Contacts of the strand formed by residues 219 - 226 (chain A) in PDB entry 3ATA
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 LYS 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A MET* 3.4 3.8 - - - +
216A ARG 2.9 32.7 + - - +
217A ASP* 3.0 13.9 + - + +
218A GLY* 1.3 85.4 + - - +
220A LEU* 1.3 62.4 + - - +
221A CYS* 3.4 5.0 - - - -
284A GLU* 3.5 44.6 - - + +
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Residues in contact with LEU 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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213A ILE* 3.9 21.1 - - + -
214A SER* 4.0 13.5 - - - -
215A MET* 3.7 25.1 - - + +
218A GLY 4.2 0.6 + - - -
219A LYS* 1.3 72.8 - - - +
221A CYS* 1.3 56.8 + - - +
284A GLU* 3.7 1.9 - - - +
285A ILE* 2.7 47.3 + - + +
294A ILE 5.5 0.2 - - - +
334A TRP* 4.0 29.6 - - + -
364A THR* 4.3 11.4 - - + -
365A PRO* 5.3 1.3 - - + +
367A LEU 4.4 3.4 - - - +
369A ALA* 4.1 31.0 - - + +
372A LEU* 4.6 10.3 - - + +
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Residues in contact with CYS 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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212A VAL 3.7 0.7 - - - +
213A ILE* 2.9 8.0 - - - +
214A SER 2.9 36.6 + - - +
216A ARG* 4.1 16.8 - - + -
219A LYS* 3.4 17.7 - - - -
220A LEU* 1.3 82.7 - - - +
222A LEU* 1.3 60.1 + - - +
223A MET* 3.9 11.1 - - + +
282A SER* 3.6 25.4 - - - +
283A HIS 3.5 4.5 - - - +
284A GLU* 4.0 15.5 - - - -
285A ILE* 4.0 5.8 - - - -
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Residues in contact with LEU 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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211A ALA* 4.0 21.5 - - + -
212A VAL 3.3 11.4 - - - +
213A ILE* 3.9 18.6 - - + -
221A CYS* 1.3 73.1 - - - +
223A MET* 1.3 63.7 + - - +
224A PHE* 5.5 9.1 - - + -
262A ILE* 5.0 4.0 - - + -
281A ILE 4.0 0.2 - - - +
283A HIS* 2.8 53.9 + - + +
285A ILE* 3.9 7.6 - - + +
291A PHE* 4.0 20.6 - - + -
306A ILE* 3.7 33.4 - - + -
332A ILE* 4.1 10.8 - - + -
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Residues in contact with MET 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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211A ALA* 3.4 4.9 - - - +
212A VAL* 2.8 48.3 + - + +
214A SER* 3.4 33.9 - - - +
216A ARG* 3.3 44.9 - - + +
221A CYS* 3.9 19.5 - - + +
222A LEU* 1.3 79.2 - - - +
224A PHE* 1.3 62.6 + - - +
280A ILE* 3.6 11.7 - - + -
281A ILE 3.1 14.4 - - - +
282A SER* 3.6 15.9 - - - +
337A ARG* 5.6 2.9 - - + -
338A PHE* 3.2 9.1 - - + -
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Residues in contact with PHE 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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207A PHE* 4.5 9.9 - + - -
211A ALA* 4.2 5.6 - - + -
222A LEU* 5.5 8.5 - - + -
223A MET* 1.3 76.1 - - - +
225A ARG* 1.3 68.1 + - - +
226A VAL* 4.8 0.9 - - + -
239A ILE* 3.9 22.7 - - + -
241A ALA* 4.8 7.4 - - + -
262A ILE* 6.3 0.4 - - + -
264A VAL* 4.5 14.6 - - + -
280A ILE* 3.6 1.0 - - - -
281A ILE* 2.8 67.3 + - + +
283A HIS* 6.2 0.7 - - + -
306A ILE* 5.4 5.2 - - + -
308A VAL* 3.6 30.7 - - + -
327A TYR* 3.6 29.4 - + + +
338A PHE* 3.7 10.5 - - - -
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Residues in contact with ARG 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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207A PHE* 3.4 8.5 - - - +
208A SER* 3.0 41.8 + - - -
224A PHE* 1.3 76.7 - - - +
226A VAL* 1.3 65.7 + - - +
278A PRO* 3.8 22.9 + - + +
279A LEU 3.3 13.0 - - - +
280A ILE* 4.1 16.5 - - - +
338A PHE* 3.4 33.2 - - + +
339A THR 2.8 32.5 + - - +
340A PRO* 4.8 1.4 - - - +
341A VAL* 3.6 26.0 - - - +
355A SER 3.8 3.6 + - - -
356A PHE* 3.1 43.5 + - + -
358A GLU 4.0 0.8 + - - -
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Residues in contact with VAL 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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205A LEU* 4.0 6.7 - - + -
206A VAL 3.9 1.8 - - - -
207A PHE* 3.6 29.8 - - + -
224A PHE* 4.8 1.3 - - + -
225A ARG* 1.3 75.9 - - - +
227A GLY* 1.3 69.7 + - - +
239A ILE* 5.2 1.1 - - + -
273A LEU* 4.4 12.3 - - + -
275A LEU* 4.0 7.3 - - + +
278A PRO* 3.3 1.7 - - - +
279A LEU* 2.8 41.8 + - + +
281A ILE* 3.6 33.4 - - + -
310A LEU* 3.8 20.9 - - + -
356A PHE* 4.0 2.9 - - - -
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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