Contacts of the strand formed by residues 217 - 222 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A MET* 4.8 6.3 - - + -
131A LEU* 4.3 7.0 - - + -
210A GLN* 3.9 1.9 - - - +
211A VAL* 3.1 36.4 + - + -
214A LYS* 2.8 45.9 + - + +
216A SER* 1.3 86.5 - - - +
218A TYR* 1.3 67.2 + - - +
230A VAL* 3.4 30.1 - - + -
231A TYR* 3.4 10.8 - - - +
232A ASP* 4.2 11.2 - - + +
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Residues in contact with TYR 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ASP 3.3 6.8 + - - -
187A SER* 3.2 4.2 - - - -
188A LEU* 3.0 43.6 + - + -
189A VAL* 3.9 7.0 - - + -
207A VAL* 3.4 27.8 - - + -
209A HIS 3.3 16.6 - - - +
210A GLN* 2.8 43.0 + - + -
215A PRO 3.5 13.8 + - - -
216A SER* 3.4 16.8 - - - -
217A VAL* 1.3 74.3 - - - +
219A PHE* 1.3 67.4 + - - +
220A ILE* 4.0 2.0 + - + +
229A TYR 3.6 0.2 - - - +
230A VAL* 3.2 7.0 - - - +
231A TYR* 2.7 34.4 + - - +
233A LEU* 3.8 23.8 - - + -
234A VAL* 4.6 4.6 - - + +
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Residues in contact with PHE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 4.8 5.8 - - + -
131A LEU* 3.8 18.8 - - + -
132A ALA* 6.3 0.2 - - + -
142A TYR* 3.7 32.8 - + - -
151A LEU* 3.5 31.4 - - + -
207A VAL* 3.5 2.4 - - - +
208A ILE* 3.0 35.6 + - + -
209A HIS* 2.9 38.1 + + + +
211A VAL* 3.8 25.1 - - + -
218A TYR* 1.3 80.2 - - - +
220A ILE* 1.3 64.1 + - - +
228A ILE* 3.8 14.6 - - + -
229A TYR 3.2 3.6 - - - -
230A VAL* 4.1 12.6 - - + -
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Residues in contact with ILE 220 (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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193A VAL* 4.0 22.4 - - + -
206A MET 3.4 9.0 - - - +
207A VAL* 4.0 15.3 - - + -
208A ILE* 4.7 0.7 - - - -
218A TYR 4.8 2.2 - - - +
219A PHE* 1.3 80.4 - - - +
221A LYS* 1.3 67.2 + - - +
222A PHE* 3.5 34.5 + - + -
228A ILE* 3.7 7.2 - - - +
229A TYR* 2.7 38.4 + - + +
231A TYR* 3.7 31.2 - - + +
233A LEU* 4.1 26.5 - - + -
43B PRO* 5.8 2.0 - - + -
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Residues in contact with LYS 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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61A LEU* 4.1 26.0 - - + -
74A GLY 3.5 25.1 - - - -
75A LEU* 5.6 0.2 - - - +
205A GLY* 3.2 2.1 - - - -
206A MET* 2.9 34.2 + - + +
208A ILE* 4.1 21.4 - - + +
220A ILE* 1.3 75.0 - - - +
222A PHE* 1.3 69.1 + - - +
223A ASP* 4.0 8.0 + - - +
225A ASP 3.0 28.8 + - - +
226A PHE* 4.1 1.9 - - - +
227A HIS 4.3 2.2 - - - +
228A ILE* 4.0 17.9 - - + -
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Residues in contact with PHE 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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193A VAL* 4.2 11.9 - - + -
194A GLU* 5.2 1.1 - - - -
195A TYR* 3.5 33.4 - + - -
203A ARG* 3.6 32.8 - - + +
204A THR 3.5 16.6 - - - +
205A GLY 4.2 0.4 - - - -
220A ILE* 3.5 27.9 + - + -
221A LYS* 1.3 95.6 + - - +
223A ASP* 1.3 59.9 + - - +
224A ASP* 3.1 20.5 + - - +
225A ASP* 3.1 12.9 + - + +
227A HIS 4.9 2.4 + - - -
229A TYR* 3.6 27.8 - + + -
231A TYR* 3.6 25.6 - + - -
43B PRO* 5.8 1.6 - - + -
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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