Contacts of the strand formed by residues 220 - 226 (chain A) in PDB entry 2NN6
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 LEU 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A LYS* 6.3 1.6 - - - +
146A ILE* 5.2 6.5 - - + -
195A SER* 3.5 29.6 - - - +
196A PHE* 3.1 29.2 - - - +
197A ALA* 3.3 17.0 - - + +
198A PHE* 3.8 2.5 - - - -
209A PRO* 4.7 11.0 - - + -
214A GLU* 5.9 0.7 - - - +
217A MET* 3.1 22.1 - - + +
219A GLY* 1.3 71.1 - - - -
221A LEU* 1.3 66.3 + - - +
222A VAL* 4.0 10.5 - - + -
235A GLN* 3.7 0.7 - - - +
237A SER* 2.5 52.2 + - - +
240A ILE* 5.2 1.3 - - - -
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Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A SER* 2.9 3.1 - - - -
196A PHE* 2.4 66.2 + - + -
198A PHE* 3.5 19.0 - - + -
220A LEU* 1.3 74.1 - - - +
222A VAL* 1.3 78.4 + - - +
223A ILE* 3.9 14.1 - - + -
234A ILE* 4.4 4.3 - - + -
235A GLN 3.2 26.7 - - - +
236A SER* 4.2 5.6 - - - +
240A ILE* 6.2 0.2 - - + -
242A LEU* 5.7 4.0 - - + -
247A VAL* 5.7 1.3 - - - +
250A CYS* 4.3 12.6 - - + -
198B LEU* 3.7 22.2 - - + -
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Residues in contact with VAL 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU* 4.8 10.1 - - + -
146A ILE* 5.2 10.1 - - + -
147A ASP* 5.0 0.7 - - - +
193A CYS* 4.2 14.6 - - + -
194A VAL 3.1 15.0 - - - +
195A SER* 3.3 21.5 - - - +
220A LEU* 4.0 8.3 - - + -
221A LEU* 1.3 98.3 - - - +
223A ILE* 1.3 74.0 + - - +
234A ILE* 3.4 2.7 - - - -
235A GLN* 2.9 48.3 + - + +
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Residues in contact with ILE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ILE 3.2 4.7 - - - +
193A CYS* 3.4 5.2 - - - +
194A VAL* 2.8 33.7 + - + +
196A PHE* 3.9 2.5 - - + -
221A LEU* 3.9 21.8 - - + -
222A VAL* 1.3 73.3 - - - +
224A ALA* 1.3 63.4 + - - +
225A MET* 3.7 18.8 - - + -
231A ILE* 4.9 4.9 - - + -
233A THR 3.1 7.6 - - - -
234A ILE* 3.2 25.1 - - + -
247A VAL 5.5 0.4 - - - +
251A SER* 3.2 42.2 - - - +
254A ALA* 3.3 30.3 - - + -
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Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A CYS* 4.2 11.7 - - + -
191A PRO* 5.0 3.4 - - + -
192A ILE 3.3 9.4 - - - +
193A CYS* 5.5 2.7 - - - -
223A ILE* 1.3 76.2 - - - +
225A MET* 1.3 60.0 + - - +
226A ASN 4.3 0.2 - - - -
231A ILE* 2.8 9.5 - - - +
232A CYS* 2.7 36.4 + - + -
233A THR* 2.5 42.1 + - - +
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Residues in contact with MET 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A MET 4.2 0.7 - - - +
191A PRO* 4.1 3.3 - - - +
192A ILE* 3.6 18.9 + - - +
223A ILE* 3.7 11.6 - - + +
224A ALA* 1.3 79.9 - - - +
226A ASN* 1.3 63.0 + - - +
229A ARG* 3.3 34.8 - - - +
230A GLU 3.0 7.2 - - - +
231A ILE* 4.3 9.9 - - + -
251A SER* 3.4 13.5 - - - +
254A ALA* 3.7 6.5 - - - -
255A GLY* 2.9 44.6 - - - -
258A VAL* 3.3 32.4 - - + +
206B GLU* 3.4 19.1 - - + -
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Residues in contact with ASN 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A SER* 3.5 3.4 + - - +
189A HIS* 2.7 29.0 - - - +
190A MET* 2.4 51.5 + - - +
191A PRO* 3.1 13.9 - - + +
225A MET* 1.3 74.0 - - - +
227A LYS* 1.3 67.0 + - - +
228A HIS* 2.4 27.7 + - - -
229A ARG* 2.9 9.2 + - - -
230A GLU* 2.7 35.2 + - - +
232A CYS* 4.7 5.9 - - - -
258A VAL* 4.9 1.8 - - - +
203B ARG* 6.2 0.2 - - - -
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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