Contacts of the strand formed by residues 240 - 246 (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 ILE 240 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A HIS* 3.9 35.4 - - + +
234A PHE* 3.8 35.2 - - + +
235A SER* 4.0 3.1 - - - +
238A GLY 3.3 3.5 + - - +
239A GLN* 1.3 89.2 + - - +
241A LEU* 1.3 64.5 + - - +
242A ASP* 3.3 26.2 - - - +
243A ILE* 4.2 7.0 - - + -
257A VAL* 4.1 10.8 - - + -
258A ILE 3.3 10.3 - - - +
259A PHE* 3.4 24.9 - - + -
62E U 4.8 3.1 - - - +
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Residues in contact with LEU 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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239A GLN* 4.2 14.6 - - - +
240A ILE* 1.3 78.6 - - - +
242A ASP* 1.3 71.7 + - - +
258A ILE* 2.7 21.4 + - + +
260A LYS* 3.8 38.1 - - + +
293A ILE* 3.9 22.2 - - + +
294A ILE* 3.7 29.4 - - + -
297A MET* 5.2 9.6 - - + -
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Residues in contact with ASP 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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227A LYS* 4.7 2.1 + - - -
240A ILE* 3.3 8.8 - - - +
241A LEU* 1.3 86.3 - - + +
243A ILE* 1.3 70.2 + - - +
244A LEU* 3.1 30.6 - - + +
256A PHE 3.8 0.5 - - - +
258A ILE* 2.9 44.4 + - + +
293A ILE* 5.0 5.8 - - + -
62E U 4.0 17.6 + - - +
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Residues in contact with ILE 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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227A LYS* 2.8 65.2 + - + +
230A LEU* 3.9 30.1 - - + -
231A HIS* 3.5 27.4 - - + +
240A ILE* 4.2 10.3 - - + -
242A ASP* 1.3 83.6 - - - +
244A LEU* 1.3 62.8 - - - +
245A VAL* 4.2 7.6 - - + -
255A ALA* 4.8 0.9 - - + -
256A PHE 3.3 9.9 - - - +
257A VAL* 4.3 11.2 - - + -
62E U 3.4 21.1 + - - +
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Residues in contact with LEU 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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227A LYS* 4.1 7.4 - - - +
242A ASP* 3.1 22.2 - - - +
243A ILE* 1.3 76.0 - - - +
245A VAL* 1.3 61.9 + - - +
246A SER 4.4 0.2 + - - -
251A MET* 4.6 2.8 - - - +
255A ALA* 3.6 5.0 - - - -
256A PHE* 3.0 44.6 + - + +
258A ILE* 3.8 27.4 - - + -
293A ILE* 5.9 0.4 - - + -
28E A 4.3 19.3 - - + +
29E C 4.5 14.4 - - + +
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Residues in contact with VAL 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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223A LYS* 3.9 29.8 - - + +
226A LEU* 3.7 35.0 - - + -
227A LYS* 3.8 32.9 + - + +
243A ILE* 3.9 12.4 + - + -
244A LEU* 1.3 79.0 - - - +
246A SER* 1.3 71.3 + - - +
247A ARG* 4.9 3.1 - - + -
253A GLY 6.2 0.4 - - - +
254A GLN 4.0 12.3 - - - +
255A ALA* 4.5 6.7 - - + -
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Residues in contact with SER 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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245A VAL* 1.3 81.1 - - - +
247A ARG* 1.3 62.3 + - - +
248A SER* 2.6 31.3 + - - -
251A MET* 2.5 57.7 + - - +
252A ARG* 3.2 4.0 - - - -
253A GLY 4.3 1.2 + - - -
254A GLN 4.5 1.3 + - - +
32E C 4.6 1.6 + - - -
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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