Contacts of the strand formed by residues 223 - 229 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98E VAL* 6.1 0.2 - - - +
99E GLU 4.1 3.1 - - - +
100E PRO* 3.3 11.6 - - + +
101E LYS* 2.9 40.3 + - + +
102E GLY 4.8 0.7 - - - +
104E VAL 3.4 4.6 + - - +
105E VAL* 3.5 30.1 - - + -
106E LEU* 2.8 25.6 + - - +
221E PRO* 3.9 1.7 - - - +
222E LYS* 1.3 81.5 - - + +
224E VAL* 1.3 65.5 + - - +
225E TRP* 3.2 27.7 + - + +
250E THR* 2.5 34.1 + - - +
278E LYS* 4.3 9.5 + - - -
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Residues in contact with VAL 224 (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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106E LEU* 3.3 25.8 - - + +
108E VAL* 4.3 11.2 - - + -
210E LYS* 4.8 4.5 - - + -
221E PRO* 4.3 14.8 - - + +
222E LYS 5.4 0.2 - - - +
223E GLU* 1.3 79.9 - - - +
225E TRP* 1.3 62.7 + - - +
247E VAL* 3.8 28.3 - - + +
248E GLY 3.4 19.5 - - - +
249E LEU* 3.6 23.3 - - + -
250E THR* 2.8 34.5 + - + +
251E GLY 3.5 0.9 + - - +
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Residues in contact with TRP 225 (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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98E VAL* 4.8 4.9 - - + -
100E PRO* 4.9 5.4 - - + -
105E VAL* 3.6 25.6 - - + -
106E LEU 2.8 12.1 + - - +
107E VAL* 3.5 10.0 - - + +
108E VAL* 3.0 26.4 + - - -
122E LEU* 3.8 31.0 - - + -
126E TYR* 4.1 15.5 - + - -
189E PHE* 4.3 3.8 - + - -
223E GLU* 3.2 40.5 + - + -
224E VAL* 1.3 81.9 - - - +
226E LEU* 1.3 63.6 + - - +
227E VAL 3.8 0.2 + - - -
250E THR* 3.5 7.1 + - - -
251E GLY* 3.3 17.7 - - - +
253E ILE* 3.6 26.9 - - + -
278E LYS* 3.8 25.7 - - + +
279E PHE* 3.9 18.2 - + - -
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Residues in contact with LEU 226 (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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108E VAL* 3.4 12.8 - - + +
109E GLY* 4.1 4.0 - - - -
224E VAL 4.1 0.6 + - - -
225E TRP* 1.3 73.0 - - - +
227E VAL* 1.3 77.2 + - - +
228E LEU* 4.3 17.5 - - + +
239E GLN* 4.7 7.0 - - + +
240E ALA* 3.9 32.1 - - + +
243E PHE* 4.0 33.7 - - + -
249E LEU* 3.9 20.9 - - + +
251E GLY 2.9 7.7 + - - -
252E VAL* 3.4 21.9 - - + +
253E ILE* 2.8 29.8 + - - +
269E ILE* 5.5 0.9 - - + -
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Residues in contact with VAL 227 (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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107E VAL* 3.5 31.9 - - + -
108E VAL 2.8 10.5 + - - +
109E GLY* 4.1 3.5 - - - -
113E VAL* 3.4 34.6 - - + +
114E GLY 4.0 8.3 - - - -
115E LYS* 3.8 18.4 - - + -
118E THR* 4.2 12.8 - - + +
225E TRP 4.4 0.4 - - - +
226E LEU* 1.3 87.8 - - - +
228E LEU* 1.3 61.9 - - - +
239E GLN* 4.8 2.9 - - - +
253E ILE* 3.5 9.4 - - + +
255E THR* 3.6 29.2 - - + -
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Residues in contact with LEU 228 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113E VAL* 4.6 1.1 - - - -
226E LEU* 3.9 15.0 + - + -
227E VAL* 1.3 74.6 - - - +
229E ASP* 1.3 64.4 + - - +
230E ALA* 6.1 0.4 - - - -
232E THR* 4.9 2.5 - - - +
236E GLY* 3.9 31.9 - - - +
239E GLN* 4.2 12.1 - - + +
252E VAL* 4.2 10.8 - - + -
253E ILE 2.9 10.7 + - - +
254E VAL* 3.1 11.3 - - + -
255E THR* 2.7 34.7 + - - -
263E GLY* 5.5 0.9 - - - +
265E VAL* 3.9 16.2 - - + -
266E LEU* 4.0 24.5 - - + -
269E ILE* 3.7 23.1 - - + -
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Residues in contact with ASP 229 (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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107B GLN 4.3 1.9 - - - +
219B ASP* 5.7 0.2 - - - +
221B MET* 4.5 8.0 - - + +
112E GLY 5.2 0.3 - - - -
113E VAL* 3.9 25.2 - - + +
228E LEU* 1.3 76.1 - - - +
230E ALA* 1.3 66.4 + - - +
231E VAL* 3.0 30.6 + - - +
232E THR* 2.5 35.5 + - - +
239E GLN* 5.7 0.2 + - - -
254E VAL* 4.6 0.4 - - - -
255E THR* 3.3 9.2 + - - +
256E LYS* 2.6 45.4 + - - +
265E VAL* 5.6 0.5 - - - +
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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