Contacts of the strand formed by residues 133 - 140 (chain C) in PDB entry 3DC5
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C ARG* 3.7 11.4 - - - +
99C ASP* 3.4 15.5 - - - +
127C TYR* 3.6 6.6 - - - -
128C CYS* 2.8 30.2 + - + +
131C ASP* 3.5 30.1 - - + +
132C LYS* 1.3 81.7 - - - +
134C LEU* 1.3 64.1 + - - +
135C LYS* 3.7 32.8 - - + -
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Residues in contact with LEU 134 (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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92C LEU* 4.2 4.9 - - + -
95C THR* 3.7 19.5 - - + +
96C ILE* 3.7 45.8 - - + +
99C ASP* 2.8 15.1 + - - +
100C PHE* 3.6 27.3 - - + -
125C LEU* 4.2 8.3 - - + -
126C GLY 3.3 6.1 - - - +
127C TYR* 3.9 6.0 - - + -
133C ILE* 1.3 80.1 - - - +
135C LYS* 1.3 67.2 + - - +
151C LEU* 3.5 32.8 - - + -
189C PHE* 3.8 15.9 - - + -
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Residues in contact with LYS 135 (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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100C PHE* 4.1 5.4 - - - -
125C LEU* 3.6 4.7 - - - +
126C GLY 2.8 31.6 + - - -
128C CYS* 3.6 32.0 - - + -
131C ASP* 4.6 7.5 + - - -
133C ILE* 3.7 28.9 - - + +
134C LEU* 1.3 80.5 - - - +
136C ILE* 1.3 67.2 + - - +
148C MET* 3.7 28.9 - - + +
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Residues in contact with ILE 136 (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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100C PHE* 3.9 16.0 - - + -
106C LEU* 3.6 28.5 - - + -
109C ARG* 3.7 53.8 - - + +
110C LEU* 3.7 10.3 - - + +
113C ILE* 3.9 19.6 - - + +
124C TRP 3.2 11.2 - - - +
125C LEU* 4.2 5.2 - - + -
135C LYS* 1.3 82.0 - - - +
137C ALA* 1.3 65.3 + - - +
148C MET* 5.1 0.5 - - - +
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Residues in contact with ALA 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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113C ILE* 3.7 7.5 - - - +
123C GLY* 3.6 2.1 - - - -
124C TRP* 2.8 33.1 + - - +
136C ILE* 1.3 77.5 - - - +
138C THR* 1.3 68.8 + - - +
145C LEU* 4.0 24.2 - - + -
148C MET* 4.1 14.1 - - + -
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Residues in contact with THR 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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113C ILE* 3.5 44.6 - - + +
114C THR 4.2 1.3 - - - +
117C VAL* 3.7 18.2 - - + +
122C TRP 3.1 11.9 - - - +
123C GLY* 4.3 2.7 - - - -
124C TRP* 5.2 0.2 - - - -
137C ALA* 1.3 83.0 - - - +
139C CYS* 1.3 71.6 + - - +
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Residues in contact with CYS 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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117C VAL* 5.0 2.4 - - - +
121C GLY* 3.2 3.8 - - - -
122C TRP* 2.9 35.6 + - + +
124C TRP* 3.7 20.6 - - - +
138C THR* 1.3 82.5 - - - +
140C ALA* 1.3 59.5 + - - +
141C ASN 5.1 0.2 - - - -
143C ASP* 3.2 31.9 - - + +
144C PRO 4.1 2.5 - - - -
145C LEU* 3.7 31.9 - - - -
146C GLU 5.2 0.2 - - - -
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Residues in contact with ALA 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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117C VAL* 5.8 1.8 - - - -
120C SER 3.9 6.1 - - - +
139C CYS* 1.3 73.6 - - - +
141C ASN* 1.3 78.7 + - - +
143C ASP* 2.9 36.8 + - - +
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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