Contacts of the strand formed by residues 234 - 239 (chain E) 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 VAL 234 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94E GLN* 3.6 31.4 - - + +
95E LEU 3.4 14.4 - - - +
96E VAL* 4.5 8.1 - - + -
109E TRP* 4.1 3.6 - - - -
144E PHE* 4.6 7.9 - - + -
145E PHE* 3.1 7.1 - - - +
146E GLN* 2.9 46.2 + - + +
231E GLY 4.0 3.4 - - - +
232E ALA 3.4 14.3 + - - +
233E THR* 1.3 80.9 - - - +
235E LEU* 1.3 65.2 + - - +
236E GLY 4.4 0.7 - - - +
202F ARG* 3.7 25.8 - - + +
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Residues in contact with LEU 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E GLN* 3.3 1.7 - - - -
95E LEU* 2.7 38.4 + - + +
109E TRP* 3.6 27.3 - - + +
133E LEU* 4.5 28.3 - - + -
143E VAL* 4.0 22.0 - - + -
144E PHE 3.6 10.5 - - - +
145E PHE* 4.0 10.8 - - + -
165E LEU* 4.3 17.7 - - + -
212E LEU* 5.3 4.3 - - + +
214E VAL* 3.8 22.9 - - + -
234E VAL* 1.3 75.2 - - - +
236E GLY* 1.3 65.6 + - - +
237E LEU* 5.7 1.1 - - + -
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Residues in contact with GLY 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E ALA 3.4 11.9 - - - -
94E GLN* 4.0 3.4 - - - -
143E VAL* 3.5 3.5 - - - +
144E PHE* 2.8 59.0 + - - +
235E LEU* 1.3 76.4 - - - +
237E LEU* 1.3 64.6 + - - +
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Residues in contact with LEU 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E PHE* 3.3 4.6 - - - +
93E ALA* 2.9 50.1 + - + +
124E LEU* 3.9 26.2 - - + -
133E LEU* 3.8 24.7 - - + -
135E VAL* 4.9 2.5 - - + -
141E TYR* 4.1 13.7 - - + -
142E TYR 3.2 13.9 - - - +
143E VAL* 3.9 27.6 - - + -
144E PHE* 3.8 2.8 - - - -
206E LEU* 4.4 16.6 - - + -
212E LEU* 5.8 4.5 - - + -
235E LEU* 5.7 2.2 - - + -
236E GLY* 1.3 75.0 - - - +
238E PHE* 1.3 64.8 - - - +
203F LEU* 4.2 1.4 - - - +
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Residues in contact with PHE 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C PHE* 3.8 31.2 - + - -
91E MET 3.6 6.5 - - - +
92E PHE* 3.6 15.7 - - + +
141E TYR* 3.3 7.3 - - - -
142E TYR* 3.0 63.6 + + + -
144E PHE* 4.3 4.3 - + - -
237E LEU* 1.3 79.1 - - - +
239E ARG* 1.3 72.8 + - - +
240E VAL* 4.5 2.9 - - + -
142F TYR* 4.1 22.2 - + + -
203F LEU* 4.2 15.9 - - + -
238F PHE* 3.9 18.6 - + - -
240F VAL* 3.9 18.6 - - + -
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Residues in contact with ARG 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E MET* 3.0 29.2 + - + +
140E VAL 3.8 2.5 - - - +
141E TYR* 3.4 29.3 - - + +
238E PHE* 1.3 80.4 - - - +
240E VAL* 1.3 62.3 + - - +
241E THR 4.1 13.2 - - - +
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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