Contacts of the strand formed by residues 234 - 244 (chain A) in PDB entry 3ATF
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 ILE 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A LEU* 3.8 29.2 - - + -
229A LEU* 3.8 28.9 - - + +
232A SER 4.3 0.9 - - - +
233A HIS* 1.3 80.4 + - - +
235A VAL* 1.3 62.1 + - - +
236A GLU 3.8 0.3 + - - -
237A ALA* 3.5 22.8 + - + +
273A LEU 5.2 1.0 - - - +
275A LEU* 4.4 27.5 + - + +
310A LEU* 4.6 5.6 - - + -
311A GLU 5.0 0.4 - - - -
312A GLY* 3.6 28.3 - - - +
313A MET 3.2 12.8 - - - +
314A VAL* 5.0 5.2 - - + -
321A CYS* 4.8 8.5 - - - -
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Residues in contact with VAL 235 (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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233A HIS* 5.2 1.8 - - + -
234A ILE* 1.3 72.0 - - - +
236A GLU* 1.3 80.3 + - + +
237A ALA 3.1 1.4 + - - -
312A GLY* 3.4 0.7 - - - -
313A MET* 2.8 52.3 + - + +
315A GLU* 3.8 33.9 - - + +
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Residues in contact with GLU 236 (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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2A CS 3.0 33.7 - - - -
234A ILE 3.8 0.2 + - - -
235A VAL* 1.3 87.8 - - + +
237A ALA* 1.3 61.0 + - - +
311A GLU 3.4 2.1 - - - +
312A GLY* 3.7 1.3 - - - -
313A MET* 4.9 5.8 - - + +
382A MG 3.9 16.5 - - - -
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Residues in contact with ALA 237 (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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234A ILE* 3.5 27.7 + - + +
235A VAL 3.1 3.0 + - - -
236A GLU* 1.3 78.9 - - - +
238A SER* 1.3 62.3 + - - +
272A ARG* 3.5 8.1 - - - +
273A LEU* 3.1 46.5 + - + +
275A LEU* 4.9 7.0 - - + +
310A LEU* 4.5 9.9 - - + -
311A GLU 3.4 6.3 - - - +
312A GLY* 4.2 0.4 - - - -
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Residues in contact with SER 238 (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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2A CS 2.9 27.9 - - - -
237A ALA* 1.3 77.5 - - - +
239A ILE* 1.3 63.3 + - - +
240A ARG* 5.4 4.1 - - - +
271A ASP* 3.1 19.3 - - - -
272A ARG* 4.7 4.7 - - - -
273A LEU* 4.4 1.1 - - - +
309A ILE 3.8 0.9 - - - +
310A LEU* 3.4 7.5 - - - +
311A GLU* 2.9 35.3 + - - +
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Residues in contact with ILE 239 (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* 4.3 14.4 - - + -
224A PHE* 3.9 34.5 - - + -
226A VAL* 5.1 2.5 - - + -
238A SER* 1.3 77.1 - - - +
240A ARG* 1.3 72.2 + - - +
264A VAL* 3.6 13.8 - - + +
270A ASP 5.0 0.2 - - - +
271A ASP* 3.1 38.9 + - - +
273A LEU* 3.7 26.2 - - + -
281A ILE* 4.4 17.7 - - + -
309A ILE 3.6 19.1 - - - +
310A LEU* 4.4 7.9 - - + +
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Residues in contact with ARG 240 (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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238A SER* 5.4 4.7 - - - +
239A ILE* 1.3 83.6 - - - +
241A ALA* 1.3 63.2 + - - +
242A LYS* 4.9 16.3 - - - +
261A ASP* 4.7 14.2 + - - +
264A VAL* 4.0 7.6 - - - -
308A VAL* 3.7 1.2 - - - -
309A ILE* 3.0 57.8 + - + +
311A GLU* 2.7 43.7 + - + +
322A GLN* 5.3 1.4 - - - +
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Residues in contact with ALA 241 (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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224A PHE* 4.9 4.3 - - + -
240A ARG* 1.3 77.3 - - - +
242A LYS* 1.3 64.9 + - - +
261A ASP* 3.5 8.3 - - - +
262A ILE* 3.0 45.7 + - + +
264A VAL* 4.5 12.7 - - + +
306A ILE* 4.5 9.0 - - + -
307A VAL 3.0 12.1 - - - +
308A VAL* 4.4 12.3 - - + -
309A ILE* 5.4 0.7 - - - -
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Residues in contact with LYS 242 (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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240A ARG* 4.9 18.2 - - + +
241A ALA* 1.3 78.2 - - - +
243A LEU* 1.3 61.9 + - - +
244A ILE* 3.9 12.3 - - + -
259A GLN* 3.9 32.6 - - + +
260A THR* 3.4 5.7 - - - +
261A ASP* 2.7 42.1 + - - +
262A ILE* 3.9 5.1 - - - +
306A ILE* 3.4 5.0 - - - -
307A VAL* 2.8 37.7 + - + +
309A ILE* 4.5 16.4 - - + -
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Residues in contact with LEU 243 (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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242A LYS* 1.3 71.4 - - - +
244A ILE* 1.3 60.5 + - - +
245A LYS* 4.2 20.1 - - + +
258A ASN 3.0 14.6 - - - +
259A GLN* 3.3 1.4 - - - -
260A THR* 2.7 43.0 + - - +
262A ILE* 3.9 14.8 - - + +
290A PRO* 3.5 31.9 - - + -
291A PHE* 4.5 14.8 - - + -
304A LEU* 3.9 36.1 - - + -
305A GLU 3.7 10.8 - - - +
306A ILE* 4.7 0.7 - - + -
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Residues in contact with ILE 244 (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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242A LYS* 4.5 6.1 - - + -
243A LEU* 1.3 73.0 - - - +
245A LYS* 1.3 65.0 + - - +
257A LEU* 3.6 43.1 - - + +
258A ASN 3.4 1.3 - - - +
259A GLN* 3.7 35.4 - - + +
304A LEU* 3.5 3.3 - - - +
305A GLU* 2.9 39.9 + - + +
307A VAL* 3.8 30.1 - - + -
384A EOH 3.6 15.5 + - - +
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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