Contacts of the strand formed by residues 243 - 249 (chain A) in PDB entry 1UCU
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 GLY 243 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ALA 3.5 1.0 - - - +
232A LYS* 3.7 5.6 - - - +
233A VAL 3.0 31.3 + - - -
241A LYS 3.7 2.2 + - - -
242A ASP* 1.3 74.1 - - - +
244A TYR* 1.3 69.5 + - - -
245A TYR* 3.8 6.4 - - - -
265A PRO* 4.0 7.9 - - - -
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Residues in contact with TYR 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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221A LYS* 3.9 16.3 + - - -
230A TYR* 5.5 0.2 - - + -
231A ALA 3.6 14.6 - - - -
232A LYS* 3.7 36.6 - - + +
243A GLY* 1.3 75.9 - - - -
245A TYR* 1.3 61.7 + - - +
265A PRO* 3.6 7.7 - - - +
266A LEU* 2.8 38.5 + - + +
269A GLY* 3.8 26.8 - - - +
270A LEU* 3.4 54.0 - - + +
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Residues in contact with TYR 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 3.3 35.7 - - + +
230A TYR* 3.1 7.3 - - - +
231A ALA* 2.7 36.8 + - - +
233A VAL* 3.4 37.2 - - + -
241A LYS* 2.9 30.3 + - - -
243A GLY 3.8 4.9 - - - -
244A TYR* 1.3 78.8 - - - +
246A GLU* 1.3 60.9 + - - +
247A VAL* 5.1 3.1 - - + -
258A LEU* 3.5 28.5 - - + -
262A ALA* 4.0 14.4 - - + -
264A SER* 3.6 19.8 - - - -
265A PRO* 3.0 27.0 - - + +
266A LEU* 4.7 1.8 - - - -
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Residues in contact with GLU 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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228A LYS* 2.8 48.7 + - + +
229A TYR 3.5 13.0 - - - +
230A TYR* 3.8 19.9 + - + -
245A TYR* 1.3 73.7 - - - +
247A VAL* 1.3 67.3 + - - +
248A SER* 5.6 0.2 + - - -
258A LEU* 4.2 4.2 - - - +
259A ALA* 2.9 40.7 + - + +
266A LEU* 4.6 13.5 - - + +
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Residues in contact with VAL 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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202A PHE* 4.2 17.3 - - + -
220A LEU* 3.8 24.2 - - + -
229A TYR* 2.9 46.1 + - + +
230A TYR 4.0 3.4 - - - +
231A ALA* 3.8 21.5 - - + -
245A TYR* 4.4 2.2 - - + +
246A GLU* 1.3 83.1 - - - +
248A SER* 1.3 60.2 + - - +
249A VAL* 3.9 3.0 + - + -
256A VAL* 3.8 19.3 - - + -
257A THR 3.4 10.5 - - - +
258A LEU* 4.5 0.9 - - - -
259A ALA* 3.8 3.1 - - - -
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Residues in contact with SER 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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246A GLU* 5.6 0.2 + - - -
247A VAL* 1.3 72.7 - - - +
249A VAL* 1.3 60.9 + - - +
255A GLU 3.4 4.5 - - - +
256A VAL* 3.5 2.6 - - - -
257A THR* 2.8 46.6 + - - -
258A LEU 5.0 0.2 - - - -
259A ALA* 3.4 21.1 - - - +
260A GLY 5.1 0.3 + - - -
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Residues in contact with VAL 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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197A LEU* 3.9 16.4 - - + -
220A LEU* 4.3 2.2 - - + -
229A TYR* 3.7 53.3 - - + +
247A VAL* 3.9 2.1 + - + +
248A SER* 1.3 77.9 - - - +
250A ASP* 1.3 63.2 + - - +
251A LYS* 3.1 22.9 + - + +
254A GLY 4.7 0.9 - - - +
255A GLU 3.4 3.8 - - - +
256A VAL* 4.3 11.2 - - + -
281A VAL* 3.5 33.9 - - + -
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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