Contacts of the strand formed by residues 139 - 146 (chain C) in PDB entry 6CU0
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 GLY 139 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138C ALA* 1.3 78.8 - - - +
140C VAL* 1.3 61.5 + - - -
141C TYR* 3.7 8.4 - - - -
205C HIS* 3.5 2.5 - - - +
206C LEU* 2.8 34.7 + - - +
241C THR* 4.4 13.9 - - - -
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Residues in contact with VAL 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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139C GLY* 1.3 73.9 - - - -
141C TYR* 1.3 67.2 - - - +
203C LEU* 4.0 29.6 - - + -
204C LEU 3.5 7.2 - - - +
205C HIS* 4.0 21.1 - - + -
239C ARG* 3.8 1.2 - - - +
240C VAL* 2.9 25.2 + - + -
241C THR* 3.2 22.1 + - - +
92F PHE* 3.5 39.0 - - + -
119F SER* 5.6 4.3 - - - +
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Residues in contact with TYR 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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91C MET* 4.3 11.6 - - + +
124C LEU* 5.1 4.5 - - + +
135C VAL* 3.4 14.8 - - + +
137C LYS* 2.6 35.2 + - - +
138C ALA 4.2 2.2 + - - -
139C GLY* 3.7 23.6 - - - -
140C VAL* 1.3 79.0 - - - +
142C TYR* 1.3 61.4 + - - +
143C VAL* 3.5 17.9 + - + +
203C LEU* 3.2 7.2 - - - -
204C LEU* 2.8 33.5 + - - +
206C LEU* 3.6 25.4 - - + -
237C LEU* 4.1 20.6 - - + -
238C PHE 3.3 9.2 - - - +
239C ARG* 3.4 37.7 - - + +
240C VAL 4.3 0.7 - - - +
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Residues in contact with TYR 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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141C TYR* 1.3 69.4 - - - +
143C VAL* 1.3 58.0 + - - +
144C PHE* 3.9 16.5 - + + -
199C PHE* 3.8 5.2 - - - -
201C GLY* 3.9 20.8 - - - -
202C ARG 3.6 13.5 - - - -
203C LEU* 4.0 12.3 - - + +
236C GLY 4.1 0.2 - - - +
237C LEU* 3.2 4.2 - - - -
238C PHE* 3.0 63.7 + + + -
240C VAL* 4.0 2.7 - - + +
142E TYR* 3.3 35.3 + + - -
142F TYR* 3.3 27.9 + + - -
144F PHE* 4.0 14.8 - + - -
199F PHE* 3.4 16.1 - - - -
238F PHE* 3.7 16.8 - + + -
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Residues in contact with VAL 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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141C TYR* 3.9 17.9 - - + +
142C TYR* 1.3 74.6 - - - +
144C PHE* 1.3 64.5 + - - +
165C LEU* 4.1 19.3 - - + -
179C LEU* 3.8 8.9 - - + +
201C GLY* 3.1 1.7 - - - -
202C ARG 2.9 30.3 + - - +
204C LEU* 3.7 27.8 - - + -
206C LEU* 4.6 4.7 - - + -
235C LEU* 4.0 19.7 - - + -
236C GLY 3.5 10.1 - - - +
237C LEU* 3.9 22.9 - - + -
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Residues in contact with PHE 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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94C GLN* 3.6 18.8 - - - -
142C TYR* 3.9 22.4 - + + -
143C VAL* 1.3 75.2 - - - +
145C PHE* 1.3 66.3 + - - +
146C GLN* 5.3 2.0 - - + -
179C LEU* 4.1 3.4 - - - -
199C PHE* 3.6 31.6 - + + -
200C GLN 3.1 12.8 - - - +
201C GLY* 3.7 3.8 - - - -
234C VAL* 4.6 6.5 - - + -
235C LEU* 3.6 2.3 - - - +
236C GLY* 2.8 63.5 + - - +
237C LEU* 3.8 4.7 - - - -
238C PHE* 4.3 4.5 - + - -
142E TYR* 4.0 13.7 - + - -
201E GLY 4.0 1.6 - - - -
202E ARG* 3.8 20.9 - - + -
203E LEU* 3.9 18.4 - - + -
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Residues in contact with PHE 145 (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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109C TRP* 5.9 0.2 - - + -
144C PHE* 1.3 75.5 - - - +
146C GLN* 1.3 60.8 + - - +
163C LEU* 3.7 39.7 - - + -
165C LEU* 3.8 24.2 - - + -
179C LEU* 3.6 44.6 - - + +
180C ALA* 3.9 7.2 - - - -
181C LEU* 3.7 27.5 - - + +
199C PHE* 3.5 5.4 - - - -
200C GLN* 2.8 37.1 + - + +
214C VAL* 4.1 12.1 - - + -
234C VAL 3.2 14.4 - - - +
235C LEU* 4.0 17.5 - - + -
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Residues in contact with GLN 146 (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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144C PHE* 5.5 2.0 - - + -
145C PHE* 1.3 75.3 - - - +
147C LEU* 1.3 65.3 + - - +
148C GLU* 5.6 0.7 - - + +
163C LEU* 4.1 3.0 - - - +
181C LEU* 4.8 0.7 - - - -
198C GLY 3.3 7.2 - - - +
199C PHE* 4.1 9.1 - - + +
232C ALA* 3.3 21.0 + - - +
233C THR* 3.5 6.1 - - - +
234C VAL* 2.9 35.2 + - + +
200E GLN* 3.3 37.4 + - - +
201E GLY 2.8 28.9 + - - +
202E ARG* 3.4 36.1 - - - +
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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