Contacts of the strand formed by residues 223 - 229 (chain F) in PDB entry 2CNW
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 GLU 223 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99F GLU 4.3 1.9 - - - +
100F PRO* 3.4 13.3 - - + +
101F LYS* 2.7 34.5 + - - +
102F GLY 5.1 0.2 - - - +
104F VAL 3.4 6.3 + - - +
105F VAL* 3.7 27.4 - - + -
106F LEU 3.0 22.3 + - - -
221F PRO* 3.7 4.7 - - - +
222F LYS* 1.3 80.1 - - + +
224F VAL* 1.3 64.8 + - - +
225F TRP* 2.7 39.0 + - + +
250F THR* 2.7 32.0 + - - +
278F LYS* 4.3 8.2 + - - -
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Residues in contact with VAL 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F LEU* 3.3 15.5 - - + +
108F VAL* 4.3 9.2 - - + -
210F LYS* 3.9 17.7 - - - +
221F PRO* 4.3 12.6 - - + +
222F LYS 4.0 2.4 + - - +
223F GLU* 1.3 77.2 - - - +
225F TRP* 1.3 63.5 + - - +
247F VAL* 3.7 28.0 - - + +
248F GLY 3.3 25.8 - - - +
249F LEU* 3.5 20.8 - - + -
250F THR* 2.8 33.7 + - + -
251F GLY 3.5 1.9 + - - +
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Residues in contact with TRP 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F VAL* 4.8 3.6 - - + -
99F GLU 5.6 0.4 - - - -
100F PRO* 4.6 13.5 - - + -
105F VAL* 3.6 22.2 - - + -
106F LEU 2.7 12.8 + - - +
107F VAL* 3.4 11.5 - - + +
108F VAL* 3.0 25.3 + - - -
122F LEU* 4.1 16.6 - - + -
126F TYR* 4.1 12.6 - - - -
189F PHE* 4.5 4.5 - + - -
223F GLU* 2.7 41.7 + - + -
224F VAL* 1.3 81.7 - - - +
226F LEU* 1.3 64.0 + - - +
227F VAL* 5.7 0.4 - - + -
250F THR* 3.4 6.9 + - - -
251F GLY* 3.5 17.9 - - - +
253F ILE* 3.8 25.4 - - + -
278F LYS* 3.8 27.7 - - + +
279F PHE* 3.6 29.8 - + - -
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Residues in contact with LEU 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F VAL* 3.4 17.6 - - + +
109F GLY* 3.9 13.9 - - - -
224F VAL 4.0 1.4 + - - -
225F TRP* 1.3 72.2 - - - +
227F VAL* 1.3 69.6 + - - +
228F LEU* 4.2 18.4 - - + -
239F GLN* 4.7 6.5 - - + +
240F ALA* 3.9 31.9 - - + +
243F PHE* 4.0 27.6 - - + -
249F LEU* 3.7 22.8 - - + +
251F GLY 2.9 11.3 + - - +
252F VAL* 3.4 15.3 - - + +
253F ILE* 2.8 28.4 + - - +
269F ILE* 5.5 0.7 - - + -
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Residues in contact with VAL 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F VAL* 3.6 30.1 - - + -
108F VAL 2.6 11.5 + - - -
109F GLY* 4.0 9.0 - - - -
110F VAL 4.6 0.7 + - - -
113F VAL* 3.4 37.3 - - + +
114F GLY 4.2 0.4 - - - -
115F LYS* 3.7 24.5 - - + +
118F THR* 4.4 8.3 - - + +
225F TRP* 4.4 1.8 - - + +
226F LEU* 1.3 80.2 - - - +
228F LEU* 1.3 62.8 - - - +
239F GLN* 4.8 1.9 - - - +
253F ILE* 3.5 15.5 - - + +
255F THR* 3.7 28.5 - - + -
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Residues in contact with LEU 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F VAL* 5.1 0.7 - - - -
226F LEU* 4.2 13.2 - - + -
227F VAL* 1.3 74.6 - - - +
229F ASP* 1.3 69.5 + - - +
232F THR* 4.8 2.0 - - - +
236F GLY* 3.8 29.4 - - - +
239F GLN* 3.8 18.4 - - - +
252F VAL* 4.2 10.8 - - + -
253F ILE 2.7 14.0 + - - +
254F VAL* 3.1 8.9 - - + +
255F THR* 2.8 29.8 + - - -
263F GLY* 6.3 0.4 - - - -
265F VAL* 3.8 14.1 - - + -
266F LEU* 3.6 31.9 - - + -
269F ILE* 3.6 17.0 - - + -
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Residues in contact with ASP 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C GLN 4.5 0.7 - - - +
219C ASP* 5.3 2.4 - - - +
221C MET* 4.3 8.0 - - + +
112F GLY 4.3 2.4 - - - +
113F VAL* 3.8 22.3 - - + +
228F LEU* 1.3 77.2 - - - +
230F ALA* 1.3 67.4 + - - +
231F VAL* 3.1 29.7 + - - +
232F THR* 2.6 35.1 + - - +
239F GLN* 5.4 0.6 + - - -
254F VAL* 4.7 0.4 - - - -
255F THR* 3.6 8.1 - - - -
256F LYS* 2.8 43.2 + - - +
265F VAL* 5.5 0.9 - - - +
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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