Contacts of the strand formed by residues 243 - 249 (chain A) in PDB entry 3UJK
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 HIS 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A PHE* 4.4 6.7 - + - -
201A TRP* 3.6 40.9 - + + -
202A GLN* 5.2 11.5 + - + +
238A VAL 4.0 0.4 - - - +
240A PHE* 2.8 35.3 + - + +
242A THR* 1.3 107.8 + - - +
244A ILE* 1.3 65.1 + - - +
245A PHE* 4.1 11.7 - - + -
322A SER* 5.5 2.8 + - - -
323A VAL 3.4 10.5 + - - +
324A ARG* 3.2 56.7 + - + +
325A ARG* 3.7 3.8 - - - +
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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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237A ALA* 4.7 0.4 - - + -
238A VAL 3.4 7.2 - - - +
239A VAL* 4.4 11.2 - - + -
243A HIS* 1.3 78.7 - - - +
245A PHE* 1.3 71.5 + - - +
246A VAL* 4.1 13.2 + - + -
256A LEU* 4.4 11.4 - - + -
265A LEU* 4.2 7.4 - - + +
321A THR* 4.0 0.5 - - - +
322A SER* 3.4 2.4 - - - -
323A VAL* 2.9 46.2 + - + +
325A ARG* 3.8 20.9 - - + -
329A ASP* 5.1 1.6 - - - +
332A LEU* 4.1 23.6 - - + -
411A LEU* 3.7 35.4 - - + -
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Residues in contact with PHE 245 (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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201A TRP* 3.6 38.4 - + - -
202A GLN* 3.6 28.9 - - + -
205A TRP* 3.6 20.6 - + + -
206A LYS* 3.9 12.6 - - + -
209A LEU* 3.6 21.7 - - + +
236A VAL 3.9 0.4 - - - +
237A ALA* 3.1 6.4 - - - +
238A VAL* 2.8 39.2 + - + +
240A PHE* 3.7 25.4 - + - -
243A HIS* 4.1 8.3 - - + -
244A ILE* 1.3 76.9 - - - +
246A VAL* 1.3 61.9 + - - +
247A ALA 4.4 0.2 - - - -
321A THR 3.3 5.6 - - - +
322A SER* 3.4 29.6 - - - -
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Residues in contact with VAL 246 (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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209A LEU* 5.1 0.4 - - - -
235A VAL* 4.2 5.4 - - + -
236A VAL 3.2 8.7 - - - +
237A ALA* 4.2 9.9 - - + -
244A ILE* 4.1 7.4 + - + +
245A PHE* 1.3 77.7 - - - +
247A ALA* 1.3 70.7 + - - +
248A ASN 4.7 0.2 - - - +
254A ALA* 3.8 25.1 - - + -
265A LEU* 3.7 52.2 - - + +
266A SER* 4.4 4.0 - - - -
319A GLU 3.7 1.4 - - - +
320A VAL* 3.3 4.6 - - - -
321A THR* 2.8 41.3 + - + +
332A LEU* 5.0 1.1 - - + -
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Residues in contact with ALA 247 (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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209A LEU* 4.1 21.9 - - + +
213A PHE* 3.7 28.9 - - + -
235A VAL* 3.5 1.9 - - - -
236A VAL* 2.9 32.5 + - + +
246A VAL* 1.3 74.7 - - - +
248A ASN* 1.3 60.4 + - - +
318A PRO* 4.4 2.7 - - + -
319A GLU 3.4 4.7 - - - -
320A VAL* 4.0 19.1 - - + +
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Residues in contact with ASN 248 (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 SER 3.4 4.9 - - - +
235A VAL* 3.4 20.7 - - + +
246A VAL* 4.7 0.7 - - + -
247A ALA* 1.3 76.4 - - - +
249A CYS* 1.3 66.7 + - - +
250A GLY 3.3 21.4 + - - -
252A SER 3.3 19.5 + - - +
266A SER* 3.5 29.0 - - - -
267A VAL 3.7 18.0 + - - +
269A HIS* 3.3 10.7 + - + -
318A PRO* 3.0 7.5 - - - +
319A GLU* 2.9 36.0 + - + +
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Residues in contact with CYS 249 (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 PHE* 3.9 8.5 - - + -
233A THR* 3.4 3.5 - - - -
234A SER 2.8 39.4 + - - +
248A ASN* 1.3 77.1 - - - +
250A GLY* 1.3 59.7 + - - +
269A HIS* 3.5 5.2 - - - -
303A ARG* 4.1 9.2 - - + -
304A SER* 3.8 17.0 - - - -
305A ILE* 3.7 26.7 - - - -
316A PRO 3.6 26.7 - - - +
317A ASP 4.1 4.7 - - - +
318A PRO* 4.1 5.2 - - + -
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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