7.6 - - - +
149A ALA* 4.0 7.0 - - - +
189A TYR* 4.1 5.8 - + + -
193A ILE* 3.7 26.2 - - + -
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Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A GLU 3.5 7.9 - - - +
103A LYS* 5.0 1.3 - - + +
116A PHE* 3.5 28.3 - - + -
124A MET* 4.3 6.5 - - + -
135A PHE* 1.3 88.2 - - - +
137A ILE* 1.3 69.2 + - - +
138A ILE* 3.2 26.5 - - + +
146A PHE* 3.5 2.6 - - - -
147A LEU* 2.9 44.7 + - + +
149A ALA* 5.4 0.4 - - - -
152A LEU* 3.6 37.7 - - + -
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 4.3 18.4 - - + -
100A PHE* 3.4 32.1 - - + -
101A GLU 2.9 8.5 + - - +
102A ALA* 3.2 7.9 - - + +
103A LYS 2.9 25.5 + - - -
135A PHE* 3.4 24.0 - - + -
136A VAL* 1.3 76.1 - - - +
138A ILE* 1.3 63.2 + - - +
139A SER* 4.2 1.1 + - - +
144A VAL* 3.8 26.2 - - + -
145A TYR 3.4 4.7 - - - +
146A PHE* 4.4 6.3 - - + -
179A ILE* 4.2 4.9 - - + -
187A ILE* 5.2 3.1 - - + -
189A TYR* 4.0 25.1 - - + -
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Residues in contact with ILE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS 3.1 10.3 - - - +
111A PHE* 3.7 40.2 - - + -
136A VAL* 3.2 38.1 - - + +
137A ILE* 1.3 76.8 - - - +
139A SER* 1.3 63.3 + - - +
140A ALA* 3.7 9.0 + - + +
143A GLN 3.7 1.2 - - - +
144A VAL* 3.4 2.1 - - - +
145A TYR* 2.8 44.1 + - + +
147A LEU* 3.6 28.9 - - + +
172A LEU* 4.1 20.4 - - + -
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Residues in contact with SER 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG 3.6 4.5 + - - +
32A GLY 2.9 36.3 + - - -
33A MET 5.6 0.2 - - - -
103A LYS 2.9 9.9 + - - -
104A GLU* 3.1 16.0 - - - +
105A THR 2.9 24.6 + - - +
137A ILE* 4.2 1.5 - - - -
138A ILE* 1.3 73.6 - - - +
140A ALA* 1.3 59.2 + - - +
143A GLN 3.6 8.3 + - - -
144A VAL* 4.4 18.3 - - - +
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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