Contacts of the strand formed by residues 254 - 259 (chain A) in PDB entry 3K0J
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 GLN 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A TYR* 2.4 32.8 + - + +
214A ILE 3.2 10.3 - - - +
215A ASN* 4.0 1.8 - - + -
217A LEU* 3.6 6.7 - - - +
226A LEU* 5.4 0.2 - - - +
245A VAL* 4.0 15.1 - - - +
246A SER 4.5 2.3 + - - -
250A LYS 2.9 27.5 + - - -
251A MET* 3.0 39.6 + - + +
252A ARG 3.1 5.3 + - - -
253A GLY* 1.3 84.2 + - - +
255A ALA* 1.3 66.8 + - - +
26E G 3.0 44.6 - - + +
27E C 3.8 7.8 - - - +
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Residues in contact with ALA 255 (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 ILE 4.0 0.2 - - - +
213A TYR* 3.8 4.2 - - - -
214A ILE* 3.0 36.3 + - + +
217A LEU* 3.8 8.5 - - + -
230A LEU* 3.7 29.8 - - + -
243A ILE* 4.8 2.0 - - + -
244A LEU 3.6 12.6 - - - +
245A VAL* 4.5 8.3 - - + -
251A MET* 5.4 0.4 - - - -
254A GLN* 1.3 79.3 - - - +
256A PHE* 1.3 69.5 + - - +
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Residues in contact with PHE 256 (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 THR* 3.8 16.8 - - + -
212A ILE 3.6 4.7 - - - -
213A TYR* 3.7 20.6 - + - -
242A ASP 3.8 1.2 - - - +
243A ILE* 3.3 5.2 - - - +
244A LEU* 3.0 44.2 + - + +
251A MET* 3.4 27.6 - - + -
254A GLN* 5.4 0.4 - - + -
255A ALA* 1.3 79.9 - - - +
257A VAL* 1.3 63.3 + - - +
258A ILE* 3.9 2.1 + - + +
287A ALA* 4.6 2.7 - - + -
27E C 3.6 34.8 - - - -
28E A 3.3 66.6 - + + -
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Residues in contact with VAL 257 (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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210A HIS 3.6 1.9 - - - +
211A THR* 3.2 3.9 - - - -
212A ILE* 3.1 43.2 + - + +
214A ILE* 3.8 25.8 - - + -
230A LEU* 4.6 4.5 - - + -
234A PHE* 4.3 11.7 - - + -
240A ILE* 4.1 36.1 - - + -
242A ASP 3.7 2.7 - - - +
243A ILE* 4.3 19.7 - - + -
256A PHE* 1.3 77.1 - - - +
258A ILE* 1.3 63.0 + - - +
259A PHE* 3.7 15.7 + - + -
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Residues in contact with ILE 258 (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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210A HIS* 5.0 0.2 - - + -
211A THR* 3.4 21.8 - - + +
240A ILE* 3.3 7.7 - - - +
241A LEU* 2.7 58.2 + - + -
242A ASP* 2.9 28.0 + - + +
244A LEU* 3.8 25.8 - - + -
256A PHE* 4.8 2.0 - - + +
257A VAL* 1.3 73.2 - - - +
259A PHE* 1.3 58.6 + - - +
291A SER* 3.8 14.4 - - - +
293A ILE* 3.3 26.5 - - + -
294A ILE* 3.9 21.3 - - + -
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Residues in contact with PHE 259 (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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210A HIS* 2.9 42.4 + - - +
212A ILE* 4.2 12.6 - - + -
234A PHE* 3.6 28.7 - - + -
237A PHE* 4.1 4.7 - - + -
238A GLY 3.8 12.6 - - - -
239A GLN 3.8 8.3 - - - -
240A ILE* 3.4 30.7 - - + -
241A LEU* 4.1 7.4 - - - +
257A VAL* 4.4 8.5 - - + -
258A ILE* 1.3 74.4 - - - +
260A LYS* 1.3 65.3 + - - +
261A GLU 3.1 15.5 - - - +
264A SER* 3.8 9.0 - - - -
265A ALA* 3.3 36.3 - - + -
268A ALA* 3.6 22.2 - - + -
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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