Contacts of the strand formed by residues 226 - 236 (chain A) in PDB entry 3ZJU
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 ARG 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A ASP* 3.7 16.2 + - - -
203A LEU* 4.0 30.9 - - + +
221A ARG 4.7 1.0 + - - -
224A ILE* 3.5 2.5 - - + +
225A GLY* 1.3 75.5 - - - +
227A SER* 1.3 60.5 + - - +
228A GLU* 2.7 39.7 + - - +
413A VAL* 3.9 25.7 - - + +
414A ASN 3.6 3.8 - - - -
415A TYR* 3.5 37.3 + - + -
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Residues in contact with SER 227 (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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225A GLY 3.9 3.8 - - - -
226A ARG* 1.3 75.0 - - - +
228A GLU* 1.3 60.9 + - - +
246A TYR* 2.7 18.7 + - - -
248A THR* 3.4 10.4 - - - +
330A TYR* 3.4 12.3 - - - -
413A VAL* 3.3 7.4 - - - +
414A ASN 2.8 35.1 + - - -
76B DJF 2.6 32.3 + - - -
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Residues in contact with GLU 228 (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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226A ARG* 2.7 35.3 + - - +
227A SER* 1.3 73.2 + - - +
229A GLY* 1.3 58.4 + - - +
246A TYR* 3.5 1.8 + - - -
248A THR* 4.3 11.8 - - - +
396A PHE* 4.2 18.6 - - + -
412A LYS 3.9 2.7 - - - -
413A VAL* 4.3 11.7 - - + +
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Residues in contact with GLY 229 (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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228A GLU* 1.3 75.1 - - - +
230A VAL* 1.3 70.5 + - - +
246A TYR* 3.2 15.6 + - - -
247A THR 3.3 11.2 - - - -
248A THR* 4.3 1.1 - - - -
396A PHE* 4.4 6.6 - - - -
411A ARG* 3.3 7.6 - - - +
412A LYS 2.8 31.3 + - - -
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Residues in contact with VAL 230 (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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229A GLY* 1.3 80.2 - - - +
231A GLU* 1.3 73.6 + - - +
232A ILE* 4.0 12.6 - - + -
245A VAL 3.9 0.3 - - - +
246A TYR* 3.7 3.5 - - - -
247A THR* 2.8 37.8 + - + +
250A PRO* 3.6 33.0 - - + -
396A PHE* 4.2 7.0 - - + -
400A ALA* 4.0 29.6 - - + -
403A LEU* 4.9 3.8 - - + -
409A GLY* 4.7 2.7 - - - -
410A GLU 3.3 20.6 - - - +
411A ARG* 4.4 3.6 - - + -
412A LYS 4.4 0.2 - - - +
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Residues in contact with GLU 231 (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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230A VAL* 1.3 78.1 - - - +
232A ILE* 1.3 60.9 + - - +
233A THR* 4.3 0.9 - - - -
244A THR* 3.8 13.0 - - + +
245A VAL 3.2 10.8 - - - +
246A TYR* 4.3 4.7 - - + +
331A GLY 5.1 1.4 - - - +
332A THR* 3.2 28.5 - - + +
409A GLY* 3.1 6.3 - - - -
410A GLU* 2.8 52.7 + - + +
412A LYS* 3.6 45.3 + - + +
414A ASN* 4.7 4.3 + - - -
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Residues in contact with ILE 232 (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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230A VAL* 4.0 10.3 - - + +
231A GLU* 1.3 80.1 - - - +
233A THR* 1.3 66.1 + - - +
234A PHE* 3.5 26.0 - - + -
244A THR* 4.1 0.4 - - - -
245A VAL* 3.0 36.6 + - + +
247A THR* 3.9 24.2 - - + -
250A PRO* 4.9 4.5 - - + -
253A PHE* 3.8 36.1 - - + -
312A PRO* 4.6 4.5 - - + -
336A MET* 4.4 4.0 - - + -
403A LEU* 3.8 28.7 - - + -
408A VAL 3.5 9.2 - - - +
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Residues in contact with THR 233 (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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231A GLU 5.4 0.5 - - - -
232A ILE* 1.3 77.8 - - - +
234A PHE* 1.3 66.7 + - - +
242A THR* 3.4 38.1 - - + +
243A LEU 3.2 7.0 - - - +
244A THR* 2.9 20.6 + - - +
312A PRO* 4.7 4.9 - - - +
408A VAL* 2.9 42.8 + - + +
409A GLY* 5.7 0.3 - - - -
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Residues in contact with PHE 234 (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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232A ILE* 3.5 27.8 - - + -
233A THR* 1.3 79.0 - - - +
235A ASN* 1.3 69.6 + - - +
236A VAL* 5.0 0.2 - - + -
242A THR* 3.2 11.4 - - - -
243A LEU* 2.6 41.0 + - + +
245A VAL* 3.9 17.0 - - + -
253A PHE* 3.8 26.2 - + - -
256A CYS* 4.6 1.6 - - - -
259A LEU* 3.7 37.9 - - + -
309A ALA* 4.1 9.9 - - + -
310A VAL 3.5 22.4 - - - -
311A HIS* 3.9 8.1 - + - -
312A PRO* 3.7 16.2 - - + -
318A ILE* 4.6 7.6 - - + -
336A MET* 4.7 0.9 - - + -
408A VAL* 6.4 0.2 - - - -
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Residues in contact with ASN 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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234A PHE* 1.3 75.0 - - - +
236A VAL* 1.3 61.6 + - - +
241A ASN 5.3 0.2 - - - -
242A THR* 3.7 20.9 - - - +
309A ALA* 3.4 4.0 - - - +
310A VAL* 2.9 46.2 + - + +
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Residues in contact with VAL 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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234A PHE 4.2 0.7 - - - +
235A ASN* 1.3 80.3 - - - +
237A ASN* 1.3 71.3 + - - +
238A ASP 3.8 0.7 - - - -
239A TYR* 3.2 46.2 - - + +
241A ASN 4.4 4.9 + - - +
243A LEU* 4.0 34.1 - - + +
267A LEU* 4.4 8.5 - - + -
307A PHE* 3.7 28.5 - - + -
308A LYS 3.3 16.4 - - - +
309A ALA* 4.4 7.6 - - + +
310A VAL* 5.9 0.2 - - - -
320A VAL* 4.6 2.0 - - + -
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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