Contacts of the strand formed by residues 215 - 224 (chain A) in PDB entry 3R9X
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 ALA 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A ARG* 4.4 1.1 - - - +
214A ILE* 1.3 75.6 - - - +
216A VAL* 1.3 72.1 + - - +
237A ILE* 3.5 1.7 - - - -
238A ILE* 2.8 34.6 + - + +
287A TRP* 3.7 15.2 - - + -
297A PHE* 3.4 35.2 - - + -
299A TYR* 3.4 16.4 - - - +
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Residues in contact with VAL 216 (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 ALA* 3.2 46.3 - - + +
198A VAL* 3.6 35.2 - - + -
199A ARG* 3.7 21.9 - - + +
214A ILE* 4.3 4.7 - - + -
215A ALA* 1.3 83.0 - - - +
217A LYS* 1.3 66.7 + - - +
218A ILE* 4.9 4.0 - - + -
236A GLU 3.5 11.0 - - - +
237A ILE* 4.2 9.2 - - + -
279A LEU* 5.5 2.5 - - + -
297A PHE* 4.7 12.7 - - - +
299A TYR* 3.5 10.2 + - - +
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Residues in contact with LYS 217 (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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191A ARG* 4.5 21.6 + - - +
192A LEU* 5.9 2.0 - - - +
216A VAL* 1.3 75.1 - - - +
218A ILE* 1.3 76.2 + - - +
219A ASN* 3.8 19.8 + - - +
235A GLY* 3.2 2.9 - - - -
236A GLU* 2.8 47.7 + - + +
238A ILE* 4.9 2.5 - - + +
296A LEU* 3.6 45.2 + - + +
297A PHE* 4.0 25.0 - - + +
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Residues in contact with ILE 218 (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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191A ARG* 3.3 41.0 + - + +
194A ALA* 4.0 15.7 - - + +
195A ALA* 3.8 19.1 - - + +
198A VAL* 5.5 2.7 - - + -
216A VAL* 4.2 4.2 + - + -
217A LYS* 1.3 95.2 + - - +
219A ASN* 1.3 64.5 + - - +
220A GLU 4.0 7.9 - - - +
221A ILE* 4.0 24.0 - - + -
233A ILE* 3.8 23.6 - - + -
234A LYS 3.8 5.2 - - - +
235A GLY* 4.4 9.2 - - - +
277A LEU* 5.4 4.9 - - + -
279A LEU* 5.8 1.1 - - + -
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Residues in contact with ASN 219 (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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217A LYS* 3.8 20.9 - - - +
218A ILE* 1.3 76.0 - - - +
220A GLU* 1.3 59.4 + - + +
234A LYS* 2.7 35.6 + - + +
236A GLU* 3.2 41.0 + - - +
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Residues in contact with GLU 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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218A ILE* 3.7 2.2 - - - +
219A ASN* 1.3 84.1 - - + +
221A ILE* 1.3 72.0 + - - +
222A LYS* 2.8 46.2 - - + +
232A VAL 3.8 1.5 - - - +
233A ILE* 3.6 1.9 - - - +
234A LYS* 3.0 43.1 + - + +
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Residues in contact with ILE 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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190A LEU* 3.8 29.6 - - + -
191A ARG* 4.1 28.5 - - + +
194A ALA* 6.2 0.2 - - + -
218A ILE* 4.0 11.2 - - + -
220A GLU* 1.3 80.2 - - - +
222A LYS* 1.3 65.9 + - - +
231A LEU* 3.6 33.4 - - + -
232A VAL 3.9 2.2 - - - -
233A ILE* 4.4 16.4 - - + -
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Residues in contact with LYS 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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220A GLU* 2.8 34.3 - - + +
221A ILE* 1.3 79.2 - - - +
223A PRO* 1.3 80.4 - - + +
225A ASP* 2.9 40.5 + - - +
231A LEU* 3.4 8.6 - - - +
232A VAL* 3.0 45.7 + - + +
234A LYS* 6.5 0.4 - - - -
1538C C 3.2 19.4 - - - +
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Residues in contact with PRO 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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222A LYS* 1.3 98.1 - - + +
224A GLY* 1.3 67.9 + - - +
225A ASP* 3.2 6.1 + - - +
228A PRO* 4.3 24.0 - - + +
230A MET 4.2 2.2 - - - +
231A LEU* 4.2 7.8 - - + -
273A ARG* 4.5 10.1 - - - +
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Residues in contact with GLY 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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222A LYS 3.6 0.2 + - - -
223A PRO* 1.3 71.0 - - - +
225A ASP* 1.3 69.6 + - - +
226A ALA 3.0 4.5 + - - -
227A ASN 3.2 22.1 + - - -
228A PRO* 3.7 7.5 - - - +
230A MET* 2.8 25.8 + - - -
232A VAL* 3.4 13.0 - - - -
1538C C 3.3 9.6 - - - -
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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