Contacts of the strand formed by residues 217 - 222 (chain B) in PDB entry 2NS2
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 217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B MET* 4.8 7.2 - - + -
131B LEU* 4.5 4.7 - - + -
210B GLN* 3.7 2.3 - - - +
211B VAL* 2.8 43.1 + - + -
214B LYS* 2.9 43.5 + - + +
216B SER* 1.3 81.8 - - - +
218B TYR* 1.3 70.6 + - - +
230B VAL* 3.4 32.3 - - + -
231B TYR 3.4 8.3 - - - +
232B ASP* 3.9 14.8 - - + +
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Residues in contact with TYR 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B VAL 4.8 2.3 + - - -
186B ASP 3.5 6.8 + - - -
187B SER* 3.5 3.9 - - - -
188B LEU* 3.2 43.3 + - + +
189B VAL* 4.0 3.1 - - + -
207B VAL* 3.4 24.0 - - + -
209B HIS 3.2 19.1 - - - +
210B GLN* 3.2 38.9 + - + -
211B VAL 4.7 0.7 - - - +
215B PRO 3.6 12.4 + - - -
216B SER* 3.8 9.2 - - - -
217B VAL* 1.3 76.5 - - - +
219B PHE* 1.3 66.8 + - - +
220B ILE* 3.9 5.2 + - + +
229B TYR 3.5 0.9 - - - +
230B VAL* 3.3 5.9 - - - +
231B TYR 2.8 36.6 + - - +
233B LEU* 3.5 34.8 - - + -
234B VAL* 5.4 2.5 - - + -
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Residues in contact with PHE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU* 5.0 2.7 - - + -
131B LEU* 3.9 11.4 - - + -
132B ALA* 6.2 0.7 - - + -
142B TYR* 3.8 29.2 - + + -
151B LEU* 3.6 25.8 - - + -
207B VAL* 3.7 1.6 - - - +
208B ILE* 2.9 37.0 + - + -
209B HIS* 2.9 37.6 + + + +
211B VAL* 3.8 24.9 - - + -
218B TYR* 1.3 77.3 - - - +
220B ILE* 1.3 63.7 + - - +
228B ILE* 3.8 19.7 - - + -
229B TYR 3.2 2.9 - - - -
230B VAL* 3.6 28.7 - - + -
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Residues in contact with ILE 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B VAL* 4.0 23.6 - - + -
195B TYR* 4.5 2.7 - - + +
206B MET 3.4 10.1 - - - +
207B VAL* 4.3 10.5 - - + -
208B ILE* 4.8 0.7 - - - -
218B TYR* 4.6 7.0 - - + +
219B PHE* 1.3 79.3 - - - +
221B LYS* 1.3 65.6 + - - +
222B PHE* 3.8 31.1 + - + -
228B ILE* 3.8 6.1 - - - +
229B TYR* 2.7 42.4 + - + +
231B TYR* 3.9 31.0 - - + +
233B LEU* 4.1 24.9 - - + -
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Residues in contact with LYS 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.7 29.2 - - + -
74B GLY 3.3 24.2 + - - -
75B LEU* 5.2 0.4 - - - +
76B GLU* 5.7 3.6 - - - +
205B GLY* 3.4 0.7 - - - -
206B MET* 2.9 39.4 + - + +
208B ILE* 4.1 20.6 - - + +
220B ILE* 1.3 74.6 - - - +
222B PHE* 1.3 72.7 + - - +
223B ASP* 3.9 7.7 + - - +
225B ASP 2.8 28.9 + - - +
226B PHE* 4.5 0.4 - - - +
227B HIS 4.3 3.4 - - - +
228B ILE* 4.0 18.8 - - + -
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Residues in contact with PHE 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B VAL* 4.6 2.5 - - + -
195B TYR* 3.5 33.4 - + - -
203B ARG* 3.5 54.1 - - + +
204B THR 3.5 19.1 - - - +
205B GLY* 3.6 10.1 - - - -
220B ILE* 3.8 18.7 + - + -
221B LYS* 1.3 94.5 + - - +
223B ASP* 1.3 65.3 + - - +
224B ASP* 3.2 17.8 + - - +
225B ASP 3.3 8.5 + - - +
227B HIS 4.9 0.4 + - - -
229B TYR* 3.7 31.6 - + + -
231B TYR* 3.8 19.3 - + - -
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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